Zinc finger domain libraries

Abstract

Disclosed are libraries of chimeric zinc finger domains. The libraries can include two or more zinc finger domains from naturally occurring proteins, e.g., mammalian proteins and particularly human proteins. Useful chimeric zinc finger domains can be identified from the library. Also disclosed are the amino acid sequences of zinc finger domains that recognize particular sites.

Description

TECHNICAL FIELD

[0002] This invention relates to DNA-binding proteins such as transcription factors.

BACKGROUND

[0003] Most genes are regulated at the transcriptional level by polypeptide transcription factors that bind to specific DNA sites within in the gene, typically in promoter or enhancer regions. These proteins activate or repress transcriptional initiation by RNA polymerase at the promoter, thereby regulating expression of the target gene. Many transcription factors, both activators and repressors, are modular in structure. Such modules can fold as structurally distinct domains and have specific functions, such as DNA binding, dimerization, or interaction with the transcriptional machinery. Effector domains such as activation domains or repression domains retain their function when transferred to DNA-binding domains of heterologous transcription factors (Brent and Ptashne, (1985) Cell 43:729-36; Dawson et al, (1995) Mol. Cell Biol. 15:6923-31). The three-dimensional structures of many DNA-binding domains, including zinc finger domains, homeodomains, and helix-turn-helix domains, have been determined from NMR and X-ray crystallographic data.

SUMMARY

[0004] The invention provides a rapid and scalable cell-based method for identifying and constructing chimeric proteins, e.g., transcription factors. Such transcription factors can be used, for example, for altering the expression of endogenous genes in biomedical and bioengineering applications. The transcription factors are assayed in vivo, i.e., in intact, living cells in culture. A database can be constructed from the results of the assays. The database can be used to design other chimeric transcription factors. Libraries of chimeric transcription factors can be prepared and screened. It is also possible that the chimeric proteins bind and regulate molecules other than DNA, e.g., proteins and RNA, in particular small non-coding RNAs (ncRNAs).

[0005] In one aspect, the invention features libraries of nucleic acids that encode chimeric zinc finger proteins. The term “library” refers to a physical collection of similar, but non-identical biomolecules. The collection can be, for example, together in one vessel or physically separated (into groups or individually) in separate vessels or on separate locations on a solid support. Duplicates of individual members of the library may be present in the collection.

[0006] A first library includes a plurality of nucleic acids, each nucleic acid encoding a polypeptide comprising at least a first, second, and third zinc finger domains. As used herein, “first, second and third” denotes three separate domains that can occur in any order in the polypeptide: e.g., each domain can occur N-terminal or C-terminal to either or both of the others. The first zinc finger domain varies among nucleic acids of the plurality. The second zinc finger domain varies among nucleic acids of the plurality. At least 10 different first zinc finger domains are represented in the library. In one implementation, at least 0.5, 1, 2, 5%, 10%, or 25% of the members of the library have one or both of the following properties: (1) each represses transcription of at least one p1G reporter plasmid at least 1.25 fold in vivo; and (2) each binds at least one target site with a dissociation constant of no more than 7, 5, 3, 2, 1, 0.5, or 0.05 nM. The first and second zinc finger domains can be from different naturally-occurring proteins or are positioned in a configuration that differs from their relative positions in a naturally occurring protein. For example, the first and second zinc finger domains may be adjacent in the polypeptide, but may be separated by one or more intervening zinc finger domains in a naturally occurring protein.

[0007] As used herein, the “dissociation constant” refers to the equilibrium dissociation constant of a polypeptide for binding to a 28-basepair double-stranded DNA that includes one 9-basepair target site. The dissociation constant is determined by gel shift analysis using a purified protein that is bound in 20 mM Tris pH 7.7, 120 mM NaCl, 5 mM MgCl2, 20 μM ZnSO4, 10% glycerol, 0.1% Nonidet P-40, 5 mM DTT, and 0.10 mg/mL BSA (bovine serum albumin) at room temperature. Additional details are provided in Example 10 and Rebar and Pabo ((1994) Science 263:671-673).

[0008] As used herein, the “repression of transcription of a p1G reporter plasmid” refers to the fold repression of the luciferase reporter gene of a p1G reporter plasmid that has a given 9-basepair target site positioned downstream of the TATA box as depicted in FIG. 12. The fold repression is determined by the assay set forth in Example 68, requiring the transfection of HEK 293 cells with appropriate expression and reporter plasmids.

[0009] The first and second zinc finger domains can be naturally occurring domains, e.g., as described below.

[0010] A second featured library includes a plurality of nucleic acids, each nucleic acid encoding a polypeptide that includes at least first and second zinc finger domains. The first and second zinc finger domains of each polypeptide (1) are identical to zinc finger domains of different naturally occurring proteins (and generally do not occur in the same naturally occurring protein or are positioned in a configuration that differs from their relative positions in a naturally-occurring protein), (2) differ by no more than four, three, two, or one amino acid residues from domains of naturally occurring proteins, or (3) are non-adjacent zinc finger domains from a naturally occurring protein. Identical zinc finger domains refer to zinc finger domains that are identical at each amino acid from the first metal coordinating residue (typically cysteine) to the last metal coordinating residue (typically histidine). Examples of differing configurations include placement of non-adjacent domains in positions adjacent to one another, placement of a domain that is N-terminal to another domain at a C-terminal position to the other domain, and placement of adjacent domain in positions non-adjacent to each other (e.g., by inserting another domain between them).

[0011] The first zinc finger domain varies among nucleic acids of the plurality, and the second zinc finger domain varies among nucleic acids of the plurality. The naturally occurring protein can be any eukaryotic zinc finger protein: for example, a fungal (e.g., yeast), plant, or animal protein (e.g., a mammalian protein, such as a human or murine protein). Each polypeptide can further include a third, fourth, fifth, and/or sixth zinc finger domain. Each zinc finger domain can be a mammalian, e.g., human, zinc finger domain.

[0012] For the first and second featured libraries described above, the first and/or second zinc finger domain of each polypeptide can be selected from Tables 5, 6, and 7. In another example, the first and/or second zinc finger domain of at least one polypeptide can be selected from Tables 5, 6, and 7. In one embodiment, at least 1%, 5%, 10%, 25%, 50%, 75%, or all of the zinc finger domains listed in Tables 5, 6, and 7 are encoded by at least one nucleic acid of the plurality. The plurality of first zinc finger domains encoded by respective members of the plurality of nucleic acids can include a sufficient number of different zinc finger domains to bind specifically to at least 10, 20, 30, 40, or 50 different 3-base pair DNA sites.

[0013] A given zinc finger domain is said to “bind specifically” to a given 3-base pair DNA site if a chimeric protein that includes fingers 1 and 2 of Zif268 and the given zinc finger domain has an affinity of at least 5 nM for a target site that includes both the given 3-base pair DNA site and the 5-bp sequence, 5′-GGGCG-3′, that is recognized by fingers 1 and 2 of Zif268. Fingers 1 and 2 of Zif268 have the polypeptide sequence: ERPYACPVESCDRRFSRSDELTRHIRIHTGQKPFQCRICMRNFSRSDHLTTHIRTH (SEQ ID NO: 198). The terms “recognize” and “specifically bind” are used interchangeably and refer to the discrimination for a bind site of a zinc finger domain in the above Zif268 fusion assay.

[0014] Optionally, the plurality of nucleic acids collectively encode a sufficient number of different zinc finger domains to recognize at least 10, 20, 30, 40, or 50 different 3-base pair DNA sites. In one embodiment, the plurality of nucleic acids collectively encode a sufficient number of different zinc finger domains to recognize no more than 40, 30, 20, 10, or 5 different 3-base pair DNA sites.

[0015] The plurality of nucleic acids can collectively encode at least 5, 10, 20, 30, or 40 different first zinc finger domains and/or at least 5, 10, 20, 30, or 40 different second zinc finger domains. The plurality of nucleic acids can include at least 10, 50, 200, 500, 1000, 5000, 10 000, 20 000, 25 000, or 40 000 different nucleic acids (i.e., with different sequences). In some cases, the plurality can include no more than 100, 500, 2000, 5000, 15 000, 30 000, or 50 000 nucleic acids. The plurality of nucleic acids can constitute at least 20%, 50%, 70%, 80%, 90%, 95%, or 100% of the library by molar ratio.

[0016] In one embodiment, the polypeptides encoded by nucleic acids of the plurality include different numbers of zinc finger domains. For example, polypeptides encoded by a first subset can include four zinc finger domains, and polypeptides encoded by a second subset can include five zinc finger domains. Another combination is one with three, four, and five domains, or four, five and six domains.

[0017] In one embodiment, the polypeptides encoded by nucleic acids of the plurality include different types of transcriptional regulatory domains. For example, polypeptides encoded by a first subset can include a transcriptional activation domain, and polypeptides encoded by a second subset can include a transcriptional repression domain. Still another subset can be devoid of a transcriptional regulatory domain. This embodiment enables screening of the library without bias for a particular type of transcription factor.

[0018] In one embodiment, each nucleic acid is immobilized on a solid support. In still another embodiment, each nucleic acid is attached to the polypeptide that it encodes. The attachment can be covalent or non-covalent. For example, the polypeptide encoded by each nucleic acid can be attached to the exterior of a virus or viral particle, and the nucleic acid is packaged within the virus or viral particle. A “virus” refers to a genetic entity that can infect a host cell and replicate. A “virus particle” refers to a genetic entity that can infect a host cell, but cannot replicate. An example of a virus particle is a filamentous phage coat package that includes a phagemid nucleic acid. A virus or virus particle can infect a mammalian cell (e.g., a retrovirus and adenovirus) or a bacterial cell (e.g., a bacteriophage). In another example, the polypeptide is covalently attached to the nucleic acid, e.g., by a puromycin linkage.

[0019] In another embodiment, each polypeptide further includes an activation or repression domain. The first and the second zinc finger domains of each polypeptide can be adjacent to each other or separated, e.g., by an intervening domain or linker.

[0020] In one embodiment, each nucleic acid of the library is in a cell. The nucleic acid can be expressed within the cell. The cell can also include a heterologous reporter construct that includes a target DNA site operably linked to a reporter gene. The cell can be a yeast cell; an animal cell such as a cell of a mammal, a bird, or an insect; a bacterial cell; or a plant cell.

[0021] All nucleic acids of the library can be located within a single container or on a single surface. In another implementation, subsets of the plurality of nucleic acids are located in separate containers, on separate surfaces, or on separate parts of the same surface. In still another implementation, each nucleic acid of the library is addressable, e.g., uniquely addressable. An “addressable” element is located at a defined spatial location that can be accessed under appropriate conditions to retrieve the addressed element. For example, each nucleic acid can be located in a well of a microtitre plate, on a planar array, or within a frozen sample of cells.

[0022] Each nucleic acid of the library can be referenced in a machine-readable medium by a pointer associated with information about the ability of the polypeptide encoded by the nucleic acid to recognize a target site. The information can include, for example, a value representing the binding affinity of the polypeptide for the target site, a value predictive of the ability of the polypeptide to recognize the target site, or a set of values reflecting the effect of the polypeptide on the expression of endogenous genes within a cell (e.g., a human cell).

[0023] Similarly, the invention provides a library of polypeptides. The library includes a plurality of polypeptides that are each encoded by a nucleic acid of a nucleic acid library featured herein. The polypeptide library can also include any of appropriate feature of a nucleic acid library described herein, except that the feature is embodied at the protein level.

[0024] The invention also provides a kit that includes a library described herein, and a machine readable medium that includes, encoded therein, information about the ability of a polypeptide to recognize a target DNA site, wherein each nucleic acid or polypeptide of the library is referenced in a machine readable medium by a pointer associated with information about the ability of the respective polypeptide encoded by the nucleic acid to recognize a target DNA site. For example, the information can include a value representing the binding affinity of the polypeptide for the target site or a value predictive of the ability of the polypeptide to recognize the target site. The kit can further include computer-readable instructions that enable a user to interface with the information.

[0025] In another aspect, the invention features a polypeptide that includes a first and a second zinc finger domain. Each zinc finger domain has a sequence selected from Tables 5, 6, and 7. The first and second zinc finger domains are from different naturally occurring polypeptides. The polypeptide can further include third, fourth, and fifth zinc finger domains. Each of these domains can also have a sequence selected from Tables 5, 6, and 7. Typically, the zinc finger domains are positioned adjacent to each other to form an array of zinc finger domains. Such an array is a polypeptide unit that is uninterrupted by other types of structural or functional protein domains. Typically the array, e.g., in its entirety, does not occur in a naturally occurring protein.

[0026] The invention also features a polypeptide that includes a first, second, and third zinc finger domains. Each domain is naturally occurring. At least two of the domains occur in different naturally occurring polypeptides. Further, the polypeptide has one or both of the following properties: (1) each represses transcription of at least one p1G reporter plasmid at least 1.25, 1.5, 1.7, 1.9, 2.0, or 2.5 fold in vivo; and (2) each binds at least one target nucleic acid site with a dissociation constant of no more than 7, 5, 3, 2, 1, 0.5, or 0.05 nM. The target site can be DNA or RNA. The first, second, and/or third finger can be selected from Tables 5, 6, and 7. In one embodiment, the first, second, and third zinc finger domains of each given polypeptide are represented by the domains listed together in a row of Table 10, e.g., a row above row 113, e.g., a row that includes all human zinc finger domains. In one embodiment, the polypeptide only includes domains from naturally occurring polypeptides (e.g. mammalian, e.g., human polypeptides).

[0027] In one embodiment, the first domain is N-terminal to the second domain, the second domain is N-terminal to the third domain, and the second domain occurs in a different naturally occurring polypeptide than the first domain. Each of the first, second, and third domains can occur in a different naturally occurring polypeptide than the other two.

[0028] With respect to any featured polypeptide, the polypeptide can further include a heterologous sequence, e.g., a nuclear localization signal, a small molecular binding domain (e.g., a steroid binding domain), an epitope tag or purification handle, a catalytic domain (e.g., a nucleic acid modifying domain, a nucleic acid cleavage domain, or a DNA repair catalytic domain), a transcriptional function domain (e.g., an activation domain, a repression domain, and so forth), a protein transduction domain (e.g., from HIV tat), and/or a regulatory site (e.g., a phosphorylation site, ubiquitination site, or protease cleavage site).

[0029] The polypeptide can be attached (covalently or non-covalently) to a solid support, e.g., a bead, matrix, or planar array. The polypeptide can also be attached to a label such as a radioactive compound, a fluorescent compound, another detectable entity, or a component of a detection system (e.g., a chemiluminescent agent).

[0030] The invention also includes an isolated nucleic acid sequence encoding one of the aforementioned polypeptides. The nucleic acid can further include an operably linked regulatory sequence, e.g., a promoter, a transcriptional enhancer, a 5′ untranslated region, a 3′ untranslated region, a virus packaging sequence, and/or a selectable marker. The nucleic acid can be packaged in a virus, e.g., a virus that can infect a mammalian cell, e.g., a lentivirus, retrovirus, pox virus, or adenovirus.

[0031] The invention further provides a cell that contains the nucleic acid. The cell can be within a tissue in a subject organism or in culture. The cell can be an animal (e.g., mammalian), plant, or microbial (e.g., fungal or bacterial) cell. The invention still further includes a non-human transgenic mammal, e.g., a mouse, rat, pig, rabbit, cow, goat, or sheep. The genetic complement of the transgenic mammal includes the nucleic acid sequence encoding the chimeric zinc finger polypeptide described above and elsewhere herein. The invention also includes method of producing the polypeptide, e.g., by expressing the nucleic acid, and of using the polypeptide, e.g., to regulate endogenous genes or viral genes in a cell.

[0032] In still another aspect, the invention features a method of evaluating one or more polypeptides encoded by a nucleic acid library. The method includes: providing the library, in which each of a plurality of library nucleic acids is located in a cell (with one or more (but not all) of the members of the library in any given cell); expressing each of the plurality of nucleic acids in the cell in which it resides; and identifying a cell having altered expression of the reporter gene relative to a cell that is void of a library member, thereby identifying a nucleic acid encoding a polypeptide that recognizes the target DNA site.

[0033] In another aspect, the invention features a method of constructing a library of chimeric zinc finger proteins. The method includes: providing a set of nucleic acids, each comprising a sequence encoding a zinc finger domain selected from Tables 5, 6, and 7; and joining each nucleic acid of the set to one or more, preferably two, three, or four other nucleic acids of the set to form a plurality of chimeric nucleic acids. Each chimeric nucleic acid can be located in a vector, e.g., a mammalian expression vector.

[0034] In one embodiment, the method further includes, after the joining, introducing one or more of the plurality of chimeric nucleic acids into cells and expressing the one or more chimeric nucleic acids. In another embodiment, the method further includes individually introducing one or more of the chimeric nucleic acids into a cell, e.g., a mammalian cell; expressing the chimeric nucleic acids; and monitoring expression of a gene or protein in the cell. The cell can include a reporter construct, e.g., a construct that includes a target site inferred to be recognized by the polypeptide encoded by the chimeric nucleic acid such that the polypeptide binds to the target site and either induces or represses expression of the reporter gene.

[0035] In yet another aspect, the invention features a method of characterizing a chimeric zinc finger protein, e.g., a zinc finger protein described herein. The method includes: introducing a nucleic acid that encodes the protein into a cell; expressing the nucleic acid; and determining the profile of expression of endogenous genes in the cell. Such an expression profile includes a plurality of values, wherein each value corresponds to the level of expression of a different gene, splice-variant or allelic variant of a gene (i.e., mRNA level) or the abundance of a translation product (i.e., protein level). The value can be a qualitative or quantitative assessment of the level of expression of the gene or the translation product of the gene, i.e., an assessment of the abundance of 1) an mRNA transcribed from the gene, or 2) the polypeptide encoded by the gene.

[0036] The method can further include comparing the determined expression profile to at least one reference expression profile, to thereby characterize the chimeric zinc finger protein. The reference profile can be the expression profile of a related cell that lacks a heterologous chimeric zinc finger protein or that includes a control vector. The comparison can identify the regulation of one or more genes as altered by the chimeric zinc finger protein. In one embodiment, the sample expression profile is compared to a reference profile to produce a difference profile. The sample expression profile can also be compared in multi-dimensional space to a cluster of reference profiles. In one embodiment, the sample expression profile is determined using a nucleic acid array. In another embodiment, the sample expression profile is determined using a method and/or apparatus that does not require an array (e.g., SAGE or quantitative PCR with multiple primers).

[0037] The method can further include determining or inferring a target binding site for the polypeptide, and identifying occurrences of the target binding site in a regulatory nucleic acid sequence of a gene whose regulation is altered by the polypeptide. The method can be used to distinguish direct from indirect targets.

[0038] In another aspect, the invention features a method that includes: providing a plurality of nucleic acids, each nucleic acid of the plurality encoding a polypeptide comprising a first and a second zinc finger domain, wherein the first and second zinc finger domains of the polypeptide encoded by each nucleic acid of the plurality are identical to zinc finger domains from different naturally occurring mammalian proteins, the first zinc finger domain varies among nucleic acids of the plurality, and the second zinc finger domain varies among nucleic acids of the plurality; introducing each nucleic acid of the plurality into a cell that has a given trait prior to the introducing thereby providing a plurality of cells; expressing the introduced nucleic acid in each cell of the plurality of cells; and identifying a cell from the plurality of cells in which the given trait is altered. The method can include other features described herein. Exemplary traits include enhanced sensitivity or resistance to a condition (e.g., stress), altered proliferative ability, altered pathogenicity, and altered product production (e.g., metabolite production).

[0039] In yet another aspect, the invention features a method of identifying a chimeric zinc finger protein that can bind to a particular target site. The method includes: providing data records, each record associating an identifier for a naturally-occurring human zinc finger domain and at least one 3- or 4-basepair subsite that is recognized by the zinc finger domain referenced by the identifier; parsing the target site into at least two 3- or 4-basepair subsites; for each of the subsites, retrieving a set of the identifiers from the data records, the set comprising identifiers for the zinc finger domains that recognize the subsite; and designing a polypeptide that comprises a zinc finger domain for each of the subsites, the zinc finger domain being referenced by an identifier from the set for the respective subsite.

[0040] The data records can include a record that identifies a human zinc finger domain selected from Tables 5, 6, and 7. The method can further include the step of synthesizing a nucleic acid that encodes the polypeptide and/or synthesizing the polypeptide in vitro. The method can also include the step of assessing the binding of the polypeptide to the target site, e.g., using an in vitro binding assay or an in vivo assay such as an assay for reporter gene expression. The synthesized polypeptide can further include an activation or repression domain.

[0041] In one embodiment, the method further includes assessing the ability of the polypeptide to alter the expression of one or more endogenous genes. The assessing can include profiling the expression of multiple endogenous genes, e.g., using nucleic acid microarrays. The method can also further include contacting the polypeptide with a DNA that includes the target site, e.g., in vitro.

[0042] In another embodiment, the method further includes retrieving a nucleic acid encoding the polypeptide from an addressed library of nucleic acids, each nucleic acid of the library including a sequence encoding first and second zinc finger domains.

[0043] The invention also features a method that includes: storing data records in a machine readable medium, each record associating a zinc finger domain identifier and at least one 3- or 4-basepair subsite that is recognized by the zinc finger domain referenced by the identifier; retrieving from the stored records one or more identifiers that are associated with a subsite of interest; and constructing a nucleic acid encoding a polypeptide that includes (a) a zinc finger domain referenced by one of the one or more retrieved identifiers and (b) a second DNA binding domain. The second DNA binding domain can be a zinc finger domain.

[0044] The constructing can include constructing a plurality of nucleic acids, each nucleic acid of the plurality comprising a sequence encoding a zinc finger domain referenced by the retrieved identifiers. The method can further include, for each nucleic acid of the plurality, expressing the nucleic acid in a cell and assessing the change in the level of transcription of a given gene when the nucleic acid is expressed, relative to the level of transcription of the given gene when the nucleic acid is absent or not expressed. The assessing can further include assessing the level of transcription of multiple genes, e.g., by profiling.

[0045] In another aspect, the invention features a computer-based method that includes: storing information that includes associations between (a) each of a plurality of naturally occurring zinc finger domains referenced in Tables 5, 6, and 7 and (b) one or more subsites recognized by the domain; receiving a user query that comprises a string specifying a target nucleic acid sequence; and filtering the information to identify combinations of zinc finger domains predicted to recognize a site within the target nucleic acid sequence.

[0046] The method can further include displaying the combinations to a user or physically locating a library nucleic acid or polypeptide that includes one of the identified combinations of zinc finger domains from an addressed library of nucleic acids or polypeptides.

[0047] In still another aspect, the invention features a database that is stored on machine-readable medium. The database includes (i) data representing (a) individual naturally-occurring zinc finger domains, (b) nucleic acid sites, and (c) chimeric polypeptides that comprise a plurality of naturally-occurring zinc finger domains; and (ii) associations that relate (1) individual zinc finger domains and nucleic acid sites recognized by the respective individual domains; (2) chimeric polypeptides and their respective component zinc finger domains; and (3) chimeric polypeptides and nucleic acid sites recognized by the respective chimeric polypeptides. The database can enable a user to identify combinations of zinc finger domains predicted to recognize a site within the target nucleic acid sequence.

[0048] The data can further represent (d) addressable locations, the locations being associated with resident chimeric polypeptides of an arrayed polypeptide library or (e) an expression profile, as described above. Each expression profile can be associated with a chimeric polypeptide.

[0049] Also featured is a library that includes a plurality of polypeptides, each polypeptide comprising a first and a second zinc finger domain, wherein the first and second zinc finger domains of each polypeptide are identical to mammalian zinc finger domains that are from different naturally occurring polypeptides, the first zinc finger domain varies among polypeptides of the plurality, and the second zinc finger domain varies among polypeptides of the plurality. Each polypeptide of the library can be attached to a solid support (e.g., a bead, matrix, or planar array).

[0050] The invention further provides a method of profiling a test nucleic acid. The method includes: contacting the test nucleic acid with the polypeptides of a library described herein; and identifying one or more polypeptides that specifically bind to the test nucleic acid. The polypeptides can be immobilized on an addressable array or attached to a virus particle.

[0051] The invention features a method of identifying a peptide domain that recognizes a target site on a DNA. This method is sometimes referred to herein as the “domain selection method” or the “in vivo screening method.” The method includes providing (1) cells containing a reporter construct and (2) a plurality of hybrid nucleic acids. The reporter construct has a reporter gene operably linked to a promoter that has both a recruitment site and a target site. The reporter gene is expressed above a given level when a transcription factor recognizes (i.e., binds to a degree above background) both the recruitment site and the target site of the promoter, but not when the transcription factor recognizes only the recruitment site of the promoter. Each hybrid nucleic acid of the plurality encodes a non-naturally occurring protein with the following elements: (i) a transcription activation domain, (ii) a DNA binding domain that recognizes the recruitment site, and (iii) a test zinc finger domain. The amino acid sequence of the test zinc finger domain varies among the members of the plurality of hybrid nucleic acids. The method further includes: contacting the plurality of nucleic acids with the cells under conditions that permit at least one of the plurality of nucleic acids to enter at least one of the cells; maintaining the cells under conditions permitting expression of the hybrid nucleic acids in the cells; and identifying a cell that expresses the reporter gene above the given level as an indication that the cell contains a hybrid nucleic acid encoding a test zinc finger domain that recognizes the target site.

[0052] The DNA binding domain, i.e., the domain that recognizes the recruitment site and does not vary among members of the plurality, can include, for example, one, two, three, or more zinc finger domains. The cells utilized in the method can be prokaryotic or eukaryotic. Exemplary eukaryotic cells are yeast cells, e.g. Saccharomyces cerevisiae, Schizosaccharomyces pombe, or, Pichia pasteuris; insect cells such as Sf9 cells; and mammalian cells such as fibroblasts or lymphocytes.

[0053] The “given level” is the amount of expression observed when the transcription factor recognizes the recruitment site, but not the target site. The “given level” in some cases may be zero (at least within the limits of detection of the assay used).

[0054] The method can include an additional step of amplifying a source nucleic acid encoding the test zinc finger domain from a nucleic acid, e.g., genomic DNA, an mRNA mixture, or a cDNA mixture, to produce an amplified fragment. The source nucleic acid can be amplified using an oligonucleotide primer. The oligonucleotide primer can be one of a set of degenerate oligonucleotides (e.g., a pool of specific oligonucleotides having different nucleic acid sequences, or a specific oligonucleotide having a non-natural base such as inosine) that anneals to a nucleic acid encoding a conserved domain boundary. Alternatively, the primer can be a specific oligonucleotide. The amplified fragments are utilized to produce a hybrid nucleic acid for inclusion in the plurality of hybrid nucleic acids used in the aforementioned method.

[0055] The method can further include the steps of (i) identifying a candidate zinc finger domain amino acid sequence in a sequence database; (ii) providing a candidate nucleic acid encoding the candidate zinc finger domain amino acid sequence; and (iii) utilizing the candidate nucleic acid to construct a hybrid nucleic acid for inclusion in the plurality of hybrid nucleic acids used in the aforementioned method. The database can include records for multiple amino acid sequences, e.g., known and/or predicted proteins, as well as multiple nucleic acid sequences such as cDNAs, ESTs, genomic DNA, or genomic DNA computationally processed to remove predicted introns.

[0056] If desired, the method can be repeated to identify a second test zinc finger domain that recognizes a second target site, e.g., a site other than that recognized by the first test zinc finger domain. Subsequently, a nucleic acid can be constructed that encodes both the first and the second identified test zinc finger domains. The encoded hybrid protein would specifically recognize a target site that includes the target site of the first test zinc finger domain and the target site of the second test zinc finger domain.

[0057] The invention also features a method of determining whether a test zinc finger domain recognizes a target site on a promoter. This method is sometimes referred to herein as the “site selection method.” The method includes the steps of providing a reporter construct and a hybrid nucleic acid. The reporter gene is operably linked to a promoter that includes a recruitment site and a target site, and is expressed above a given level when a transcription factor recognizes both the recruitment site and the target site of the promoter, but not when the transcription factor recognizes only the recruitment site of the promoter. The hybrid nucleic acid encodes a non-naturally occurring protein with the following elements: (i) a transcription activation domain, (ii) a DNA binding domain that recognizes the recruitment site, and (iii) a test zinc finger domain. The method further includes: contacting the reporter construct with a cell under conditions that permit the reporter construct to enter the cell; prior to, after, or concurrent with the aforementioned step, contacting the hybrid nucleic acid with the cell under conditions that permit the hybrid nucleic acid to enter the cell; maintaining the cell under conditions permitting expression of the hybrid nucleic acid in the cell; and detecting reporter gene expression in the cell. A level of reporter gene expression greater than the given level is an indication that the test zinc finger domain recognizes the target site.

[0058] The reporter construct and the hybrid nucleic acid can be contained in separate plasmids. The two plasmids can be introduced into the cell simultaneously or consecutively. One or both plasmids can contain selectable markers. The reporter construct and the hybrid nucleic acid can also be contained on the same plasmid, in which case only one contacting step is required to introduce both nucleic acids into a cell. In yet another implementation, one or both of the nucleic acids are stably integrated into a genome of a cell. For this method, as for any in vivo method described herein, the transcriptional activation domain can be replaced with a transcriptional repression domain, and a cell is identified in which the level of reporter gene expression is decreased to a level below the given level.

[0059] Another method of the invention facilitates the rapid determination of a binding preference of a test zinc finger domain by fusing two cells. The method includes: providing a first cell containing the reporter gene; providing a second cell containing the hybrid nucleic acid; fusing the first and second cells to form a fused cell; maintaining the fused cells under conditions permitting expression of the hybrid nucleic acids in the fused cell; and detecting reporter gene expression in the fused cell, wherein a level of reporter gene expression greater than the given level is an indication that the test zinc finger domain recognizes the target site. For example, the first and second cells can be tissue culture cells or fungal cells. An exemplary implementation of the method utilizes S. cerevisiae cells. The first cell has a first mating type, e.g., MATa; the second cell has a second mating type different from the first, e.g., MATα. The two cells are contacted with one another, and yeast mating produces a single cell (e.g., MATa/α) with a nucleus containing the genomes of both the first and second cells. The method can including providing multiple first cells, all of the same first mating type where each first cell has a reporter construct with a different target site. Multiple second cells, all of the same second mating type and each having a different test zinc finger domain, are also provided. A matrix is generated of multiple pair-wise matings, e.g., all possible pair-wise matings. The method is applied to determine the binding preference of multiple test zinc finger domains for multiple binding sites, e.g., a complete set of possible target sites.

[0060] The invention also provides a method of assaying a binding preference of a test zinc finger domain. The method includes providing (1) cells, essentially all of which contain a hybrid nucleic acid, and (2) a plurality of reporter constructs. Each reporter construct of the plurality has a reporter gene operably linked to a promoter with a recruitment site and a target site. The reporter gene is expressed above a given level when a transcription factor recognizes both the recruitment site and the target site of the promoter, but not when the transcription factor binds only the recruitment site of the promoter. The second target site varies among the members of the plurality of reporter constructs. The hybrid nucleic acid encodes a hybrid protein with the following elements: (i) a transcription activation domain, (ii) a DNA binding domain that recognizes the recruitment site, and (iii) a test zinc finger domain. The method further includes: contacting the plurality of reporter constructs with the cells under conditions that permit at least one of the plurality of reporter constructs to enter at least one of the cells; maintaining the cells under conditions permitting expression of the nucleic acids in the cells; identifying a cell that contains a reporter construct in the cell and that expresses the reporter construct above the given level as an indication that the reporter construct in the cell has a target site recognized by the zinc finger domain.

[0061] A plurality of cells, each with a different target site, can be identified by the above method if the test zinc finger domain has a binding preference for more than one target site. The method can further include identifying the cell that exhibits the highest level of reporter gene expression. Alternatively, a threshold level of reporter gene expression is determined, e.g., an increase in reporter gene expression of 2, 4, 8, 20, 50, 100, 1000 fold or greater, and all cells exhibiting reporter gene expression above the threshold are selected.

[0062] The target binding site, for example, can be between two and six nucleotides long. The plurality of reporter constructs can include every possible combination of A, T, G, and C nucleotides at two, three, or four or more positions of the target binding site.

[0063] In another aspect, the invention features a method of identifying a plurality of zinc finger domains. The method includes: carrying out the domain selection method to identify a first test zinc finger domain and carrying out the domain selection method again to identify a second test zinc finger domain that recognizes a target site different from a target site of the first test zinc finger domain. Also featured is a method of generating a nucleic acid encoding a chimeric zinc finger protein, the method includes carrying out the domain selection method twice to identify a first and second test zinc finger domain and constructing a nucleic acid encoding a polypeptide including the first and second test zinc finger domains. The nucleic acid can encode a hybrid protein that includes the two domains that specifically recognize a site that includes two subsites. The subsites are the target site of the first test zinc finger domain and target site of the second test zinc finger domain. The method can be repeated to identify additional zinc finger domains and construct a nucleic acid encoding a polypeptide including three, four, five, six, or more zinc finger domain, e.g., to specifically recognize a nucleic acid binding site.

[0064] In still another aspect, the invention features a method of identifying a DNA sequence recognized by zinc finger domains. The method includes: carrying out the site selection method to identify a first binding preference for a first test zinc finger domain, and carrying out the site selection method again to identify a second binding preference for a second test zinc finger domain. A nucleic acid can be constructed which encodes both the first and the second identified test zinc finger domains. The nucleic acid can encode a hybrid protein including the two domains that specifically recognizes a site that includes the target site of the first test zinc finger domain and target site of the second test zinc finger domain. The method can be repeated to identify additional zinc finger domains and construct a nucleic acid encoding a polypeptide including three, four, five, six, or more zinc finger domains, e.g., to specifically recognize a nucleic acid binding site.

[0065] The invention also features a method of identifying a peptide domain that recognizes a target site on a DNA. The method includes providing (1) cells containing a reporter construct and (2) a plurality of hybrid nucleic acids. The reporter construct has a reporter gene operably linked to a promoter that has both a recruitment site and a target site. The reporter gene is expressed below a given level when a transcription factor recognizes (i.e., binds to a degree above background) both the recruitment site and the target site of the promoter, but not when the transcription factor recognizes only the recruitment site of the promoter. Each hybrid nucleic acid of the plurality encodes a non-naturally occurring protein with the following elements: (i) a transcription repression domain, (ii) a DNA binding domain that recognizes the recruitment site, and (iii) a test zinc finger domain. The amino acid sequence of the test zinc finger domain varies among the members of the plurality of hybrid nucleic acids. The method further includes: contacting the plurality of nucleic acids with the cells under conditions that permit at least one of the plurality of nucleic acids to enter at least one of the cells; maintaining the cells under conditions permitting expression of the hybrid nucleic acids in the cells; and identifying a cell that expresses the reporter gene below the given level as an indication that the cell contains a hybrid nucleic acid encoding a test zinc finger domain that recognizes the target site. Additional embodiments of this method are as for the similar method utilizing a transcription activation domain. Likewise, any other selection method described herein can be performed using a transcriptional repression domain in place of a transcriptional activation domain.

[0066] In another aspect, the invention features certain purified polypeptides and isolated nucleic acids. A purified polypeptide of the invention can include a polypeptide having one or more of the following amino acid sequences:

[0067] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Cys-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:68),

[0068] Xa-X-Cys-X2-5-Cys-X3-Xa-X-His-X-Ser-Asn-Xb-X-Lys-His-X3-5-His (SEQ ID NO:69),

[0069] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ser-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:70),

[0070] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Thr-Xb-X-Val-His-X3-5-His (SEQ ID NO:71),

[0071] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Val-X-Ser-Xc-Xb-X-Arg-His-X3-5-His (SEQ ID NO:72),

[0072] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:73),

[0073] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO:74),

[0074] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Xc-Xb-X-Arg-His-X3-5-His (SEQ ID NO:75),

[0075] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ala-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 150),

[0076] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Phe-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:151),

[0077] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO: 152),

[0078] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Val-His-X3-5-His (SEQ ID NO: 153),

[0079] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Ile-His-X3-5-His (SEQ ID NO: 154),

[0080] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:155),

[0081] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Thr-His-Xb-X-Gln-His-X3-5-His (SEQ ID NO:156),

[0082] Cys-X2-5-Cys-X3-Xa-X-Gln-X-Thr-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 157),

[0083] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-Lys-Xb-X-Ile-His-X3-5-His (SEQ ID NO: 158),

[0084] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:159),

[0085] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Gly-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 161),

[0086] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-Glu-Xb-X-Arg-His-X3-5-His (SEQ ID NO:162),

[0087] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:163),

[0088] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO: 164),

[0089] Xa-X-Cys-X2-5Cys-X3-Xa-X-Arg-X-Asp-Lys-Xb-X-Arg-His-X3-5-His (SEQ ID NO:165),

[0090] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Ser-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:166),

[0091] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Thr-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:160),

[0092] Xa-X-Cys-X2-5-Cys-X3-Xa-X-His-X-Ser-Ser-Xb-X-Arg-His-X3-5-His (SEQ ID NO:167),

[0093] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 168),

[0094] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Lys-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 169),

[0095] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Lys-His-X3-5-His (SEQ ID NO:170),

[0096] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO:171),

[0097] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Val-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO:172),

[0098] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Cys-Xb-X-Arg-His-X3-5-His (SEQ ID NO:193),

[0099] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO:194),

[0100] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Trp-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:195), or

[0101] Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Ala-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 196),

[0102] wherein Xa is phenylalanine or tyrosine, Xb is a hydrophobic residue, and Xc is serine or threonine. Nucleic acids of the invention include nucleic acids encoding the aforementioned polypeptides. In one embodiment, the amino acid sequence listed above is a naturally occurring sequence.

[0103] In addition, purified polypeptides of the invention can have an amino acid sequence at least 50%, 60%, 70%, 80%, 90%, 93%, 95%, 96%, 98%, 99%, or 100% identical to SEQ ID NOs: 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 103, 105, 107, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 141, 143, 145, 147, 149, 173, 175, 177, 179, 181, 183, 185, 187, 189, or 191. The polypeptides can be identical to SEQ ID NOs: 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 103, 105, 107, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 141, 143, 145, 147, 149, 173, 175, 177, 179, 181, 183, 185, 187, 189, or 191 at the amino acid positions corresponding to the nucleic acid contacting residues of the polypeptide. Alternatively, the polypeptides differ from SEQ ID NOs: 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61, 63, 65, 67, 103, 105, 107, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 141, 143, 145, 147, 149, 173, 175, 177, 179, 181, 183, 185, 187, 189, or 191 at at least one of the residues corresponding to the nucleic acid contacting residues of the polypeptide. The polypeptides can also differ at at least one residue other than a DNA contacting residue (see below for further explanation). For example, within a given zinc finger domain, the polypeptide may differ by a single amino acid from the amino acid sequences referenced above, or by two, three, or four amino acids from the sequences referenced above. The difference may be due to a conservative substitution as defined herein. In one embodiment, the amino acids differences with respect to the sequences referenced above are located between the second zinc-coordinating cysteine and the −1 DNA contacting position (referring to the numbering system for DNA contacting positions described below). The comparison of sequences and determination of percent identity between two sequences can be accomplished using a mathematical algorithm. In particular, the percent identity between two amino acid sequences is determined using the Needleman and Wunsch ((1970) J. Mol. Biol. 48:444-453) algorithm which has been incorporated into the GAP program in the GCG software package, using a Blossum 62 scoring matrix with a gap penalty of 12, a gap extend penalty of 4, and a frameshift gap penalty of 5.

[0104] The purified polypeptides can also include one or more of the following: a heterologous DNA binding domain, a nuclear localization signal, a small molecular binding domain (e.g., a steroid binding domain), an epitope tag or purification handle, a catalytic domain (e.g., a nucleic acid modifying domain, a nucleic acid cleavage domain, or a DNA repair catalytic domain) and/or a transcriptional function domain (e.g., an activation domain, a repression domain, and so forth). In one embodiment, the polypeptide further include a second zinc finger domain, e.g., a domain having a sequence described herein. For example, the polypeptide can include an array of zinc fingers that include two or more zinc finger domains. Each domain can have a sequence selected from the group consisting of SEQ ID NOs:68-75, 150-172, and 193-196, or subsets thereof. Further, each domain can have a sequence selected from the group consisting of SEQ ID NOs: 23, 25, 27, 29, 31, 33, 35, 37, 39, 41, 43, 45, 47, 49, 51, 53, 55, 57, 59, 61,63, 65, 67, 103, 105, 107, 111, 113, 115, 117, 119, 121, 123, 125, 127, 129, 131, 133, 135, 137, 141, 143, 145, 147, 149, 173, 175, 177, 179, 181, 183, 185, 187, 189, and 191, and subsets thereof.

[0105] As described herein, the polypeptide can be produced in a cell and can regulate a gene in the cell, e.g., an endogenous gene, by binding to a target site, e.g., a site that includes a subsite that the respective zinc finger domain(s) recognizes. See, e.g., Tables 5, 6, and 7.

[0106] The invention also includes isolated nucleic acid sequences encoding the aforementioned polypeptides, and isolated nucleic acid sequences that hybridize under high stringency conditions to a single stranded probe, the sequence of the probe consisting of SEQ ID NO:22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 42, 44, 46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 102, 104, 106, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 140, 142, 144, 146, 148, 150, 174, 176, 178, 180, 182, 184, 186, 188, 190, 192 or the complements thereof. The invention further includes a method of expressing in a cell a polypeptide of the invention fused to a heterologous nucleic acid binding domain. The method includes introducing into a cell a nucleic acid encoding the aforementioned fusion protein. A nucleic acid of the invention can be operably regulated by a heterologous nucleic acid sequence, e.g., an inducible promoter (e.g., a steroid hormone regulated promoter, a small-molecule regulated promoter, or an engineered inducible system such as the tetracycline Tet-On and Tet-Off systems).

[0107] The term “base contacting positions,” “DNA contacting positions,” or “nucleic acid contacting positions” refers to the four amino acid positions of zinc finger domains that structurally correspond to the positions of amino acids arginine 73, aspartic acid 75, glutamic acid 76, and arginine 79 of SEQ ID NO:21. These positions are also referred to as positions −1, 2, 3, and 6, respectively. To identify positions in a query sequence that correspond to the base contacting positions, the query sequence is aligned to the zinc finger domain of interest such that the cysteine and histidine residues of the query sequence are aligned with those of finger 3 of Zif268. The ClustalW WWW Service at the European Bioinformatics Institute (Thompson et al. (1994) Nucleic Acids Res. 22:4673-4680) provides one convenient method of aligning sequences.

[0108] Conservative amino acid substitutions refer to the interchangeability of residues having similar side chains. For example, a group of amino acids having aliphatic side chains is glycine, alanine, valine, leucine, and isoleucine; a group of amino acids having aliphatic-hydroxyl side chains is serine and threonine; a group of amino acids having amide-containing side chains is asparagine and glutamine; a group of amino acids having aromatic side chains is phenylalanine, tyrosine, and tryptophan; a group of amino acids having basic side chains is lysine, arginine, and histidine; a group of amino acids having acidic side chains is aspartic acid and glutamic acid; and a group of amino acids having sulfur-containing side chains is cysteine and methionine. Depending on circumstances, amino acids within the same group may be interchangeable. Some additional conservative amino acids substitution groups are: valine-leucine-isoleucine; phenylalanine-tyrosine; lysine-arginine; alanine-valine; aspartic acid-glutamic acid; and asparagine-glutamine.

[0109] The term “heterologous polypeptide” refers either to a polypeptide with a non-naturally occurring sequence (e.g., a hybrid polypeptide) or a polypeptide with a sequence identical to a naturally occurring polypeptide but present in a milieu in which it does not naturally occur.

[0110] The term “hybrid” refers to a non-naturally occurring polypeptide that comprises amino acid sequences derived from either (i) at least two different naturally occurring sequences; (ii) at least one artificial sequence (i.e., a sequence that does not occur naturally) and at least one naturally occurring sequence; or (iii) at least two artificial sequences (same or different). Examples of artificial sequences include mutants of a naturally occurring sequence and de novo designed sequences.

[0111] As used herein, the term “hybridizes under stringent conditions” refers to conditions for hybridization in 6×sodium chloride/sodium citrate (SSC) at 45° C., followed by two washes in 0.2×SSC, 0.1% SDS at 65° C.

[0112] The term “binding preference” refers to the discriminative property of a polypeptide for selecting one nucleic acid binding site relative to another. For example, when the polypeptide is limiting in quantity relative to two different nucleic acid binding sites, a greater amount of the polypeptide will bind the preferred site relative to the other site in an in vivo or in vitro assay described herein.

[0113] As used herein, “degenerate oligonucleotides” refers to both (a) a population of different oligonucleotides that each encode a particular amino acid sequence, and (b) a single species of oligonucleotide that can anneal to more than one sequence, e.g., an oligonucleotide with an unnatural nucleotide such as inosine.

[0114] The present invention provides numerous benefits. The ability to select a DNA binding domain that recognizes a particular sequence permits the design of novel polypeptides that bind to specific site on a DNA. Thus, the invention facilitates the customized generation of novel polypeptides that can regulate the expression of a selected target, e.g., a gene required by a pathogen can be repressed, a gene required for cancerous growth can be repressed, a gene poorly expressed or encoding an unstable protein can be activated and overexpressed, and so forth.

[0115] The use of zinc finger domains is particularly advantageous. First, the zinc finger motif recognizes very diverse DNA sequences. Second, the structure of naturally occurring zinc finger proteins is modular. For example, the zinc finger protein Zif268, also called “Egr-1,” is composed of a tandem array of three zinc finger domains. FIG. 1 is the x-ray crystallographic structure of zinc finger protein Zif268, consisting of three fingers complexed with DNA (Pavletich and Pabo, (1991) Science 252:809-817). Each finger independently contacts 3-4 basepairs of the DNA recognition site. High affinity binding is achieved by the cooperative effect of having multiple zinc finger modules in the same polypeptide chain.

[0116] It is frequently the ultimate goal to obtain a DNA binding polypeptide that functions within a cell. Advantageously, the in vivo selection method identifies up-front DNA binding polypeptides that are functional at a specific DNA site within a cell. The factors associated with recognition in a cell, particularly a eukaryotic cell, can be vastly different from the factors present during an in vitro selection scenario. For example, in a eukaryotic nucleus, a polypeptide must compete with the myriad other nuclear proteins for a specific nucleic acid binding site. A nucleosome or another chromatin protein can occupy, occlude, or compete for the binding site. Even if unbound, the conformation of a nucleic acid in the cell is subject to bending, supercoiling, torsion, and unwinding. The polypeptide itself is exposed to proteases and chaperones, among other factors. Moreover, the polypeptide is confronted with an entire genome of possible binding sites, and hence must be endowed with a high specificity for the desired site in order to survive the selection process. In contrast to in vivo selection, an in vitro selection can select for the highest affinity binder rather than the highest specificity binder.

[0117] The use of a reporter gene to indicate the binding ability of an expressed polypeptide chimera not only is efficient and simple, but also obviates the need to develop a complex interaction code that accounts for the energetics of the protein-nucleic acid interface and the immense number of peripheral factors, such as surrounding residues and nucleotides that also affect the binding interface. (Segal et al. (1999) Proc. Natl. Acad. Sci. USA 96:2758-2763).

[0118] The present invention avails itself of all the zinc finger domains present in the human genome, or any other genome. This diverse sampling of sequence space occupied by the zinc finger domain structural fold may have the additional advantages inherent in eons of natural selection. Moreover, by utilizing domains from the host species, a DNA binding protein engineered for a gene therapy application by the methods described herein has a reduced likelihood of being regarded as foreign by the host immune response.

[0119] A DNA binding protein identified by a method described herein can be used in a variety of applications. For example, the DNA binding protein can be used to alter the expression of an endogenous gene in a cultured cell or in a cell in a host organism. The DNA binding protein can be used to alter the phenotype of a cell, e.g., enhanced sensitivity or resistance to a condition (e.g., stress), altered proliferative ability, altered pathogenicity, and altered product production (e.g., metabolite production).

[0120] All patents, patent applications, and references cited herein are incorporated by reference in their entirety for all purposes. The details of one or more embodiments of the invention are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the invention will be apparent from the description and drawings, and from the claims.

DESCRIPTION OF DRAWINGS

[0121] FIG. 1 is a depiction of the three dimensional structure of the Zif268 zinc finger protein that consists of three finger domains and binds the DNA sequence, 5′-GCG TGG GCG T-3′ (SEQ ID NO:197). The black circles represent the location of the zinc ion.

[0122] FIG. 2 is an illustration of the hydrogen-bonding interactions between amino acid residues of Zif268 and DNA bases. Amino acid residues at positions −1, 2, 3, and 6 along the α-helix interact with the bases at specific positions. The bold lines represent ideal hydrogen bonding, while the dotted lines represent potential hydrogen bonding.

[0123] FIG. 3 is a recognition code table that summarizes the interactions between DNA bases and amino acid residues at positions −1, 2, 3, and 6 along the α-helix of a zinc finger domain.

[0124] FIG. 4 is a depiction of the positions of amino acid residues and their corresponding 3 base triplets. The bold lines represent the main interactions observed, while the dotted line represents an auxiliary interaction.

[0125] FIG. 5 is a diagram illustrating the principles of the in vivo selection system disclosed herein. Of the various zinc finger mutants, zinc finger domain A recognizes the target sequence (designated XXX X) and activates the transcription of HIS3 reporter gene. As a result, yeast colonies grow on a medium lacking histidine. In contrast, zinc finger domain B does not recognize the target sequence and thus the reporter gene remains repressed. As a result, no colonies grow on a medium lacking histidine. AD represents the transcriptional activation domain.

[0126] FIG. 6 is a list of 10-bp sequences (SEQ ID NOs:1-5, respectively) found in long terminal repeats (LTR) of HIV-1 and in the promoter region of CCR5, a human gene encoding a coreceptor for HIV-1. The underlined portions represent 4-bp target sequences used in the present selection.

[0127] FIG. 7 is a depiction of the base sequences of the binding sites linked to the reporter gene (SEQ ID NOs:6-17, respectively). Each binding site consists of a tandem array of 4 composite binding sequences. Each composite binding sequence was constructed by connecting truncated binding sequence 5′-GG GCG-3′ recognized by finger 1 and finger 2 of Zif268 to 4-bp target sequences.

[0128] FIG. 8 is a diagram of pPCFMS-Zif, a plasmid that can be used for the construction of a library of hybrid plasmids (SEQ ID NOs: 18 and 19).

[0129] FIG. 9 is a representation of the base sequence for the gene coding for Zif268 zinc finger protein inserted into pPCFMS-Zif and the corresponding translated amino acid sequences (SEQ ID NOs:20 and 21, respectively). Sites recognized by restriction enzymes are underlined.

[0130] FIG. 10 is a photograph of a culture plate having yeast cells obtained from retransformation and cross transformation using zinc finger proteins selected by the in vivo selection system.

[0131] FIG. 11A is a listing of the nucleotide sequence of polylinker region of P3 (SEQ ID NO:251). The sequence outside of this region is identical to that of the parental vector, pcDNA3 (Invitrogen). Each enzyme site is italicized and HA tag is underlined. Both initiation and stop codons are indicated by bold letters. The nuclear localization signal (NLS) is also indicated.

[0132] FIG. 11B is a schematic of one exemplary method for zinc finger protein library construction.

[0133] FIG. 12 is a schematic of reporter constructs and segments of their sequence in the initiator region. 5XGal4, TATA and Inr indicate: five GAL4 binding sites, the TATA box and the transcriptional initiator, respectively. NNNNNNNNN indicates the site for the cognate binding site for a specific ZFP. The positions are numbered with respect to the transcription start point (+1) and identical nucleotides are indicated by “−”. “>” represents a deletion of a corresponding nucleotide.

DETAILED DESCRIPTION

[0134] The invention features a novel screening method for determining the nucleic acid binding preferences of test zinc finger domains. The method is easily adapted to a variety of protein domains, a variety of sources for these domains, and a number of library designs, reporter genes, and selection and screening systems. The screening method can be implemented as a high-throughput platform. Information obtained from the screening method is readily applied to a method of designing artificial nucleic acid binding proteins, typically DNA binding proteins, but also in some cases RNA binding proteins or even proteins that interact with other proteins. The design method appropriates the binding preferences of test zinc finger domains to guide the modular assembly of a chimeric nucleic acid binding protein. A designed protein can be further optimized or varied with the screening method.

[0135] DNA Binding Domains

[0136] The invention utilizes collections of nucleic acid binding domains with differing binding specificities. A variety of protein structures are known to bind nucleic acids with high affinity and high specificity. These structures are used repeatedly in a myriad of different proteins to specifically control nucleic acid function (for reviews of structural motifs which recognize double stranded DNA, see, e.g., Pabo and Sauer (1992) Annu. Rev. Biochem. 61:1053-95; Patikoglou and Burley (1997) Annu. Rev. Biophys. Biomol. Struct. 26:289-325; Nelson (1995) Curr Opin Genet Dev. 5:180-9). A few non-limiting examples of nucleic acid binding domains include:

[0137] Zinc fingers. Zinc fingers are small polypeptide domains of approximately 30 amino acid residues in which there are four residues, either cysteine or histidine, appropriately spaced such that they can coordinate a zinc ion (FIG. 1; for reviews, see, e.g., Klug and Rhodes, (1987) Trends Biochem. Sci. 12:464-469(1987); Evans and Hollenberg, (1988) Cell 52:1-3; Payre and Vincent, (1988) FEBS Lett. 234:245-250; Miller et al., (1985) EMBO J. 4:1609-1614; Berg, (1988) Proc. Natl. Acad. Sci. U.S.A. 85:99-102; Rosenfeld and Margalit, (1993) J. Biomol. Struct. Dyn. 11:557-570). Hence, zinc finger domains can be categorized according to the identity of the residues that coordinate the zinc ion, e.g., as the Cys2-His2 class, the Cys2-Cys2 class, the Cys2-CysHis class, and so forth. The zinc coordinating residues of Cys2-His2 zinc fingers are typically spaced as follows:

[0138] Xa-X-C-X2-5-C-X3-Xa-X5-ψ-X2-H-X3-5-H.

[0139] where ψ (psi) is a hydrophobic residue (Wolfe et al, (1999) Annu. Rev. Biophys. Biomol. Struct. 3:183-212) (SEQ ID NO:76), “X” represents any amino acid, Xa is phenylalanine or tyrosine, the subscript number indicates the number of amino acids, and a subscript with two hyphenated numbers indicates a typical range of intervening amino acids. Typically, the intervening amino acids fold to form an anti-parallel β-sheet that packs against an α-helix, although the anti-parallel β-sheets can be short, non-ideal, or non-existent. The fold positions the zinc-coordinating side chains so they are in a tetrahedral conformation appropriate for coordinating the zinc ion. The base contacting residues are at the N-terminus of the finger and in the preceding loop region (FIG. 2).

[0140] For convenience, the primary DNA contacting residues of a zinc finger domain are numbered: −1, 2, 3, and 6 based on the following example:

−1 1 2 3 4 5 6

[0141] Xa- α-5-X3-Xa-X—C—X—S—N-Xb-X—R—H—X3- -H (SEQ ID NO:68),

[0142] As noted in the example above, the DNA contacting residues are Cys (C), Ser (S), Asn (N), and Arg (R). The above motif can be abbreviated CSNR. As used herein, such abbreviation is a shorthand that refers to a particular polypeptide sequence from the second residue preceding the first cysteine (Xa, above, initial residue of SEQ ID NO:68) to the ultimate metal-chelating histidine (ultimate residue of SEQ ID NO:68). Where two different sequences have the same motif, a number may be used to indicate each sequence (e.g., CSNR1, CSNR2). In certain contexts where made explicitly apparent, the four-letter abbreviation refers to the motif in general.

[0143] A zinc finger DNA-binding protein may consist of a tandem array of three or more zinc finger domains.

[0144] The zinc finger domain (or “ZFD”) is one of the most common eukaryotic DNA-binding motifs, found in species from yeast to higher plants and to humans. By one estimate, there are at least several thousand zinc finger domains in the human genome alone, possibly at least 4,500. Zinc finger domains can be identified in or isolated from zinc finger proteins. Non-limiting examples of zinc finger proteins include CF2-II; Kruppel; WT1; basonuclin; BCL-6/LAZ-3; erythroid Kruppel-like transcription factor; transcription factors Sp1, Sp2, Sp3, and Sp4; transcriptional repressor YY1; EGR1/Krox24; EGR2/Krox20; EGR3/Pilot; EGR4/AT133; Evi-1; GLI1; GLI2; GLI3; HIV-EP1/ZNF40; HIV-EP2; KR1; ZfX; ZfY; and ZNF7.

[0145] Computational methods described below can be used to identify all zinc finger domains encoded in a sequenced genome or in a nucleic acid database. Any such zinc finger domain can be utilized. In addition, artificial zinc finger domains have been designed, e.g., using computational methods (e.g., Dahiyat and Mayo, (1997) Science 278:82-7).

[0146] Although many zinc finger domains bind to DNA sites, a number of zinc finger domains can bind other ligands, e.g., RNA sites and other proteins. In some implementations, a chimeric zinc finger domain protein is engineered to bind to a non-DNA ligand, e.g., a target protein or a target RNA site. The target RNA site can be a site on a ncRNA, e.g., a naturally occurring ncRNA.

[0147] Homeodomains. Homeodomains are simple eukaryotic domains that consist of a N-terminal arm that contacts the DNA minor groove, followed by three α-helices that contact the major groove (for a review, see, e.g., Laughon, (1991) Biochemistry 30:11357-67). The third α-helix is positioned in the major groove and contains critical DNA-contacting side chains. Homeodomains have a characteristic highly conserved motif present at the turn leading into the third α-helix. The motif includes an invariant tryptophan that packs into the hydrophobic core of the domain. This motif is represented in the Prosite database (see Falquet et al. (2002) Nucleic Acids Res. 30:235-238) as PDOC00027 ([L/I/V/MIF/Y/G]-[A/S/L/V/R]-X(2)-[L/IV/M/S/T/A/C/N]-X-[L/I/V/M]-X(4)-[L/I/V]-[R/K/N/Q/E/S/T/A/I/Y]-[L/I/V/F/S/T/N/K/H]-W-[F/Y/V/C]-X-[N/D/Q/T/A/H]-X(5)-[R/K/N/A/I/M/W]; SEQ ID NO:77). Homeodomains are commonly found in transcription factors that determine cell identity and provide positional information during organismal development. Such classical homeodomains can be found in the genome in clusters such that the order of the homeodomains in the cluster approximately corresponds to their expression pattern along a body axis. Homeodomains can be identified by alignment with a homeodomain, e.g., Hox-1, or by alignment with a homeodomain profile or a homeodomain hidden Markov Model (HMM; see below), e.g., PF00046 of the Pfam database or “HOX” of the SMART database, or by the Prosite motif PDOC00027 as mentioned above.

[0148] Helix-turn-helix proteins. This DNA binding motif is common among many prokaryotic transcription factors. There are many subfamilies, e.g., the LacI family, the AraC family, to name but a few. The two helices in the name refer to a first α-helix that packs against and positions a second α-helix in the major groove of DNA. These domains can be identified by alignment with a HMM, e.g., HTH_ARAC, HTH_ARSR, HTH_ASNC, HTH_CRP, HTH_DEOR, HTH_DTXR, HTH_GNTR, HTH_ICLR, HTH_LACI, HTH_LUXR, HTH_MARR, HTH_MERR, and HTH_XRE profiles available in the SMART database.

[0149] Helix-loop-helix proteins. This DNA binding domain is commonly found among homo- and hetero-dimeric transcription factors, e.g., MyoD, fos, jun, E11, and myogenin. The domain consists of a dimer, each monomer contributing two α-helices and intervening loop. The domain can be identified by alignment with a HMM, e.g., the “HLH” profile available in the SMART database. Although helix-loop-helix proteins are typically dimeric, monomeric versions can be constructed by engineering a polypeptide linker between the two subunits such that a single open reading frame encodes both the two subunits and the linker.

[0150] Identification of DNA-Binding Domains

[0151] A variety of methods can be used to identify structural domains.

[0152] Computational Methods. The amino acid sequence of a DNA binding domain isolated by a method described herein can be compared to a database of known sequences, e.g., an annotated database of protein sequences or an annotated database which includes entries for nucleic acid binding domains. In another implementation, databases of uncharacterized sequences, e.g., unannotated genomic, EST or full-length cDNA sequence; of characterized sequences, e.g., SwissProt or PDB; and of domains, e.g., Pfam, ProDom (Corpet et al. (2000) Nucleic Acids Res. 28:267-269), and SMART (Simple Modular Architecture Research Tool, Letunic et al. (2002) Nucleic Acids Res 30, 242-244) can provide a source of nucleic acid binding domain sequences. Nucleic acid sequence databases can be translated in all six reading frames for the purpose of comparison to a query amino acid sequence. Nucleic acid sequences that are flagged as encoding candidate nucleic acid binding domains can be amplified from an appropriate nucleic acid source, e.g., genomic DNA or cellular RNA. Such nucleic acid sequences can be cloned into an expression vector. The procedures for computer-based domain identification can be interfaced with an oligonucleotide synthesizer and robotic systems to produce nucleic acids encoding the domains in a high-throughput platform. Cloned nucleic acids encoding the candidate domains can also be stored in a host expression vector and shuttled easily into an expression vector, e.g., into a translational fusion vector with Zif268 fingers 1 and 2, either by restriction enzyme-mediated subcloning or by site-specific recombinase-mediated subcloning (see U.S. Pat. No. 5,888,732). The high-throughput platform can be used to generate multiple microtitre plates containing nucleic acids encoding different candidate nucleic acid binding domains.

[0153] Detailed methods for the identification of domains from a starting sequence or a profile are well known in the art. See, for example, Prosite (Hofmann et al., (1999) Nucleic Acids Res. 27:215-219), FASTA, BLAST (Altschul et al., (1990) J. Mol. Biol. 215:403-10.), etc. A simple string search can be done to find amino acid sequences with identity to a query sequence or a query profile, e.g., using Perl to scan text files. Sequences so identified can be at least about 30%, 40%, 50%, 60%, 70%, 80%, 90%, or greater identical to an initial input sequence.

[0154] Domains similar to a query domain can be identified from a public database, e.g., using the XBLAST programs (version 2.0) of Altschul et al., (1990) J. Mol. Biol. 215:403-10. For example, BLAST protein searches can be performed with the XBLAST parameters as follows: score=50, wordlength=3. Gaps can be introduced into the query or searched sequence as described in Altschul et al., (1997) Nucleic Acids Res. 25(17):3389-3402. Default parameters for XBLAST and Gapped BLAST programs are available at National Center for Biotechnology Information (NCBI), National Institutes of Health, Bethesda Md.

[0155] The Prosite profiles PS00028 and PS50157 can be used to identify zinc finger domains. In a SWISSPROT release of 80,000 protein sequences, these profiles detected 3189 and 2316 zinc finger domains, respectively. Profiles can be constructed from a multiple sequence alignment of related proteins by a variety of different techniques. Gribskov and co-workers (Gribskov et al., (1990) Meth. Enzymol. 183:146-159) utilized a symbol comparison table to convert a multiple sequence alignment supplied with residue frequency distributions into weights for each position. See, for example, the PROSITE database and the work of Luethy et al., (1994) Protein Sci. 3:139-1465.

[0156] Hidden Markov Models (HMM's) representing a DNA binding domain of interest can be generated or obtained from a database of such models, e.g., the Pfam database, release 2.1. A database can be searched, e.g., using the default parameters, with the HMM in order to find additional domains (see, e.g., Bateman et al. (2002) Nucleic Acids Research 30:276-280). Alternatively, the user can optimize the parameters. A threshold score can be selected to filter the database of sequences such that sequences that score above the threshold are displayed as candidate domains. A description of the Pfam database can be found in Sonhammer et al., (1997) Proteins 28(3):405-420, and a detailed description of HMMs can be found, for example, in Gribskov et al., (1990) Meth. Enzymol. 183:146-159; Gribskov et al., (1987) Proc. Natl. Acad. Sci. USA 84:4355-4358; Krogh et al., (1994) J. Mol. Biol. 235:1501-1531; and Stultz et al., (1993) Protein Sci. 2:305-314.

[0157] The SMART database of HMM's (Simple Modular Architecture Research Tool, Schultz et al., (1998) Proc. Natl. Acad. Sci. USA 95:5857 and Schultz et al., (2000) Nucl. Acids Res 28:231) provides a catalog of zinc finger domains (ZnF_C2H2; ZnF_C2C2; ZnF_C2HC; ZnF_C3H1; ZnF_C4; ZnF_CHCC; ZnF_GATA; and ZnF_NFX) identified by profiling with the hidden Markov models of the HMMer2 search program (Durbin et al., (1998) Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge University Press).

[0158] Hybridization-based Methods. A collection of nucleic acids encoding various forms of a DNA binding domain can be analyzed to profile sequences encoding conserved amino- and carboxy-terminal boundary sequences. Degenerate oligonucleotides can be designed to hybridize to sequences encoding such conserved boundary sequences. Moreover, the efficacy of such degenerate oligonucleotides can be estimated by comparing their composition to the frequency of possible annealing sites in known genomic sequences. Multiple rounds of design can be used to optimize the degenerate oligonucleotides. For example, comparison of known Cys2-His2 zinc fingers revealed a common sequence in the linker region between adjacent fingers in natural sequence (Agata et al., (1998) Gene 213:55-64). Such degenerate oligonucleotides are used to amplify a plurality of DNA binding domains. The amplified domains are inserted as test zinc finger domains into the hybrid nucleic acid, and subsequently assayed for binding to a target site by the methods described herein.

[0159] Collections of Nucleic Acid Binding Domains

[0160] The method permits the screening of a collection of nucleic acids encoding DNA binding domains (for example, in the form of a plasmid, phagemid, or phage library) for functional nucleic acid binding properties. The collection can encode a diverse group of DNA binding domains, even domains of different structural folds. In one instance, the collection encodes domains of a single structural fold such as a zinc finger domain. Although the following methods are described in the context of zinc finger domains, one skilled in the art would be able to adapt them to other types of nucleic acid binding domains.

[0161] Mutated Domains. In still another instance, the collection is composed of nucleic acids encoding a structural domain that is assembled from a degenerate patterned library. For example, in the instance of zinc fingers, an alignment of known zinc fingers can be utilized to identify the optimal amino acids at each position. Alternatively, structural studies and mutagenesis experiments can be used to determine the preferred properties of amino acids at each position. Any nucleic acid binding domain can be used as a structural scaffold for introducing mutations. In particular, positions in close proximity to the nucleic acid binding interface or adjacent to a position so located can be targeted for mutagenesis. A mutated test zinc finger domain can be constrained at any mutated position to a subset of possible amino acids by using a patterned degenerate library. Degenerate codon sets can be used to encode the profile at each position. For example, codon sets are available that encode only hydrophobic residues, aliphatic residues, or hydrophilic residues. The library can be selected for full-length clones that encode folded polypeptides. Cho et al. ((2000) J. Mol. Biol. 297(2):309-19) provides a method for producing such degenerate libraries using degenerate oligonucleotides, and also provides a method of selecting library nucleic acids that encode full-length polypeptides. Such nucleic acids can be easily inserted into an expression plasmid using convenient restriction enzyme cleavage sites or transposase or recombinase recognition sites for the selection methods described herein.

[0162] Selection of the appropriate codons and the relative proportions of each nucleotide at a given position can be determined by simple examination of a table representing the genetic code, or by computational algorithms. For example, Cho et al., supra, describe a computer program that accepts a desired profile of protein sequences and outputs a preferred oligonucleotide design that encodes sequences of the profile. For example, the design may include degenerate positions for an oligonucleotide population.

[0163] Isolation of a natural repertoire of domains. A library of domains can be constructed from genomic DNA or cDNA of eukaryotic organisms such as humans. Multiple methods are available for doing this. For example, a computer search of available amino acid sequences can be used to identify the domains, as described above. A nucleic acid encoding each domain can be isolated and inserted into a vector appropriate for the expression in cells, e.g., a vector containing a promoter, an activation domain, and a selectable marker. In another example, degenerate oligonucleotides that hybridize to sequences encoding a conserved motif are used to amplify, e.g., by PCR, a large number of related domains containing the motif. For example, Kruppel-like Cys2His2 zinc fingers can be amplified by the method of Agata et al., (1998) Gene 213:55-64. This method also maintains the naturally occurring zinc finger domain linker peptide sequences, e.g., sequences with the pattern: Thr-Gly-(Glu/Gln)-(Lys/Arg)-Pro-(Tyr/Phe) (SEQ ID NO:78). Moreover, screening a collection limited to domains of interest, unlike screening a library of unselected genomic or cDNA sequences, significantly decreases library complexity and reduces the likelihood of missing a desirable sequence due to the inherent difficulty of completely screening large libraries.

[0164] The human genome contains numerous zinc finger domains, many of which are uncharacterized and unidentified. It is estimated that there are thousands of genes encoding proteins with zinc finger domains (Pellegrino and Berg, (1991) Proc. Natl. Acad. Sci. USA 88:671-675). These human zinc finger domains represent an extensive collection of diverse domains from which novel DNA-binding proteins can be constructed. If each zinc finger domain recognizes a unique 3- to 4-bp sequence, the total number of domains required to bind every possible 3- to 4-bp sequence is only 64 to 256 (43 to 44). It is possible that the natural repertoire of the human genome contains a sufficient number of unique zinc finger domains to span all possible recognition sites. These zinc finger domains are a valuable resource for constructing artificial chimeric DNA-binding proteins. Naturally occurring zinc finger domains, unlike artificial mutants derived from the human genome, have evolved under natural selective pressures and therefore may be naturally optimized for binding specific DNA sequences and in vivo function.

[0165] Human zinc finger domains are much less likely to induce an immune response when introduced into humans, e.g., in gene therapy applications.

[0166] In vivo Selection of Zinc Finger Domains Possessing Specific DNA Binding Properties

[0167] Zinc finger domains with desired DNA recognition properties can be identified using the following in vivo screening system. A composite binding site of interest is inserted upstream of a reporter gene such that recruitment of a transcriptional activation domain to the composite binding site results in increased reporter gene transcription above a given level. An expression plasmid that encodes a hybrid protein consisting of a test zinc finger domain fused to a fixed DNA binding domain and a transcriptional activation domain is constructed.

[0168] The composite binding site includes at least two elements, a recruitment site and a target site. The system is engineered such that the fixed DNA binding domain recognizes the recruitment site. However, the binding affinity of the fixed DNA binding domain for the recruitment site is such that in vivo it alone is insufficient for transcriptional activation of the reporter gene. This can be verified by a control experiment.

[0169] For example, when expressed in cells, the fixed DNA binding domain (in the absence of a test zinc finger domain, or in the presence of a test zinc finger domain that is known to be nonfunctional or whose known DNA contacting residues have been replaced with an alternative amino acid such as alanine) should not be able to activate transcription of the reporter gene above a nominal level. Some leaky or low-level activation is tolerable, as the system can be sensitized by other means (e.g., by use of a competitive inhibitor of the reporter). The fixed DNA binding domain is expected not to bind stably to the recruitment site. For example, the fixed DNA binding domain can bind to the recruitment site with a dissociation constant (Kd) of at least approximately 0.1 nM, 1 nM, 1 μM, 10 μM, 100 μM, or greater. (In addition, the Kd can be less than 100 μM, or 10 μM). The Kd of the DNA binding domain for the target site can be measured in vitro by an electrophoretic mobility shift assay (EMSA) in the absence of a test zinc finger domain or in the absence of a test zinc finger domain with specificity for the second target site.

[0170] Thus, attachment of a functional test zinc finger domain that recognizes the target site, e.g., the variable site of the composite binding site, is necessary for the hybrid protein to bind stably to the composite binding site in cells, and thereby to activate the reporter gene. The binding preference of the test zinc finger domain for the target site results in an increase in reporter gene expression relative to the given level. For example, the fold increase of reporter gene expression obtained by dividing the observed level by the given level can be at least approximately 2, 4, 8, 20, 50, 100, 1000 fold or greater. When the test zinc finger domain recognizes the target site, the Kd of the transcription factor comprising the DNA binding domain and the test zinc finger domain is decreased, e.g., relative to a transcription factor lacking a test zinc finger domain with specificity for the target site. For example, the dissociation constant (Kd) of a transcription factor complexed to a target site for which it has specificity can be at or below approximately 50 nM, 10 nM, 1 nM, 0.1 nM, 0.01 nM or less. The Kd can be determined in vitro by EMSA.

[0171] The discovery that DNA binding specificity can be sensitively and accurately assayed by determining the ability of test zinc finger domains to augment the in vivo binding affinity of a fixed DNA binding domain has enabled the rapid isolation and characterization of novel zinc finger domains from the human genome.

[0172] Fixed DNA binding domains include modular domains isolated from naturally occurring DNA-binding proteins, e.g., a naturally occurring DNA-binding protein that has multiple domains or that is an oligomer. For example, an amino acid sequence that includes two known zinc fingers, e.g., fingers 1 and 2 of Zif268, can be used as the fixed DNA binding domain. A skilled artisan would be able to identify from the myriad of nucleic acid binding domains (e.g., a domain family described herein, such as a homeodomain, a helix-turn-helix domain, or a helix-loop-helix domain, or a nucleic acid binding domain well characterized in the art) a fixed DNA binding domain suitable for the system. Appropriate selection of a recruitment site that is recognized by the fixed DNA binding domain is also necessary. The recruitment site can be a subsite within the natural binding site for the naturally occurring DNA binding protein from which the fixed DNA binding domain is obtained. If necessary, mutations can be introduced either into the fixed domain or into the recruitment site, in order to sensitize the system.

[0173] Cells suitable for the in vivo screening system include both eukaryotic and prokaryotic cells. Exemplary eukaryotic cells include yeast cells, e.g., Saccharomyces cerevisiae, Saccharomyces pombe, and Pichia pastoris cells.

[0174] The yeast one-hybrid system, using Saccharomyces cerevisiae, was modified to select zinc finger domains using the aforementioned screening system. First, reporter plasmids that encode the HIS3 reporter gene were prepared. The predetermined 4-bp target DNA sequences were connected to a truncated binding sequence to provide composite binding sequences for the DNA-binding domains, and each of the composite binding sequences was operably linked to the reporter gene on separate plasmids.

[0175] The hybrid nucleic acid sequence encodes a transcriptional activation domain linked to a DNA-binding domain comprising a truncated DNA-binding domain and a zinc finger domain.

[0176] The binding sites used herein are not necessarily contiguous, although contiguous sites are frequently used. Flexible and/or extensible linkers between nucleic acid binding domains can be used to construct proteins that recognize non-contiguous sites.

[0177] According to one aspect of the present invention, a polypeptide composed of finger 1 and finger 2 of Zif268 and devoid of finger 3 can be used as a fixed DNA-binding domain. (Among the three zinc finger domains of Zif268, finger 1 refers to the zinc finger domain located at the N-terminal end, finger 2, the zinc finger domain in the middle, and finger 3 the zinc finger domain at the C-terminal end.) Alternately, any two zinc finger domains whose binding site is characterized can be used as a fixed DNA-binding domain. Many novel examples are disclosed herein.

[0178] Other useful fixed DNA-binding domains may be derived from other zinc finger proteins, such as Sp1, CF2-II, YY1, Kruppel, WT1, Egr2, or POU-domain proteins, such as Oct1, Oct2, and Pit1. These are provided by way of example and the present invention is not limited thereto.

[0179] According to one particular example of the present invention, the base sequence of 5′-GGGCG-3′, generated by deleting 4-bp from the 5′ end of the optimal Zif268 recognition sequence (5′-GCG TGG GCG-3′), can be used as a recruitment site. Any target sequence of 3 to 4 bp can be linked to this recruitment site, to yield a composite binding sequence.

[0180] Activation domains. Transcriptional activation domains that may be used in the present invention include but are not limited to the Gal4 activation domain from yeast and the VP16 domain from herpes simplex virus. In bacteria, activation domain function can be emulated by fusing a domain that can recruit a wild-type RNA polymerase alpha subunit C-terminal domain or a mutant alpha subunit C-terminal domain, e.g., a C-terminal domain fused to a protein interaction domain.

[0181] Repression domains. If desired, a repression domain instead of an activation domain can be fused to the DNA binding domain. Examples of eukaryotic repression domains include ORANGE, groucho, and WRPW (Dawson et al., (1995) Mol. Cell Biol. 15:6923-31). When a repression domain is used, a toxic reporter gene and/or a non-selectable marker can be used to screen for decreased expression.

[0182] Other Functional Domains. A protein transduction domain can be fused to the DNA binding domain, e.g., of the chimeric zinc finger protein. Protein transduction domains result in uptake of the transduction domain and attached polypeptide into cells. One example of a protein transduction domain is the HIV tat protein.

[0183] Reporter genes. The reporter gene can be a selectable marker, e.g., a gene that confers drug resistance or an auxotrophic marker. Examples of drug resistance genes include S. cerevisiae cyclohexamide resistance (CYH), S. cerevisiae canavanine resistance gene (CAN1), and the hygromycin resistance gene. S. cerevisiae auxotrophic markers include the URA3, HIS3, LEU2, ADE2 and TRP1 genes. When an auxotrophic marker is the reporter gene, cells that lack a functional copy of the auxotrophic gene and so the ability to produce a particular metabolite are utilized. Selection for constructs encoding test zinc finger domains that bind a target site is achieved by maintaining the cells in medium lacking the metabolite. For example, the HIS3 gene can be used as a selectable marker in combination with a his3− yeast strain. After introduction of constructs encoding the hybrid transcription factors, the cells are grown in the absence of histidine. Selectable markers for use in mammalian cells, such as thymidine kinase, neomycin resistance, and HPRT, are also well known to the skilled artisan.

[0184] Alternatively, the reporter gene encodes a protein whose presence can be easily detected and/or quantified. Exemplary reporter genes include lacZ, chloramphenicol acetyl transferase (CAT), luciferase, green fluorescent protein (GFP), beta-glucuronidase (GUS), blue fluorescent protein (BFP), and derivatives of GFP, e.g., with altered or enhanced fluorescent properties (Clontech Laboratories, Inc. CA). Colonies of cells expressing lacZ can be easily detected by growing the colonies on plates containing the colorimetric substrate X-gal. GFP expression can be detected by monitoring fluorescence emission upon excitation. Individual GFP expressing cells can be identified and isolated using fluorescence activated cell sorting (FACS).

[0185] The system can be constructed with two reporter genes, e.g., a selectable reporter gene and a non-selectable reporter gene. The selectable marker facilitates rapid identification of the domain of interest, as under the appropriate growth conditions, only cells bearing the domain of interest grow. The non-selectable reporter provides a means of verification, e.g., to distinguish false-positives, and a means of quantifying the extent of binding. The two reporters can be integrated at separate locations in the genome, integrated in tandem in the genome, contained on the same extrachromosomal element (e.g., plasmid) or contained on separate extrachromosomal elements.

[0186] FIG. 5 illustrates the principle of the modified one-hybrid system used to select desired zinc finger domains. The DNA-binding domain of the hybrid transcription factor is composed of (a) a truncated DNA-binding domain consisting of finger 1 and finger 2 of Zif268 and (b) zinc finger domain A or B. The base sequence of the binding site located at the promoter region of the reporter gene is a composite binding sequence (5′-XXXXGGGCG-3′), which consists of a 4-bp target sequence (nucleotides 1 to 4, 5′-XXXX-3′), and a truncated binding sequence (nucleotides 5 to 9, 5′-GGGCG-3′).

[0187] If the test zinc finger domain (A in FIG. 5) in the hybrid transcription factor recognizes the target sequence, the hybrid transcription factor can bind the composite binding sequence stably. This stable binding leads to expression of the reporter gene through the action of the activation domain (AD in FIG. 5) of the hybrid transcription factor. As a result, when HIS3 is used as a reporter gene, the transformed yeast grows in medium devoid of histidine. Alternatively, when lacZ is used as a reporter gene, the transformed yeast grows as a blue colony in a medium containing X-gal, a substrate of the lacZ protein. However, if the zinc finger domain (B in FIG. 5) of the hybrid transcription factor fails to recognize the target sequence, expression of the reporter gene is not induced. As a result, the transformed yeast cannot grow in the medium devoid of histidine (when HIS3 is used as a reporter gene) or grows as a white colony in a medium containing X-gal (when lacZ is used as a reporter gene).

[0188] The selection method using this modified one-hybrid system is advantageous because zinc finger domains selected by virtue of this procedure are demonstrated to function in the cellular milieu. Thus, the domains are presumably able to fold, enter the nucleus, and withstand intracellular proteases and other potentially damaging intracellular agents. Furthermore, the modified one-hybrid system disclosed herein allows the isolation of desired zinc finger domains quickly and easily. The modified one-hybrid system requires only a single round of transformation of yeast cells to isolate the desired zinc finger domains.

[0189] The selection method described herein can be utilized to identify a zinc finger domain from a genome e.g., a genome of a plant or animal species (e.g., a mammal, e.g., a human). The method can also be utilized to identify a zinc finger domain from a library of mutant zinc finger domains prepared, for example, by random mutagenesis. In addition, the two methods can be used in conjunction. For example, if a zinc finger domain cannot be isolated from the human genome for a particular 3-bp or 4-bp DNA sequence, a library of zinc finger domains prepared by random or directed mutagenesis can be screened for such a domain.

[0190] Although the modified one-hybrid system in yeast is a preferred means to select zinc finger domains that recognize and bind the given target sequences, it will be apparent to a person skilled in the art that systems other than yeast one-hybrid selection can be used. For example, phage display selection may be used to screen a library of naturally occurring zinc finger domains derived from a genome of a eukaryotic organism.

[0191] The present invention encompasses the use of the one-hybrid method in a variety of cultured cells. For example, a reporter gene operably linked to target sequences may be introduced into prokaryotic or animal or plant cells in culture, and the cultured cells may then be transfected with plasmids, phages, or viruses encoding a library of zinc finger domains. Desired zinc finger domains recognizing target sequences may then be obtained from the isolated cells in which the reporter gene is activated.

[0192] The examples disclosed below demonstrate that the method can identify zinc finger domains for binding sites of interest. A library of hybrid transcription factors with a variety of zinc finger domains positioned at finger 3 was prepared. Of the novel zinc finger domains (e.g., HSNK, QSTV, and VSTR zinc fingers; see below) selected from the library, none is naturally located at the C-terminus in its corresponding parent zinc finger protein. This clearly demonstrates that zinc finger domains are modular and that novel DNA-binding domains can be constructed by mixing and matching appropriate zinc finger domains.

[0193] The zinc finger domains selected via the method of the present invention can be used as building blocks to make new DNA-binding proteins by appropriate rearrangement and recombination. For example, a novel DNA-binding protein recognizing the promoter region of human CCR5, a coreceptor of HIV-1, can be constructed as follows. The promoter region of human CCR5 contains the following 10-bp sequence: 5′-AGG GTG GAG T-3′ (SEQ ID NO:4). Using the modified one-hybrid system disclosed herein, one should be able to isolate three zinc finger domains, each of which specifically recognizes one of the following 4-bp target sequences; 5′-AGGG-3′, 5′-GTGG-3′, and 5′-GAGT-3′. These target sequences are overlapping 4-bp segments of the CCR5 target sequence. These three zinc finger domains can be connected with appropriate linkers and attached to a regulatory domain such as the VP 16 domain and the GAL4 domain or repression domains such as the KRAB domain in order to generate novel transcription factors that specifically bind to the CCR5 promoter. Similarly zinc fingers can be designed to recognize the following sequences:

[0194] HIV-1 LTR (−124/−115): 5′-GAC ATC GAG C-3′ (SEQ ID NO:1)

[0195] HIV-1 LTR (−23/−14): 5′-GCA GCT GCT T-3′ (SEQ ID NO:2)

[0196] HIV-1 LTR (−95/−86): 5′-GCT GGG GAC T-3′ (SEQ ID NO:3)

[0197] Human CCR5 (−70/−79): 5′-AGG GTG GAG T-3′ (SEQ ID NO:4)

[0198] Human CCR5 (+7/+16): 5′-GCT GAG ACAT-3′ (SEQ ID NO:5)

[0199] These zinc finger proteins could be used in therapy to help prevent proliferation of HIV-1.

[0200] High Throughput Screening

[0201] The following method allows rapid measurement of the relative in vivo binding affinity for each domain in a collection for multiple possible DNA-binding sites or even all possible DNA-binding sites. A large collection of nucleic acids encoding nucleic acid binding domains is generated. Each nucleic acid binding domain is encoded as the test zinc finger domain in a hybrid nucleic acid construct, and expressed in a yeast strain of one mating type. Thus, a first set of yeast strains expressing all available or desired domains is generated. A second set of yeast strains containing reporter constructs with putative target sites for the domains in the reporter construct is constructed in the opposite mating type. The method requires performing many or all of the possible pairwise matings in order to create a matrix of fused cells, each having a different test zinc finger domain and a different target site reporter construct. Each fused cell is assayed for reporter gene expression. The method thereby rapidly and effortlessly determines the binding preferences of the tested domains.

[0202] A collection of domains is identified, e.g., by searching a genomics database for putative domains that fit a given profile. The collection can include, for example, ten to twenty domains, or all the identified domains, possibly thousands or more. Nucleic acids encoding the domains identified from the database are synthesized de novo or amplified from a sample of genomic DNA using oligonucleotides. Manual and automated methods for designing such synthetic oligonucleotides are routine in the art. Nucleic acids encoding additional domains can be similarly synthesized or amplified with degenerate primers. Nucleic acids encoding the domains of the collection are cloned into the yeast expression plasmid described above, thus creating fusion proteins of the domains and the first two fingers of Zif268 and a transcription activation domain. The amplification and cloning steps can be done in a microtitre plate format in order to clone nucleic acids encoding the multiple domains.

[0203] Alternatively, a recombinational cloning method can be used to rapidly insert multiple amplified nucleic acids encoding the domains into the yeast expression vector. This method, which is described in U.S. Pat. No. 5,888,732 and the “Gateway” manual (Life Technologies-Invitrogen, CA, USA), entails including customized sites for a site-specific recombinase at the ends of the amplification primers. The expression vector contains an additional site or sites at the position for insertion of amplified nucleic acid encoding the domain. These sites are designed to lack stop codons. Addition of the amplification product, the expression vector, and the site-specific recombinase to the recombination reaction results in insertion of the amplified sequence into the vector. Additional features, e.g., the displacement of a toxic gene upon successful insertion, make this method highly efficient and suitable for high throughput cloning.

[0204] Restriction enzyme-mediated and/or recombination cloning can be used to insert nucleic acids encoding each of the identified domains into an expression vector. The vectors can be propagated in bacteria, and frozen in indexed microtitre plates, such that each well contains a cell harboring a nucleic acid encoding one of the different, unique DNA-binding domains.

[0205] Isolated plasmid DNA is obtained for each domain and transformed into a yeast cell, e.g., a Saccharomyces cerevisiae MATαcell. As the expression vector contains a selectable marker, the transformed cells are grown in minimal medium under nutritional conditions selecting for the marker. Such cells can also be frozen and stored, e.g., in microtitre plates, for later use.

[0206] A second set of yeast strains is constructed, e.g., in a Saccharomyces cerevisiae MATα cell. This set of yeast strains contains a variety of different reporter vectors. Each yeast strain bearing an expression vector with a unique DNA-binding domain is then mated to each yeast strain of the reporter gene set. As these two strains are from opposite mating types and are engineered to have different auxotrophies, diploids can easily be selected. Such diploids have both the reporter and the expression plasmids. The cells are also maintained under nutritional conditions that select for both the reporter and the expression plasmids. Uetz et al. (2000) Nature 403:623-7 describe a complete two-hybrid map of all yeast proteins by generating such a matrix of yeast matings.

[0207] Reporter gene expression can be detected in a high-volume format, e.g., in microtitre plates. For example, when using GFP as the reporter, a plate containing the matrix of mated cells can be scanned for fluorescence.

[0208] Design of Novel DNA-Binding Proteins

[0209] A new DNA-binding protein can be rationally constructed to recognize a target 9-bp or longer DNA sequence by mixing and matching appropriate zinc finger domains. The modular structure of zinc finger domains facilitates their rearrangement to construct new DNA-binding proteins. As shown in FIG. 1a, zinc finger domains in the naturally-occurring Zif268 protein are positioned tandemly along the DNA double helix. Each domain independently recognizes a different 3-4 basepair DNA segment.

[0210] A Database of Zinc Finger Domains. The one-hybrid selection system described above can be utilized to identify one or more zinc finger domains for each possible 3- or 4-basepair binding site or a representative number of such binding sites. The results of this process can be accumulated as a series of associations between a zinc finger domain and its preferred 3- or 4-basepair binding site or sites. Examples of such associations are provided in Tables 3 to 6.

[0211] The results can also be stored in a machine as a database, e.g., a relational database, spreadsheet, or text file. Each record of such a database associates a representation of a zinc finger domain and a string indicating the sequence of the one or more preferred binding sites of the domain. The database record can include an indication of the relative affinity of the zinc finger domains that bind each site. In some implementations, the database record can also include information that indicates the physical location of the nucleic acid encoding the particular zinc finger domain. Such a physical location can be, for example, a particular well of a microtitre plate stored in a freezer.

[0212] The database can be configured so that it can be queried or filtered, e.g., using a SQL operating environment, a scripting language (such as PERL or a Microsoft Excel® macro), or a programming language. Such a database would enable a user to identify one or more zinc finger domains that recognizes a particular 3- or 4-basepair binding site. Database and other information such as can be stored on a database server can also be configured to communicate with each device using commands and other signals that are interpretable by the device. The computer-based aspects of the system can be implemented in digital electronic circuitry, or in computer hardware, firmware, software, or in combinations thereof. An apparatus of the invention, e.g., the database server, can be implemented in a computer program product tangibly embodied in a machine-readable storage device for execution by a programmable processor; and method actions can be performed by a programmable processor executing a program of instructions to perform functions of the invention by operating on input data and generating output. One non-limiting example of an execution environment includes computers running Windows XP or Windows NT 4.0 (Microsoft) or better or Solaris 2.6 or better (Sun Microsystems) operating systems.

[0213] The zinc finger domains can also be tested in the context of multiple different fusion proteins to verify their specificity. Moreover, particular binding sites for which a paucity of domains is available can be the target of additional selection screens. Libraries for such selections can be prepared by mutagenizing a zinc finger domain that binds a similar yet distinct site. A complete matrix of zinc finger domains for each possible binding site is not essential, as the domains can be staggered relative to the target binding site in order to best utilize the domains available. Such staggering can be accomplished both by parsing the binding site in the most useful 3 or 4 basepair binding sites, and also by varying the linker length between zinc finger domains. In order to incorporate both selectivity and high affinity into the design polypeptide, zinc finger domains that have high specificity for a desired site can be flanked by other domains that bind with higher affinity, but lesser specificity. The in vivo screening method described herein can used to test the in vivo function, affinity, and specificity of an artificially assembled zinc finger protein and derivatives thereof. Likewise, the method can be used to optimize such assembled proteins, e.g., by creating libraries of varied linker composition, zinc finger domain modules, zinc finger domain compositions, and so forth.

[0214] Parsing a target site. The target 9-bp or longer DNA sequence is parsed into 3- or 4-bp segments. Zinc finger domains are identified (e.g., from a database described above) that recognize each parsed 3- or 4-bp segment. Longer target sequences, e.g., 20 bp to 500 bp sequences, are also suitable targets as 9 bp, 12 bp, and 15 bp subsequences can be identified within them. In particular, subsequences amenable for parsing into sites well represented in the database can serve as initial design targets.

[0215] A scoring regime can be used to estimate the probability that a particular designed chimeric zinc finger protein would recognize the target site in the cell. The scores can be a function of each component finger's affinity for its preferred subsites, its specificity, and its success in previously designed proteins.

[0216] Computer Programs. Computer systems and software can be used to access a machine-readable database described above, parse a target site, and output one or more chimeric zinc finger protein designs.

[0217] The techniques may be implemented in programs executing on programmable machines such as mobile or stationary computers, and similar devices that each include a processor, a storage medium readable by the processor, and one or more output devices. Each program may be implemented in a high level procedural or object oriented programming language to communicate with a machine system. Some merely illustrative examples of computer languages include C, C++, Java, Fortran, and Visual Basic.

[0218] Each such program may be stored on a storage medium or device, e.g., compact disc read only memory (CD-ROM), hard disk, magnetic diskette, or similar medium or device, that is readable by a general or special purpose programmable machine for configuring and operating the machine when the storage medium or device is read by the computer to perform the procedures described in this document. The system may also be implemented as a machine-readable storage medium, configured with a program, where the storage medium so configured causes a machine to operate in a specific and predefined manner.

[0219] The computer system can be connected to an internal or external network. For example, the computer system can receive requests from a remotely located client system, e.g., using HTTP, HTTPS, or XML protocols. The requests can be an identifier for a known target gene or a string representing the sequence of a target nucleic acid. In the former case, the computer system can access a sequence database such as GenBank to retrieve the nucleic acid sequence of regulatory regions of the target gene. The sequence of the regulatory region or the directly-received target nucleic acid sequence is then parsed into subsites, and chimeric zinc finger proteins are designed, e.g., as described above.

[0220] The system can communicate the results to the remotely located client. Alternatively, the system can control a robot to physically retrieve nucleic acid encoding the designed chimeric zinc finger proteins. In this implementation, a library of nucleic acids encoding chimeric zinc finger proteins is constructed and stored, e.g., as frozen purified DNA or frozen bacterial strains harboring the nucleic acids. The robot responds to signals from the computer system by accessing specified addresses of the library. The retrieved nucleic acids can then be processed, packaged and delivered to the client. Alternatively, the retrieved nucleic acids can be introduced into cells and assayed. The computer system can then communicate the results of the assay to the client across the network.

[0221] Constructing a Protein from Selected Modules. Once a chimeric polypeptide sequence containing multiple zinc finger domains is designed, a nucleic acid sequence encoding the designed polypeptide sequence can be synthesized. Methods for constructing synthetic genes are routine in the art. Such methods include gene construction from custom synthesized oligonucleotides, PCR mediated cloning, and mega-primer PCR. Example 66, below, provides a method of serially ligating nucleic acids encoding selected zinc finger domains to form a nucleic acid encoding a chimeric polypeptide. Additional sequences can be joined to the nucleic acid encoding the designed polypeptide sequence. The additional sequence can provide regulatory functions or a sequence coding for an amino acid sequence with a desired function. Examples of such additional sequences are described herein.

[0222] Constructing Libraries of Chimeric Zinc Finger Proteins

[0223] Multiple nucleic acid sequences encoding chimeric zinc finger proteins can be synthesized, e.g., to form a library. The library of nucleic acids encoding diverse chimeric zinc finger proteins can be formed by serial ligation, e.g., as described in Example 67. The library can be constructed such that each nucleic acid encodes a protein that has at least three, four, or five zinc finger domains. In some implementations, particularly for large libraries, each zinc finger position can be designed to randomly include any one of a set of zinc finger domains. The set of zinc finger domains can be selected to represent domains with a range of specificities, e.g., covering 30, 40, 50 or more of the 64 possible 3-basepair subsites. The set can include at least about 12, 15, 20, 25, 30, 40 or 50 different zinc finger domains. Some or all of these domains can be domains isolated from naturally occurring proteins.

[0224] One exemplary library includes nucleic acids that encode a chimeric zinc finger protein having 3 fingers and 30 possible domains at each finger. In its fully represented form, this library includes 27,000 sequences (i.e., the result of 303). The library can be constructed by serial ligation in which a pool of nucleic acids encoding all 30 possible domains is added at each step. The final library can be stored as a pool.

[0225] Alternatively, individual members can be isolated, stored at an addressable location (e.g., arrayed), and sequenced. After high throughput sequencing of 40 to 50 thousand constructed library members, missing chimeric combinations can be individually assembled in order to obtain complete coverage. Once arrayed, e.g., in microtitre plates, each individual member can be recovered later for further analysis or for a particular application. In particular, each individual member can be validated by determining if it can repress transcription in vivo using the p1G reporter assay described in Example 68. If validated, the library member can be profiled using nucleic acid microarrays to determine its ability to regulate endogenous genes (see “Profiling Regulatory Properties of a Chimeric Zinc Finger Protein,” below).

[0226] Small libraries, e.g., having about 6 to 200 or 50 to 2000 members can be used to identify an optimal chimeric protein that binds a target site. These libraries can be designed by the judicious selection of combinations of nucleic acids encoding particular zinc finger domains for each positioned zinc finger in the resultant chimeric polypeptide. For example, the nucleic acids that encode a particular position can be selected to vary such that they encode different zinc finger domains whose recognition specificity is suitable for that position.

[0227] These small tailored libraries can be synthesized by serial ligation or by pooling specific library members from a prefabricated and arrayed large library. Subsequent steps (e.g., sexual PCR and “DNA Shuffling™” (Maxygen, Inc., CA)) can be used to introduce additional diversity.

[0228] Screening Libraries of Chimeric Zinc Finger Proteins

[0229] The libraries can be designed with a particular intended screening application, in which case the parental vector can be engineered to include necessary regulatory and functional sequences. In one embodiment, the library is designed such that the nucleic acid encoding the chimeric zinc finger protein is flanked by site-specific recombination sites. Recombination-mediated cloning, e.g., as described in U.S. Pat. No. 5,888,732 and the “Gateway” manual (Life Technologies-Invitrogen, CA, USA), then enables each sequence to be excised from a parent vector and inserted into an application-specific vector. Thus, once a complete library is constructed in the parent vector, it can subjected to diverse screening and selective procedures.

[0230] Library members (from a small or large library) can be screened in vivo to determine if it can regulate a target gene of interest in a cell. The cell can be cultured or within a subject. The target gene can be a reporter construct that includes a regulatory region of interest operably linked to a heterologous reporter gene, e.g., as described in Example 64. Alternatively, the target gene can be an endogenous gene. The effect of one or more proteins encoded by library members on the regulation of the endogenous gene in its normal chromosomal milieu is assessed. The screening can also include assessing if the chimeric protein encoded by the library member alters the transcription of other genes. Nucleic acid arrays can be used to monitor the expression of large numbers of such genes as described below.

[0231] The library can also be screened using a display format in order to biochemically query the chimeric proteins encoded by library members. For example, the polypeptides encoded by the library can be displayed on the surface of bacteriophages, e.g., as described in U.S. Pat. No. 5,223,409 and Rebar et al., (1996) Methods Enzymol. 267:129-49. The library can also be displayed by covalently linking each nucleic acid of the library to the polypeptide that it encodes, e.g., using the method described in WO 00/32823. Individual library members with a particular binding property can be isolated by contacting the display library to a target DNA site that is fixed to a solid support, washing the support, and recovering the bound library members. This method can be adapted to identify chimeric polypeptides that bind to other ligands, e.g., a target RNA site or a target protein.

[0232] In one embodiment, the chimeric protein encoded by each library member is produced and isolated at an address of a planar array. Methods for producing polypeptide arrays are described, e.g., in De Wildt et al., (2000) Nature Biotech. 18:989-994; Lueking et al., (1999) Anal. Biochem. 270:103-111; Ge, H. (2000) Nucleic Acids Res. 28:e3, I-VII; MacBeath and Schreiber, (2000) Science 289, 1760-1763; Haab et al., (2001) Genome Biology 2(2):research0004.1; and WO 99/51773A1. Such an array can be used to identify library members that bind a particular target DNA site. DNA including the target site is labeled and contacted to the array. The amount of label at each address of the array is quantitated to identify library members that binding to the target site. The assay can include non-specific DNA or a competitor DNA in order to increase the stringency of the selection. This method can be adapted to identify chimeric proteins that bind to targets other than DNA, e.g., by using a labeled target RNA or a labeled target protein.

[0233] The array of zinc finger proteins can also be used to profile a complex nucleic acid sample. The sample is labeled and contacted to the array. Then, binding to each address is quantified in order to generate a profile for the sample. The profile can be compared to reference profiles in order to characterize the sample.

[0234] Profiling Regulatory Properties of a Chimeric Zinc Finger Protein

[0235] A chimeric zinc finger protein can be characterized to determine its ability to regulate an endogenous gene of a cell, e.g., a mammalian cell. Nucleic acid encoding the chimeric zinc finger protein is first fused to a repression or activation domain, and then introduced into a cell of interest. After appropriate incubation and induction of expression of the coding nucleic acid, mRNA is harvested from the cell and analyzed using a nucleic acid microarray.

[0236] Nucleic acid microarrays can be fabricated by a variety of methods, e.g., photolithographic methods (see, e.g., U.S. Pat. No. 5,510,270;), mechanical methods (e.g., directed-flow methods as described in U.S. Pat. No. 5,384,261), and pin based methods (e.g., as described in U.S. Pat. No. 5,288,514). The array is synthesized with a unique capture probe at each address, each capture probe being appropriate to detect a nucleic acid for a particular expressed gene.

[0237] The mRNA can be isolated by routine methods, e.g., including DNase treatment to remove genomic DNA and hybridization to an oligo-dT coupled solid substrate (e.g., as described in Current Protocols in Molecular Biology, John Wiley & Sons, N.Y). The substrate is washed, and the mRNA is eluted. The isolated mRNA is then reversed transcribed and optionally amplified, e.g., by rtPCR, e.g., as described in (U.S. Pat. No. 4,683,202). The nucleic acid can be labeled during amplification or reverse transcription, e.g., by the incorporation of a labeled nucleotide. Examples of preferred labels include fluorescent labels, e.g., red-fluorescent dye Cy5 (Amersham) or green-fluorescent dye Cy3 (Amersham). Alternatively, the nucleic acid can be labeled with biotin, and detected after hybridization with labeled streptavidin, e.g., streptavidin-phycoerythrin (Molecular Probes).

[0238] The labeled nucleic acid is then contacted to the array. In addition, a control nucleic acid or a reference nucleic acid can be contacted to the same array. The control nucleic acid or reference nucleic acid can be labeled with a label other than the sample nucleic acid, e.g., one with a different emission maximum. Labeled nucleic acids are contacted to an array under hybridization conditions. The array is washed, and then imaged to detect fluorescence at each address of the array.

[0239] A general scheme for producing and evaluating profiles is includes detecting hybridization at each address of the array. The extent of hybridization at an address is represented by a numerical value and stored, e.g., in a vector, a one-dimensional matrix, or one-dimensional array. The vector x has a value for each address of the array. For example, a numerical value for the extent of hybridization at a particular address is stored in variable xa. The numerical value can be adjusted, e.g., for local background levels, sample amount, and other variations. Nucleic acid is also prepared from a reference sample and hybridized to the same or a different array. The vector y is construct identically to vector x. The sample expression profile and the reference profile can be compared, e.g., using a mathematical equation that is a function of the two vectors. The comparison can be evaluated as a scalar value, e.g., a score representing similarity of the two profiles. Either or both vectors can be transformed by a matrix in order to add weighting values to different genes detected by the array.

[0240] The expression data can be stored in a database, e.g., a relational database such as a SQL database (e.g., Oracle or Sybase database environments). The database can have multiple tables. For example, raw expression data can be stored in one table, wherein each column corresponds to a gene being assayed, e.g., an address or an array, and each row corresponds to a sample. A separate table can store identifiers and sample information, e.g., the batch number of the array used, date, and other quality control information.

[0241] Genes that are similarly regulated can be identified by clustering expression data to identify coregulated genes. Such cluster may be indicative of a set of genes coordinately regulated by the chimeric zinc finger protein. Genes can be clustered using hierarchical clustering (see, e.g., Sokal and Michener (1958) Univ. Kans. Sci. Bull. 38:1409), Bayesian clustering, k-means clustering, and self-organizing maps (see, Tamayo et al. (1999) Proc. Natl. Acad. Sci. USA 96:2907).

[0242] The similarity of a sample expression profile to a reference expression profile (e.g., a control cell) can also be determined, e.g., by comparing the log of the expression level of the sample to the log of the predictor or reference expression value and adjusting the comparison by the weighting factor for all genes of predictive value in the profile.

[0243] Additional Features for Designed Transcription Factors

[0244] Peptide Linkers. DNA binding domains can be connected by a variety of linkers. The utility and design of linkers are well known in the art. A particularly useful linker is a peptide linker that is encoded by nucleic acid. Thus, one can construct a synthetic gene that encodes a first DNA binding domain, the peptide linker, and a second DNA binding domain. This design can be repeated in order to construct large, synthetic, multi-domain DNA binding proteins. PCT WO 99/45132 and Kim and Pabo ((1998) Proc. Natl. Acad. Sci. USA 95:2812-7) describe the design of peptide linkers suitable for joining zinc finger domains.

[0245] Additional peptide linkers are available that form random coil, α-helical or β-pleated tertiary structures. Polypeptides that form suitable flexible linkers are well known in the art (see, e.g., Robinson and Sauer (1998) Proc Natl Acad Sci USA. 95:5929-34). Flexible linkers typically include glycine, because this amino acid, which lacks a side chain, is unique in its rotational freedom. Serine or threonine can be interspersed in the linker to increase hydrophilicity. In additional, amino acids capable of interacting with the phosphate backbone of DNA can be utilized in order to increase binding affinity. Judicious use of such amino acids allows for balancing increases in affinity with loss of sequence specificity. If a rigid extension is desirable as a linker, α-helical linkers, such as the helical linker described in Pantoliano et al. (1991) Biochem. 30:10117-10125, can be used. Linkers can also be designed by computer modeling (see, e.g., U.S. Pat. No. 4,946,778). Software for molecular modeling is commercially available (e.g., from Molecular Simulations, Inc., San Diego, Calif.). The linker is optionally optimized, e.g., to reduce antigenicity and/or to increase stability, using standard mutagenesis techniques and appropriate biophysical tests as practiced in the art of protein engineering, and functional assays as described herein.

[0246] For implementations utilizing zinc finger domains, the peptide that occurs naturally between zinc fingers can be used as a linker to join fingers together. A typical such naturally occurring linker is: Thr-Gly-(Glu or Gln)-(Lys or Arg)-Pro-(Tyr or Phe) (SEQ ID NO:78) (Agata et al., supra).

[0247] Dimerization Domains. An alternative method of linking DNA binding domains is the use of dimerization domains, especially heterodimerization domains (see, e.g., Pomerantz et al (1998) Biochemistry 37:965-970). In this implementation, DNAbinding domains are present in separate polypeptide chains. For example, a first polypeptide encodes DNA binding domain A, linker, and domain B, while a second polypeptide encodes domain C, linker, and domain D. An artisan can select a dimerization domain from the many well-characterized dimerization domains. Domains that favor heterodimerization can be used if homodimers are not desired. A particularly adaptable dimerization domain is the coiled-coil motif, e.g., a dimeric parallel or anti-parallel coiled-coil. Coiled-coil sequences that preferentially form heterodimers are also available (Lumb and Kim, (1995) Biochemistry 34:8642-8648). Another species of dimerization domain is one in which dimerization is triggered by a small molecule or by a signaling event. For example, a dimeric form of FK506 can be used to dimerize two FK506 binding protein (FKBP) domains. Such dimerization domains can be utilized to provide additional levels of regulation.

[0248] Functional Assays and Uses

[0249] In addition to biochemical assays, the function of a nucleic acid binding domain or a protein designed by a method described herein, e.g., by modular assembly, can be assayed or used in vivo. For example, domains can be selected to bind to a target site, e.g., to a promoter site of a gene required for cell proliferation. By modular assembly, a protein can be designed that includes (1) the selected domains that respectively bind to subsites spanning the target promoter site, and (2) a DNA repression domain, e.g., a WRPW domain.

[0250] A nucleic acid sequence encoding a designed protein can be cloned into an expression vector, e.g., an inducible expression vector as described in Kang and Kim, (2000) J Biol Chem 275:8742. The inducible expression vector can include an inducible promoter or regulatory sequence. Non-limiting examples of inducible promoters include steroid-hormone responsive promoters (e.g., ecdysone-responsive, estrogen-responsive, and glutacorticoid-responsive promoters), the tetracyclin “Tet-On” and “Tet-Off” systems, and metal-responsive promoters. The construct can be transfected into tissue culture cells or into embryonic stem cells to generate a transgenic organism as a model subject. The efficacy of the designed protein can be determined by inducing expression of the protein and assaying cell proliferation of the tissue culture cell or assaying for developmental changes and/or tumor growth in a transgenic animal model. In addition, the level of expression of the gene being targeted can be assayed by routine methods to detect mRNA, e.g., RT-PCR or Northern blots. A more complete diagnostic includes purifying mRNA from cells expressing and not expressing the designed protein. The two pools of mRNA are used to probe a microarray containing probes to a large collection of genes, e.g., a collection of genes relevant to the condition of interest (e.g., cancer) or a collection of genes identified in the organism's genome. Such an assay is particularly valuable for determining the specificity of the designed protein. If the protein binds with high affinity but little specificity, it may cause pleiotropic and undesirable effects by affecting expression of genes in addition to the contemplated target. Such effects are revealed by a global analysis of transcripts.

[0251] In addition, the designed protein can be produced in a subject cell or subject organism in order to regulate an endogenous gene. The designed protein is configured, as described above, to bind to a region of the endogenous gene and to provide a transcriptional activation or repression function. As described in Kang and Kim (supra), the expression of a nucleic acid encoding the designed protein can be operably linked to an inducible promoter. By modulating the concentration of the inducer for the promoter, the expression of the endogenous gene can be regulated in a concentration dependent manner.

[0252] Assaying Binding Site Preference

[0253] The binding site preference of each domain can be verified by a biochemical assay such as EMSA, DNase footprinting, surface plasmon resonance, or column binding. The substrate for binding can be a synthetic oligonucleotide encompassing the target site. The assay can also include non-specific DNA as a competitor, or specific DNA sequences as a competitor. Specific competitor DNAs can include the recognition site with one, two, or three nucleotide mutations. Thus, a biochemical assay can be used to measure not only the affinity of a domain for a given site, but also its affinity to the site relative to other sites. Rebar and Pabo, (1994) Science 263:671-673 describe a method of obtaining apparent Kd constants for zinc finger domains from EMSA.

[0254] The present invention will be described in more detail through the following practical examples. However, it should be noted that these examples are not intended to limit the scope of the present invention.

EXAMPLE 1

Construction of Plasmids for Hybrid Transcription Factor Expression

[0255] An expression plasmid expressing a zinc finger transcription factor was prepared by modification of pPC86 (Chevray and Nathans, (1991) Proc. Natl. Acad. Sci. USA 89:5789-5793). Manipulations of DNA were performed as described in Ausubel et al. (Current Protocols in Molecular Biology (1998), John Wiley and Sons, Inc.). A DNA fragment encoding Zif268 zinc finger protein was inserted between the SalI and EcoRI recognition sites of pPC86 to generate pPCFM-Zif. The result of this cloning step is a translational fusion protein encoding the yeast Gal4 activation domain followed by the three Zif268 zinc fingers. Transformation of pPCFM-Zif into yeast cells results in expression of a hybrid transcription factor comprising the yeast Gal4 activation domain and the Zif268 zinc fingers. The DNA sequence encoding the Zif268 zinc finger protein as cloned in pPCFM-Zif is shown in FIG. 9.

[0256] The plasmid pPCFMS-Zif was utilized as a vector for constructing libraries of zinc finger domains (FIG. 8). pPCFMS-Zif was constructed by insertion of an oligonucleotide cassette containing a stop codon and a PstI recognition site in front of the finger 3 coding region of pPCFM-Zif. The oligonucleotide cassette was formed by annealing two synthetic oligonucleotides: 5′-TGCCTGCAGCATTTGTGGGAGGAAGTTTG-3′ (SEQ ID NO:79); and 5′-ATGCTGCAGGCTTAAGGCTTCTCGCCGGTG-3′ (SEQ ID NO:80). The insertion of a stop codon prevents the generation of library plasmids encoding finger 3 of Zif268.

[0257] The plasmid was used as a vector for the generation of zinc finger domain libraries as described in “Example 2” below.

[0258] In addition, gap repair cloning of DNA sequences encoding individual zinc finger domains was carried out as described in Hudson et al., ((1997) Genome Research 7:1169-1173) with minor modification.

[0259] To clone an individual zinc finger domain, two overlapping oligonucleotides were synthesized. Each oligonucleotide included a 21-nucleotide-long common tail at its 5′ end for second round PCR (rePCR) and a specific sequence that annealed to the nucleic acid encoding the individual zinc finger domain. The sequences of the forward and back primers were 5′-ACCCACACTGGCCAGAAACCCN48-51-3′ (SEQ ID NO: 108) and 5′-GATCTGAATTCATTCACCGGTN42-45-3′ (SEQ ID NO: 109), respectively, where N48-51 and N42-45 correspond to the customized sequence for annealing to the nucleic acid encoding the zinc finger domain. Double stranded DNA was prepared by amplifying template nucleic acid with an equimolar mixture of two oligonucleotides. PCR conditions consisted of a first cycle at 94° C. for 3 minutes followed by 5 cycles of 94° C. for 1 minutes, 50° C. for 1 minutes, and 72° C. for 30 seconds.

[0260] The double stranded DNA encoding each zinc finger domain was then used as a template in second round PCR. The rePCR primers had two regions, one region that is identical to yeast vector pPCFM-Zif and a second region that is identical to the 21-nucleotide-long common tail sequence described above. The sequence of forward primer was 5′-TGTCGAATCTGCATGCGTAACTTCAGTCGTAGTGACCACCTTACCACCCAC ATCCGGACCCACACTGGCCAGAAACCC-3′ (SEQ ID NO:138) and that of reverse primer was 5′-GGTGGCGGCCGTTACTTACTTAGAGCTCGACGTCTTACTTACTTAGC GGCCGCACTAGTAGATCTGAATTCATTCACCGGT-3′ (SEQ ID NO:139). The reaction mixture contained 2.5 pmoles of each primer, 1.5 mM Mg2+, 2 units of Taq polymerase and 0.01 units of Pfu polymerase in 25 ul. Reactions were carried out at 94° C. for 3 min, then cycled through 20 cycles of 94° C. for 1 min, 65° C. for 1 min, and 72° C. for 30 sec or at 94° C. for 3 min, then cycled through 25 cycles of 94° C. for 30 seconds and 72° C. for 30 seconds.

[0261] Gap repair cloning was performed by transforming the mixture of rePCR products and linearized pPCFM-Zif vector that had been digested with MscI and EcoRI into yeast YW1 cells. The region identical to the yeast vector pPCFM-Zif allows for homologous recombination with the vector in the yeast cells. All constructs thus formed were confirmed by DNA sequencing.

EXAMPLE 2

Construction of a Library for Assaying an Individual Zinc Finger Domain

[0262] A plasmid library of naturally occurring zinc finger domains was prepared by cloning zinc finger domains from the human genome. DNA segments encoding zinc finger domains were amplified from template human genomic DNA (purchased from Promega Corporation, Madison, Wis., USA) using PCR and degenerate oligonucleotide primers. The DNA sequences of the degenerate PCR primers used to clone human zinc finger domains were as follows; 5′-GCGTCCGGACNCAYACNGGNSARA-3′ (SEQ ID NO:81) and 5′-CGGAATTCANNBRWANGGYYTYTC-3′ (SEQ ID NO:82), wherein R represent G and A; B represents G, C, and T; S represents G and C; W represents A and T; Y represents C and T; and N represents A, C, G, and T.

[0263] The degenerate PCR primers anneal to nucleic acid sequences coding for an amino acid profile, His-Thr-Gly-(Glu or Gln)-(Lys or Arg)-Pro-(Tyr or Phe) (SEQ ID NO:83), that is found at the junction between zinc finger domains in many naturally occurring zinc finger proteins (Agata et al. (1998) Gene 213:55-64).

[0264] The buffer composition of the PCR reaction was 50 mM KCl, 3 mM MgCl2, 10 mM Tris pH 8.3. Taq DNA polymerase was added and the reaction mixture was incubated at 94° C. for 30 seconds, at 42° C. for 60 seconds, and then at 72° C. for 30 seconds. This cycle was repeated 35 times, and was followed by a final incubation at 72° C. for 10 minutes.

[0265] The PCR products were cloned into pPCFMS-Zif as follows: The PCR products were electrophoresed, and the DNA segments corresponding to about 120 bp were isolated. After digestion with BspEI and EcoRI, the 120-bp DNA segments were ligated into pPCFMS-Zif. As a result, the DNA-binding domain of the hybrid transcription factor encoded by this plasmid library consists of finger 1 and finger 2 of Zif268 and a zinc finger domain derived from the human genome. The plasmid library was prepared from a total of 106 Escherichia coli transformants. This library construction scheme retains the naturally occurring linker sequence found between zinc finger domains.

EXAMPLE 3

Construction of a Library for Assaying an Individual Zinc Finger Domain

[0266] A library of mutant zinc finger domains was prepared by random mutagenesis. Finger 3 of Zif268 was used as a polypeptide framework. Random mutations were introduced at positions −1, 2, 3, 4, 5, and 6 along the α-helix, corresponding respectively to the arginine at position 73, aspartic acid at position 75, glutamic acid at position 76, arginine at position 77, lysine at position 78, and arginine at position 79 of SEQ ID NO:21 (within finger 3 of Zif268).

[0267] At each of the nucleic acid sequence positions encoding these amino acids, a randomized codon, 5′-(G/A/C) (G/A/C/T) (G/C)-3′, was introduced. This randomized codon encodes any one of 16 amino acids (excluding four amino acids: tryptophan, tyrosine, cysteine and phenylalanine). Also excluded are all three possible stop codons. The randomized codons were introduced with an oligonucleotide cassette constructed from two oligonucleotides:

[0268] 5′-GGGCCCGGGGAGAAGCCTTACGCATGTCCAGTCGAATCTTGTGATAGAA GATTC-3′ (SEQ ID NO:84); and

[0269] 5′-CTCCCCGCGGTTCGCCGGTGTGGATTCTGATATGSNBSNBAAGSNBSNBS NBSNBTGAGAATCTTCTATCACAAG-3′ (SEQ ID NO:85), wherein B represents G, T, and C; S represents G and C; and N represents A, G, C, and T.

[0270] After annealing these two oligonucleotides, the DNA duplex cassette was synthesized by reaction with Klenow polymerase for 30 minutes. After digestion with AvaI and SacII, the DNA duplex was ligated into pPCFMS-Zif digested with SgrAI and SacII. Plasmids were isolated from about 109 E. coli transformants.

EXAMPLE 4

Construction of Reporter Plasmids

[0271] Reporter plasmids including the yeast HIS3 gene were prepared by modification of pRS315His (Wang and Reed (1993) Nature 364:121-126). The reporter plasmids also contain the LEU2 marker under its natural promoter for the purpose of selecting transformants bearing the plasmid. First, the SalI recognition site in pRS315His was removed by ligating the small fragment of pRS315His after digestion with SalI and BamHI and the large fragment of pRS315His after digestion with BamHI and XhoI to make pRS315HisΔSal. Next, a new SalI recognition site was created within the promoter region of the HIS3 gene by inserting an oligonucleotide duplex into pRS315HisΔSal between the BamHI and SmaI site. The sequences of the two oligonucleotides that were annealed to produce the inserted duplex are

[0272] 5′-CTAGACCCGGGAATTCGTCGACG-3′ (SEQ ID NO:86); and

[0273] 5′-GATCCGTCGACGAATTCCCGGGT-3′ (SEQ ID NO:87). The resulting plasmid was named pRS315HisMCS.

[0274] Multiple reporter plasmids were constructed by inserting desired composite sequences into pRS315HisMCS. The composite sequences are inserted as a tandem array containing four copies of the composite sequence. The target sequences were derived from 10-bp DNA sequences found in the LTR region of HIV-1:

[0275] 5′-GAC ATC GAG C-3′ (SEQ ID NO:1) HIV-1 LTR (−124/−115)

[0276] 5′-GCA GCT GCT T-3′ (SEQ ID NO:2) HIV-1 LTR (−23/−14)

[0277] 5′-GCT GGG GAC T-3′ (SEQ ID NO:3) HIV-1 LTR (−95/−86))

[0278] and in the promoter of human CCR5 gene:

[0279] 5′-AGG GTG GAG T-3′ (SEQ ID NO:4) human CCR5 (−70/−79)

[0280] 5′-GCT GAG ACAT-3′ (SEQ ID NO:5) human CCR5 (+7/+16)).

[0281] Each of these 10-bp DNA sequence can be parsed into component 4-bp target sites in order to identify a zinc finger domain that recognizes each region of the site. Using the modular assembly method, such zinc finger domains can be coupled to produce a DNA binding protein that recognizes the site in vivo.

[0282] The underlined portions above depict examples of 4-bp target sequences. Each of these 4-bp target sequences was connected to the 5-bp recruitment sequence, 5′-GGGCG-3′, that is recognized by finger 1 and finger 2 of Zif268. The resulting 9-bp sequences constitute composite binding sequences. Each composite binding sequence has the following format: 5′-XXXXGGGCG-3′, where XXXX is the 4-bp target sequence and the adjacent 5′-GGGCG-3′ is the recruitment sequence.

[0283] FIG. 7 recites the DNA sequences of the inserted tandem arrays of composite binding sites, each of which was operably linked to the reporter gene in pRS315HisMCS. Each tandem array contains 4 copies of a composite binding sequence. For each binding site, two oligonucleotides were synthesized, annealed and ligated into pRS315HisMCS restricted with SalI and XmaI site to make a reporter plasmid.

EXAMPLE 5

Construction of Reporter Plasmids

[0284] A set of reporter plasmids that includes a pair of reporters (one having lacZ, the other having HIS3) for each 3 basepair subsite was constructed as follows: Reporter plasmids were constructed by inserting the desired target sequences into pRS315HisMCS and pLacZi. For each 3 basepair target site, two oligonucleotides were synthesized, annealed, and inserted into the SalI and XmaI site of pRS315HisMCS and of pLacZi to make reporter plasmids. The DNA sequences of the oligonucleotides were as follows: 5′-CCGGT NNNTGGGCG TAC NNNTGGGCG TCA NNNTGGGCG-3′ (SEQ ID NO:88) and 5′-TCGA CGCCCANNN TGA CGCCCANNN GTA CGCCCANNN A-3′ (SEQ ID NO:89). Total 64 pairs of oligonucleotides were synthesized and inserted into the two reporter plasmids.

EXAMPLE 6

Selection of Zinc Finger Domains with Desired DNA-Binding Specificity

[0285] To select zinc finger domains that specifically bind given target sequences, yeast cells were transformed first with a reporter plasmid and then a library of hybrid plasmids encoding hybrid transcription factors. Yeast transformation and screening procedures were carried out as described in Ausubel et al (Current Protocols in Molecular Biology (1998), John Wiley and Sons, Inc.). Yeast strain yWAM2 (MATα(alpha) Δgal4 Δgal80 URA3:::GAL1-lacZ lys2801 his3-Δ200 trp1-Δ63 leu2 ade2-101CYH2) was used.

[0286] In one instance, yeast cells were first transformed with a reporter plasmid containing the composite binding sequence 5′-GAGCGGGCG-3′ (the 4-bp target sequence is underlined), which was operably linked to the reporter gene. Then, the plasmid library of mutant zinc finger domains prepared by random mutagenesis was introduced into the transformed yeast cells. About 106 colonies were obtained in medium lacking both leucine and tryptophan. Because the reporter plasmid and the zinc finger domain expression plasmids contain yeast LEU2 and TRP1 genes, respectively, as a marker, yeast cells were grown in medium lacking both leucine and tryptophan in order to select for cells that contain both the reporter and the zinc finger domain expression plasmid.

[0287] In one implementation, the library of zinc finger domains derived from the human genome was transformed into cells bearing the reporter plasmids. The transformation was performed on five different host cell strains, each strain containing one of five different target sequences operably linked to the reporter gene. About 105 colonies were obtained per transformation in medium lacking both leucine and tryptophan. Transformants were grown on petri plates containing synthetic medium lacking leucine and tryptophan. After incubation, transformed cells were collected by applying a 10% sterile glycerol solution to the plates, scraping the colonies into the solution, and retrieving the solution. Cells were stored as frozen aliquots in the glycerol solution. A single aliquot was spread onto medium lacking leucine, tryptophan and histidine. 3-aminotriazole (AT) was added to the growth medium at the final concentrations of 0, 0.03, 0.1 and 0.3 mM. AT is a competitive inhibitor of His3 and titrates the sensitivity of the HIS3 selection system. AT suppressed the basal activity of His3. Such basal activity can arise from leaky expression of the HIS3 gene on the reporter plasmid. Out of about 107 yeast cells spread on medium, on the order of hundreds of colonies grew in the selective medium lacking AT. The number of colonies gradually decreased as the concentration of AT increased. On the order of tens of colonies grew in the selective medium containing 0.3 mM of AT. Several colonies were randomly picked from the medium lacking AT and from the medium containing 0.3 mM of AT. Plasmids were isolated from yeast cells and transformed into Escherichia coli strain KC8 (pyrF leuB600 trpC hisB463). The plasmids encoding zinc finger transcription factor were isolated, and the DNA sequences of selected zinc finger domains were determined.

[0288] The amino acid sequence of each selected zinc finger domain was deduced from the DNA sequence. Each zinc finger domain was named after the four amino acid residues at base-contacting positions, namely positions −1, 2, 3, and 6 along the alpha-helix. The results are shown in Table 1. Identified zinc finger domains are named by the four amino acids found at base-contacting positions. Analysis of the sequences showed that in some cases the same zinc finger domain was obtained repeatedly. The numbers in the parenthesis in Table 1 represent how many times the same zinc finger domains have been obtained. For example, two zinc fingers having CSNR at the four base contacting positions were identified as binding the GAGC nucleic acid site (see column 3, “GAGC/human genome”).

	TABLE 1
	Target Sequence
	GAGC	GAGC	GCTT	GACT	GAGT	ACAT
	origin of zinc finger domain library
	random	human	human	human	human	human
	mutagenesis	genome	genome	genome	genome	genome
amino acid	KTNR (2)	RTNR (2)	VSTR (9)	HSNK (2)	RDER (2)	QSTV (3)
residues at base	RTTR	RTNR		CSNR (7)	SSNR (5)
contacting	RPNR	CSNR (2)
positions*	HSNR	SSNR (3)
	RLKP	RSTV
	TRQR	SSGE
	TALH
	RQKA
	PARV
	RTFR
	RNNR
	DPLH
	RGNR
*The four-letter identifiers in the six columns to the right are the descriptors of the zinc finger domains isolated for each target sequence. Although these names are indicative of the amino acid residues at base contacting positions, they are not sequences of polypeptides.

[0289] The full DNA sequences encoding selected human zinc finger domains and their translated amino acid sequences are shown in FIG. 11. The DNA sequence that is complementary to the degenerate PCR primers used to amplify DNA segments encoding zinc finger domains in the human genome is underlined. This sequence may differ from the original base sequence of reported human genome sequence due to either allelic differences or alterations introducing during amplification.

[0290] Most human zinc finger domains identified by screening in accordance with the present invention either were novel polypeptides or corresponded to anonymous open reading frames. For example, zinc finger domains designated as HSNK (contained in the sequence reported in GenBank accession number AF155100) and VSTR (contained in the sequence reported in GenBank accession number AF02577) are found in proteins whose function is as yet unknown. The results described herein not only indicate that these zinc finger domains are able to function as sequence-specific DNA-binding domains, but also document their preferred binding site preference in the context of chimeric proteins.

[0291] In addition, the present invention reveals that zinc finger domains obtained from the human genome can be used as modular building blocks to construct novel DNA-binding proteins. Human zinc finger domains of the present invention were obtained as a result of their functionality in vivo when connected to the C-terminus of finger 1 and finger 2 of Zif268. Thus, the identified zinc finger domains can recognize specific sequence in an artificial context, and are suitable as modular building blocks for designing synthetic transcription factors.

EXAMPLE 7

Pairwise Mating

[0292] To facilitate identification of zinc finger domains that bind to each 3 basepair target site, yeast mating was used to eliminate the need for repetitively transforming yeast cells and to search for positive binders to each of the 64 reporter constructs with a single transformation. Two yeast strains, YWI (MATα mating type) and YPH499 (MATα mating type), were used. YW1 was derived from yWAM2 by selecting a clone resistant to 5-fluoroorotic acid (FOA) in order to generate a ura3-derivative of yWAM2.

[0293] The plasmid library of zinc finger domains were introduced into the YW1 cells by yeast transformation. Cells from approximately 106 independently transformed colonies were collected by scraping plates with a 10% glycerol solution. The solution was frozen in aliquots. Each pair of 64 reporter plasmids (derived from pLacZi or pRS315His) also was cotransfected into yeast strain YPH499. Transformants containing both reporter plasmids were harvested and frozen.

[0294] After thawing, the yeast cells were grown on minimal media to mid-log phase. The two cell types were then mixed and allowed to mate in YPD for 5 h. Diploid cells were selected on minimal media containing X-gal and AT (1 mM) but lacking tryptophan, leucine, uracil, and histidine. After several days, blue colonies that grew on the selective plate were isolated. The plasmids encoding zinc finger domains were isolated from blue colonies, and the DNA sequences of the selected zinc finger domains were determined.

[0295] The nucleic acids isolated from the blue colonies were individually retransformed into YW1 cells. For each isolated nucleic acid, retransformed YW1 cells were mated to YPH499 cells containing each of the 64 LacZ reporter plasmids in a 96-well plate, and then spread onto minimal media containing X-gal but lacking tryptophan and uracil. The DNA binding affinities and specificities of a zinc finger domain for 64 target sequences were determined by the intensity of blue color. Control experiments with the Zif268 zinc finger domains indicated that positive interactions between a zinc finger domain and a binding site yielded dark to pale blue colonies, (whose blue intensity is proportional to the binding affinity) and that negative interactions yielded white colonies.

EXAMPLE 8

Comparison of Identified Zinc Finger Domains with an Interaction Code

[0296] The amino acid residues of selected zinc finger domains at the critical base-contacting positions were compared with those anticipated from the zinc finger domain-DNA interaction code (FIG. 3). Most of zinc finger domains showed expected patterns, i.e. the amino acid residues at the critical positions match well those predicted from the code.

[0297] For example, the consensus amino acid residues in zinc finger domains selected from the library generated by random mutagenesis were R (Arg; 7 out of 14) or K (Lys; 2 out of 14) at position−1, N (Asp; 6 out of 14) at position 3, and R (9 out of 14) at position 6 (Table 1). These zinc finger domains were selected with the GAGC plasmid. (The reporter plasmid in which the composite binding sequence, 5′-GAGCGGGCG-3′, is operably linked to the reporter gene is referred to as the GAGC plasmid. Likewise, the other reporter plasmids in which the sequence, 5′-XXXXGGGCG-3′, is operably linked to the reporter gene are referred to as the XXXX plasmids.) These amino acid residues at critical base-contacting positions exactly match those expected from the code.

[0298] It is also known that amino acid residues at position 2 usually play only a minor role in base recognition (Pavletich and Pabo (1991) Science 252, 809-817). In some cases, however, position 2 may be more influential.

[0299] The amino acid residues in zinc finger domains obtained from the human genome also match those expected from the code quite well. For example, the consensus amino acid residues at position −1, 3, and 6 in the zinc finger domains obtained with the GAGC plasmid were R, N, and R, respectively (Table 1, column 3). These amino acids are exactly those anticipated from the code.

[0300] The amino acid residues at position −1, 3, and 6 in the zinc finger domain obtained with the GCTT plasmid were V, T, and R, respectively (Table 1, column 4). The T and R residues are exactly those expected from the code. The amino acid residues predicted from the code at position −1 that would interact with the base T (underlined) of the GCTT site are L, T or N. The VSTR zinc finger domain, which was selected with the GCTT plasmid, contained V (valine), a hydrophobic amino acid similar to L (leucine) at this position.

[0301] Overall, the amino acid residues in selected zinc finger domains match those predicted from the code at least at two positions out of the three critical positions. The amino acid residues in selected zinc finger domains that are expected from the code are underlined in Table 1. These results strongly suggest that the in vivo selection system disclosed herein functions as expected. However, as the in vivo selection and assay systems measure actual function of the zinc finger proteins in a cell, they may identify fingers with useful functions and DNA binding specificities that do not conform to theoretical expectations (e.g., the relationship depicted in FIG. 3).

EXAMPLE 9

Retransformation and Cross-Transformation

[0302] To rule out the possibility of false positive results and to investigate the sequence specificity of the zinc finger protein described above, retransformation and cross-transformation of yeast cells were carried out using the isolated plasmids.

[0303] Yeast cells were first co-transformed with a reporter plasmid and a hybrid plasmid encoding a zinc finger domain. Yeast transformants were inoculated into minimal medium lacking leucine and tryptophan and incubated for 36 hours. About 1,000 cells in the growth medium were spotted directly onto solid medium lacking leucine, tryptophan, and histidine (designated as −histidine in FIG. 10) and onto solid medium lacking leucine and tryptophan (designated as +histidine in FIG. 10). These cells were then incubated for 50 hours at 30° C. The results are shown in FIG. 10.

[0304] It is expected that colonies can grow in the medium lacking histidine when the zinc finger moiety of the hybrid transcription factor binds the composite binding sequence, allowing the hybrid transcription factor to activate expression of the HIS3 reporter gene. Colonies cannot grow in the medium lacking histidine when the zinc finger moiety of the transcription factor does not bind the composite binding sequence.

[0305] As shown in FIG. 10, the isolated zinc finger domains were capable of binding corresponding target sequences and showed sequence specificity markedly different from that of Zif268. Zif268 showed higher activity with the GCGT plasmid than with the other five plasmids, and relatively high activity with the GAGT plasmid. No colonies were formed by strains having reporters containing other binding sites and expressing the Zif268 protein.

[0306] The KTNR zinc finger domain isolated from the random mutant library was originally selected with the GAGC reporter plasmid. As expected, colonies were formed only with the GAGC plasmid. Zinc finger domains obtained from the library derived from the human genome also showed expected specificity. For example, HSNK, which had been selected with the GACT plasmid, allowed cell growth only with the GACT plasmid when retransformed into yeast cells. VSTR, which had been selected with the GCTT plasmid, showed the highest activity with the GCTT plasmid. RDER, which was selected with the GAGT plasmid, has the same amino acid residues at the four base-contacting positions as does finger 3 of Zif268. As expected, this zinc finger domain showed sequence specificity similar to that of finger 3. SSNR, selected with the GAGC and GAGT plasmids, allowed cell growth on histidine-deficient medium with the GAGC plasmid but not with the GAGT plasmid. QSTV, obtained with the ACAT plasmid, did not allow cell growth with any of the plasmids tested in this assay. However, this zinc finger domain was able to bind to the ACAT sequence tightly in vitro as demonstrated below.

EXAMPLE 10

Gel Shift Assays

[0307] Zinc finger proteins containing zinc finger domains selected using the modified one-hybrid system were expressed in E. Coli, purified, and used in gel shift assays. The DNA segments encoding zinc finger proteins in the hybrid plasmids were isolated by digestion with SalI and NotI and inserted into pGEX-4T2 (Pharmacia Biotech) between the SalI and NotI sites. Zinc finger proteins were expressed in E. coli strain BL21 as fusion proteins connected to GST (Glutathione-S-transferase). The fusion proteins were purified using glutathione affinity chromatography (Pharmacia Biotech, Piscataway, N.J.) and then digested with thrombin, which cleaves the connecting site between the GST moiety and zinc finger proteins. Purified zinc finger proteins contained finger 1 and finger 2 of Zif268 and selected zinc finger domains at the C-terminus.

[0308] The following probe DNAs were synthesized, annealed, labeled with 32P using T4 polynucleotide kinase, and used in gel shift assays.

GCGT;
5′-CCGGGTCGCGCGTGGGCGGTACCG-3′ (SEQ ID NO:90)
3′-CAGCGCGCACCCGCCATGGCAGCT-5′ (SEQ ID NO:91)
GAGC;
5′-CCGGGTCGCGAGCGGGCGGTACCG-3′ (SEQ ID NO:92)
3′-CAGCGCTCGCCCGCCATGGCAGCT-5′ (SEQ ID NO:93)
GCTT;
5′-CCGGGTCGTGCTTGGGCGGTACCG-3′ (SEQ ID NO:94)
3′-CAGCACGAACCCGCCATGGCAGCT-5′ (SEQ ID NO:95)
GACT;
5′-CCGGGTCGGGACTGGGCGGTACCG-3′ (SEQ ID NO:96)
3′-CAGCCCTGACCCGCCATGGCAGCT-5′ (SEQ ID NO:97)
GAGT;
5′-CCGGGTCGGGAGTGGGCGGTACCG-3′ (SEQ ID NO:98)
3′-CAGCCCTCACCCGCCATGGCAGCT-5′ (SEQ ID NO:99)
ACAT;
5′-CCGGGTCGGACATGGGCGGTACCG-3′ (SEQ ID NO:100)
3′-CAGCCTGTACCCGCCATGGCAGCT-5′ (SEQ ID NO:101)

[0309] Various amounts of a zinc finger protein were incubated with a labeled probe DNA for one hour at room temperature in 20 mM Tris pH 7.7, 120 mM NaCl, 5 mM MgCl2, 20 μM ZnSO4, 10% glycerol, 0.1% Nonidet P-40, 5 mM DTT, and 0.10 mg/mL BSA (bovine serum albumin), and then the reaction mixtures were subjected to gel electrophoresis. The radioactive signals were quantitated by PhosphorImager™ analysis (Molecular Dynamics), and dissociation constants (Kd) were determined as described (Rebar and Pabo (1994) Science 263:671-673). The results are described in Table 2. All the constants were determined in at least two separate experiments, and the standard error of the mean is indicated. Cell growth of yeast transformants on histidine-deficient minimal medium (FIG. 10) is also indicated in Table 2.

	TABLE 2
	Zinc finger	Probe	Dissociation	Growth of
	protein	DNA	Constant (nM)	Yeast
	Zif268	GCTT	2.1 ± 0.3	−
		GCGT	0.024 ± 0.004	+++
		GAGT	0.17 ± 0.04	++
		GAGC	2.3 ± 0.9	−
		GACT	4.9 ± 0.6	−
		ACAT	1.3 ± 0.3	−
	KTNR	GCGT	5.5 ± 0.7	−
		GAGC	0.17 ± 0.01	++
		GACT	30 ± 1	−
	CSNR	GCGT	2.7 ± 0.3	−
		GAGT	0.46 ± 0.04	+++
		GAGC	1.2 ± 0.1	++
		GACT	0.17 ± 0.01	+++
	HSNK	GCGT	42 ± 14	−
		GAGT	3.5 ± 0.1	−
		GACT	0.32 ± 0.08	++
	RDER	GCGT	0.027 ± 0.002	+++
		GAGT	0.18 ± 0.01	++
		GACT	28 ± 9	−
	SSNR	GCGT	3.8 ± 1.3	−
		GAGC	0.45 ± 0.09	++
		GACT	0.61 ± 0.21	+
	VSTR	GCTT	0.53 ± 0.07	++
		GCGT	0.76 ± 0.22	−
		GAGT	1.4 ± 0.2	−
	QSTV	GCTT	29 ± 3	−
		GCGT	9.8 ± 3.4	−
		ACAT	2.3 ± 0.4	−
	* +++, 20 to 100% growth;
	++, 5 to 20% growth;
	+, 1-5% growth;
	−, <1% growth.

[0310] Zinc finger proteins that allowed cell growth on histidine-deficient plates bound the corresponding probe DNAs tightly. For example, the Zif268 protein used as a control allowed cell growth with the GCGT and GAGT reporter plasmids, and the dissociation constants measured in vitro using corresponding probe DNAs were 0.024 nM and 0.17 nM, respectively. In contrast, the Zif268 protein did not allow cell growth with other plasmids, and the dissociation constants measured using corresponding probe DNAs were higher than 1 nM.

[0311] Zinc finger proteins containing novel zinc finger domains also showed similar results. For example, the KTNR protein showed strong affinity for the GAGC probe DNA, with a dissociation constant of 0.17 nM, but not for the GCGT or GACT probe DNA, with dissociation constants of 5.5 nM or 30 nM, respectively. This protein allowed cell growth only with the GAGC plasmid. The HSNK protein was able to bind the GACT probe DNA tightly (Kd=0.32 nM) but not the GCGT or GAGT probe DNA; as would be expected, the HSNK protein allowed cell growth only with the GACT plasmid.

[0312] The QSTV protein, which was selected with the ACAT reporter plasmid, was not able to promote cell growth with any of the other reporter plasmids when retransformed into yeast. Gel shift assays demonstrated that this protein bound the ACAT probe DNA more tightly than it did the other probe DNAs. That is, QSTV bound the ACAT probe DNA 13 times or 4.3 times stronger than it did the GCTT or GCGT probe DNA respectively.

[0313] In general, when a zinc finger protein, e.g., having three zinc finger domains, binds a DNA sequence with a dissociation constant lower than 1 nM, it allows cell growth, whereas when a zinc finger protein binds a DNA sequence with a dissociation constant higher than 1 nM, it does not allow cell growth. Zinc finger proteins that bind with a dissociation constant of greater than 1 nM but less than 5 nM can also be useful, e.g., in the context of a chimeric zinc finger protein having four zinc finger domains.

EXAMPLE 11

TG-ZFD-001 “CSNR1”

[0314] TG-ZFD-001 “CSNR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is YKCKQCGKAFGCPSNLRRHGRTH (SEQ ID NO:23). It is encoded by the human nucleic acid sequence: 5′-TATAAATGTAAGCAATGTGGGAAAGCTTTTGGATGTCCCTCAAACCTTCGAA GGCATGGAAGGACTCAC-3′ (SEQ ID NO:22).

[0315] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-001 “CSNR1” demonstrates recognition specificity for the 3-bp target sequence sequences GAA, GAC, and GAG Its binding site preference is GAA>GAC>GAG>GCG as determined by in vivo screening results and EMSA. In EMSA, the TG-ZFD-001 “CSNR” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 0.17 nM for the GAC containing site, 0.46 nM for the GAG containing site, and 2.7 nM for the GCG containing site.

[0316] TG-ZFD-001 “CSNR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA, GAC, or GAG.

EXAMPLE 12

TG-ZFD-002 “HSNK”

[0317] TG-ZFD-002 “HSNK” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCKECGKAFNHSSNFNKHHRIH (SEQ ID NO:25). It is encoded by the human nucleic acid sequence: 5′-TATAAGTGTAAGGAGTGTGGGAAAGCCTTCAACCACAGCTCCAACTTCAATA AACACCACAGAATCCAC-3′ (SEQ ID NO:24).

[0318] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-002 “HSNK” demonstrates recognition specificity for the 3-bp target sequence GAC. Its binding site preference is GAC>GAG>GCG as determined by in vivo screening results and EMSA. In EMSA, the TG-ZFD-002 “HSNK” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 0.32 nM for the GAC containing site, 3.5 nM for the GAG containing site, and 42 nM for the GCG containing site.

[0319] TG-ZFD-002 “HSNK” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAC.

EXAMPLE 13

TG-ZFD-003 “SSNR”

[0320] TG-ZFD-003 “SSNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECKECGKAFSSGSNFTRHQRIH (SEQ ID NO:27). It is encoded by the human nucleic acid sequence: 5′-TATGAATGTAAGGAATGTGGGAAAGCCTTTAGTAGTGGTTCAAACTTCACTC GACATCAGAGAATTCAC-3′ (SEQ ID NO:26).

[0321] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-003 “SSNR” demonstrates recognition specificity for the 3-bp target sequence GAG Its binding site preference is GAG>GAC>GCG as determined by in vivo screening results and EMSA. In EMSA, the TG-ZFD-003 “SSNR” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 0.45 nM for the GAG containing site, 0.61 nM for the GAC containing site, and 3.8 nM for the GCG containing site.

[0322] TG-ZFD-003 “SSNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAG, or GAC.

EXAMPLE 14

TG-ZFD-004 “RDER1”

[0323] TG-ZFD-004 “RDER1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YVCDVEGCTWKFARSDELNRHKKRH (SEQ ID NO:29). It is encoded by the human nucleic acid sequence: 5′-TATGTATGCGATGTAGAGGGATGTACGTGGAAATTTGCCCGCTCAGATGAGC TCAACAGACACAAGAAAAGGCAC-3′ (SEQ ID NO:28).

[0324] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-004 “RDER1” demonstrates recognition specificity for the 3-bp target sequence GCG. Its binding site preference is GCG>GTG, GAG>GAC as determined by in vivo screening results and EMSA. In EMSA, the TG-ZFD-004 “RDER1” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 0.027 nM for the GCG containing site, 0.18 nM for GAG containing site, and 28 nM for the GAC containing site.

[0325] TG-ZFD-004 “RDER1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG, GTG or GAG.

EXAMPLE 15

TG-ZFD-005 “QSTV”

[0326] TG-ZFD-005 “QSTV” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECNECGKAFAQNSTLRVHQRIH (SEQ ID NO:31). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTAATGAATGCGGGAAAGCTTTTGCCCAAAATTCAACTCTCAGAG TACACCAGAGAATTCAC-3′ (SEQ ID NO:30).

[0327] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-005 “QSTV” demonstrates recognition specificity for the 3-bp target sequence ACA. Its binding site preference is ACA>GCG>GCT as determined by EMSA. In EMSA, the TG-ZFD-005 “QSTV” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 2.3 nM for the ACA containing site, 9.8 nM for the GCG containing site, and 29 nM for the GCT containing site.

[0328] TG-ZFD-005 “QSTV” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence ACA.

EXAMPLE 16

TG-ZFD-006 “VSTR”

[0329] TG-ZFD-006 “VSTR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECNYCGKTFSVSSTLIRHQRIH (SEQ ID NO:33). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTAATTACTGTGGAAAAACCTTTAGTGTGAGCTCAACCCTTATTA GACATCAGAGAATCCAC-3′ (SEQ ID NO:32).

[0330] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-006 “VSTR” demonstrates recognition specificity for the 3-bp target sequence GCT. Its binding site preference is GCT>GCG>GAG as determined by in vivo screening results and EMSA. In EMSA, the TG-ZFD-006 “VSTR” fusion to fingers 1 and 2 of Zif268 and the GST purification handles has an apparent Kd of 0.53 nM for the GCT containing site, 0.76 for the GCG containing site, and 1.4 nM for the GAG containing site.

[0331] TG-ZFD-006 “VSTR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCT or GCG.

EXAMPLE 17

TG-ZFD-007 “CSNR2”

[0332] TG-ZFD-007 “CSNR2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YQCNICGKCFSCNSNLHRHQRTH (SEQ ID NO:35). It is encoded by the human nucleic acid sequence: 5′-TATCAGTGCAACATTTGCGGAAAATGTTTCTCCTGCAACTCCAACCTCCACAGG CACCAGAGAACGCAC-3′ (SEQ ID NO:34).

[0333] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-007 “CSNR2” demonstrates recognition specificity for 3-bp target sequences GAA, GAC, and GAG. Its binding site preference is GAA>GAC>GAG as determined by in vivo screening results.

[0334] TG-ZFD-007 “CSNR2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA, GAC, or GAG.

EXAMPLE 18

TG-ZFD-008 “QSHR1”

[0335] TG-ZFD-008 “QSHR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YACHLCGKAFTQSSHLRRHEKTH (SEQ ID NO:37). It is encoded by the human nucleic acid sequence: 5′-TATGCATGTCATCTATGTGGAAAAGCCTTCACTCAGAGTTCTCACCTTAGAAGA CATGAGAAAACTCAC-3′ (SEQ ID NO:36).

[0336] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-008 “QSHR1” demonstrates recognition specificity for 3-bp target sequences GGA, GAA, and AGA. Its binding site preference is GGA>GAA>AGA as determined by in vivo screening results.

[0337] TG-ZFD-008 “QSHR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA, GAA, or AGA.

EXAMPLE 19

TG-ZFD-009 “QSHR2”

[0338] TG-ZFD-009 “QSHR2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCGQCGKFYSQVSHLTRHQKIH (SEQ ID NO:39). It is encoded by the human nucleic acid sequence: 5′-TATAAATGCGGCCAGTGTGGGAAGTTCTACTCGCAGGTCTCCCACCTCACCCGC CACCAGAAAATCCAC-3′ (SEQ ID NO:38).

[0339] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-009 “QSHR2” demonstrates recognition specificity for the 3-bp target sequence GGA.

[0340] TG-ZFD-009 “QSHR2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA.

EXAMPLE 20

TG-ZFD-010 “QSHR3”

[0341] TG-ZFD-010 “QSHR3” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YACHLCGKAFTQCSHLRRHEKTH (SEQ ID NO:41). It is encoded by the human nucleic acid sequence: 5′-TATGCATGTCATCTATGTGGAAAAGCCTTCACTCAGTGTTCTCACCTTAGAAGA CATGAGAAAACTCAC-3′ (SEQ ID NO:40).

[0342] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-010 “QSHR3” demonstrates recognition specificity for 3-bp target sequences GGA and GAA. Its binding site preference is GGA>GAA as determined by in vivo screening results.

[0343] TG-ZFD-010 “QSHR3” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA or GAA.

EXAMPLE 21

TG-ZFD-011 “QSHR4”

[0344] TG-ZFD-011 “QSHR4” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YACHLCAKAFIQCSHLRRHEKTH (SEQ ID NO:43). It is encoded by the human nucleic acid sequence: 5′-TATGCATGTCATCTATGTGCAAAAGCCTTCATTCAGTGTTCTCACCTTAGAAGAC ATGAGAAAACTCAC-3′ (SEQ ID NO:42).

[0345] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-011 “QSHR4” demonstrates recognition specificity for 3-bp target sequences GGA and GAA. Its binding site preference is GGA>GAA as determined by in vivo screening results.

[0346] TG-ZFD-011 “QSHR4” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA or GAA.

EXAMPLE 22

TG-ZFD-012 “QSHR5”

[0347] TG-ZFD-012 “QSHR5” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YVCRECGRGFRQHSHLVRHKRTH (SEQ ID NO:45). It is encoded by the human nucleic acid sequence: 5′-TATGTTTGCAGGGAATGTGGGCGTGGCTTTCGCCAGCATTCACACCTGGTCAGA CACAAGAGGACACAT-3′ (SEQ ID NO:44).

[0348] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-012 “QSHR5” demonstrates recognition specificity for 3-bp target sequences GGA, AGA, GAA, and CGA. Its binding site preference is GGA>AGA>GAA>CGA as determined by in vivo screening results.

[0349] TG-ZFD-012 “QSHR5” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA, AGA, GAA, or CGA.

EXAMPLE 23

TG-ZFD-013 “QSNR1”

[0350] TG-ZFD-013 “QSNR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FECKDCGKAFIQKSNLIRHQRTH (SEQ ID NO:47). It is encoded by the human nucleic acid sequence: 5′-TTTGAGTGTAAAGATTGCGGGAAAGCTTTCATTCAGAAGTCAAACCTCATCAG ACACCAGAGAACTCAC-3′ (SEQ ID NO:46).

[0351] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-013 “QSNR1” demonstrates recognition specificity for the 3-bp target sequence GAA.

[0352] TG-ZFD-013 “QSNR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA.

EXAMPLE 24

TG-ZFD-014 “QSNR2”

[0353] TG-ZFD-014 “QSNR2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YVCRECRRGFSQKSNLIRHQRTH (SEQ ID NO:49). It is encoded by the human nucleic acid sequence: 5′-TATGTCTGCAGGGAGTGTAGGCGAGGTTTTAGCCAGAAGTCAAATCTCATCAGA CACCAGAGGACGCAC-3′ (SEQ ID NO:48).

[0354] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-014 “QSNR2” demonstrates recognition specificity for the 3-bp target sequence GAA.

[0355] TG-ZFD-014 “QSNR2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA.

EXAMPLE 25

TG-ZFD-015 “QSNV1”

[0356] TG-ZFD-015 “QSNV1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECNTCRKTFSQKSNLIVHQRTH (SEQ ID NO:51). It is encoded by the human nucleic acid sequence: 5′-TATGAATGTAACACATGCAGGAAAACCTTCTCTCAAAAGTCAAATCTCATTGTA CATCAGAGAACACAC-3′ (SEQ ID NO:50).

[0357] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-015 “QSNV1” demonstrates recognition specificity for 3-bp target sequences AAA and CAA. Its binding site preference is AAA>CAA as determined by in vivo screening results.

[0358] TG-ZFD-015 “QSNV1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AAA or CAA.

EXAMPLE 26

TG-ZFD-016 “QSNV2”

[0359] TG-ZFD-016 “QSNV2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YVCSKCGKAFTQSSNLTVHQKIH (SEQ ID NO:53). It is encoded by the human nucleic acid sequence: 5′-TATGTTTGCTCAAAATGTGGGAAAGCCTTCACTCAGAGTTCAAATCTGACTGTA CATCAAAAAATCCAC-3′ (SEQ ID NO:52).

[0360] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-016 “QSNV2” demonstrates recognition specificity for 3-bp target sequences AAA and CAA. Its binding site preference is AAA>CAA as determined by in vivo screening results.

[0361] TG-ZFD-016 “QSNV2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AAA or CAA.

EXAMPLE 27

TG-ZFD-017 “QSNV3”

[0362] TG-ZFD-017 “QSNV3” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCDECGKNFTQSSNLIVHKRIH (SEQ ID NO:55). It is encoded by the human nucleic acid sequence: 5′-TACAAATGTGACGAATGTGGAAAAAACTTTACCCAGTCCTCCAACCTTATTGT ACATAAGAGAATTCAT-3′ (SEQ ID NO:54).

[0363] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-017 “QSNV3” demonstrates recognition specificity for a 3-bp target sequence AAA.

[0364] TG-ZFD-017 “QSNV3” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AAA.

EXAMPLE 28

TG-ZFD-018 “QSNV4”

[0365] TG-ZFD-018 “QSNV4” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECDVCGKTFTQKSNLGVHQRTH (SEQ ID NO:57). It is encoded by the human nucleic acid sequence: 5′-TATGAATGTGATGTGTGTGGAAAAACCTTCACGCAAAAGTCAAACCTTGGTGT ACATCAGAGAACTCAT-3′ (SEQ ID NO:56).

[0366] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-018 “QSNV4” demonstrates recognition specificity for the 3-bp target sequence AAA.

[0367] TG-ZFD-018 “QSNV4” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AAA.

EXAMPLE 29

TG-ZFD-019 “QSSR1”

[0368] TG-ZFD-019 “QSSR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCPDCGKSFSQSSSLIRHQRTH (SEQ ID NO:59). It is encoded by the human nucleic acid sequence: 5′-TATAAGTGCCCTGATTGTGGGAAGAGTTTTAGTCAGAGTTCCAGCCTCATTCGC CACCAGCGGACACAC-3′ (SEQ ID NO:58).

[0369] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-019 “QSSR1” demonstrates recognition specificity for 3-bp target sequences GTA and GCA. Its binding site preference is GTA>GCA as determined by in vivo screening results.

[0370] TG-ZFD-019 “QSSR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GTA or GCA.

EXAMPLE 30

TG-ZFD-020 “QSSR2”

[0371] TG-ZFD-020 “QSSR2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECQDCGRAFNQNSSLGRHKRTH (SEQ ID NO:61). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTCAGGACTGTGGGAGGGCCTTCAACCAGAACTCCTCCCTGGGGCG GCACAAGAGGACACAC-3′ (SEQ ID NO:60).

[0372] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-020 “QSSR2” demonstrates recognition specificity for the 3-bp target sequence GTA.

[0373] TG-ZFD-020 “QSSR2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GTA.

EXAMPLE 31

TG-ZFD-021 “QSTR”

[0374] TG-ZFD-021 “QSTR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCEECGKAFNQSSTLTRHKIVH (SEQ ID NO:63). It is encoded by the human nucleic acid sequence: 5′-TACAAATGTGAAGAATGTGGCAAAGCTTTTAACCAGTCCTCAACCCTTACTAGA CATAAGATAGTTCAT-3′ (SEQ ID NO:62).

[0375] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-021 “QSTR” demonstrates recognition specificity for 3-bp target sequences GTA and GCA. Its binding site preference is GTA>GCA as determined by in vivo screening results.

[0376] TG-ZFD-021 “QSTR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GTA or GCA.

EXAMPLE 32

TG-ZFD-022 “RSHR”

[0377] TG-ZFD-022 “RSHR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCMECGKAFNRRSHLTRHQRIH (SEQ ID NO:65). It is encoded by the human nucleic acid sequence: 5′-TATAAGTGCATGGAGTGTGGGAAGGCTTTTAACCGCAGGTCACACCTCACACG GCACCAGCGGATTCAC-3′ (SEQ ID NO:64).

[0378] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-022 “RSHR” demonstrates recognition specificity for the 3-bp target sequence GGG.

[0379] TG-ZFD-022 “RSHR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGG.

EXAMPLE 33

TG-ZFD-023 “VSSR”

[0380] TG-ZFD-023 “VSSR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YTCKQCGKAFSVSSSLRRHETTH (SEQ ID NO:67). It is encoded by the human nucleic acid sequence: 5′-TATACATGTAAACAGTGTGGGAAAGCCTTCAGTGTTTCCAGTTCCCTTCGAAGA CATGAAACCACTCAC-3′ (SEQ ID NO:66).

[0381] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-023 “VSSR” demonstrates recognition specificity for 3-bp target sequences GTT, GTG and GTA. Its binding site preference is GTT>GTG>GTA as determined by in vivo screening results.

[0382] TG-ZFD-023 “VSSR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GTT, GTG, or GTA.

EXAMPLE 34

TG-ZFD-024 “QAHR”

[0383] TG-ZFD-024 “QAHR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCKECGQAFRQRAHLIRHHKLH (SEQ ID NO:103). It is encoded by the human nucleic acid sequence: 5′-TATAAGTGTAAGGAATGTGGGCAGGCCTTTAGACAGCGTGCACATCTTATTCG ACATCACAAACTTCAC-3′ (SEQ ID NO: 102).

[0384] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-024 “QAHR” demonstrates recognition specificity for the 3-bp target sequence GGA as determined by in vivo screening results.

[0385] TG-ZFD-024 “QAHR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA

EXAMPLE 35

TG-ZFD-025 “QFNR”

[0386] TG-ZFD-025 “QFNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCHQCGKAFIQSFNLRRHERTH (SEQ ID NO:105). It is encoded by the human nucleic acid sequence: 5′-TATAAGTGTCATCAATGTGGGAAAGCCTTTATTCAATCCTTTAACCTTCGAAG ACATGAGAGAACTCAC-3′ (SEQ ID NO:104).

[0387] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-025 “QFNR” demonstrates recognition specificity for the 3-bp target sequence GAG as determined by in vivo screening results.

[0388] TG-ZFD-025 “QFNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAG.

EXAMPLE 36

TG-ZFD-026 “QGNR”

[0389] TG-ZFD-026 “QGNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FQCNQCGASFTQKGNLLRHIKLH (SEQ ID NO:107). It is encoded by the human nucleic acid sequence: 5′-TTCCAGTGTAATCAGTGTGGGGCATCTTTTACTCAGAAAGGTAACCTCCTCCG CCACATTAAACTGCAC-3′ (SEQ ID NO:106).

[0390] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-026 “QGNR” demonstrates recognition specificity for the 3-bp target sequence GAA as determined by in vivo screening results.

[0391] TG-ZFD-026 “QGNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA.

EXAMPLE 37

TG-ZFD-028 “QSHT”

[0392] TG-ZFD-028 “QSHT” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCEECGKAFRQSSHLTTHKIIH (SEQ ID NO: 111). It is encoded by the human nucleic acid sequence: 5′-TACAAATGTGAAGAATGTGGCAAAGCCTTTAGGCAGTCCTCACACCTTACTAC ACATAAGATAATTCAT-3′ (SEQ ID NO:110).

[0393] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-028 “QSHT” demonstrates recognition specificity for the 3-bp target sequence AGA, CGA, TGA, and GGA. Its binding site preference is (AGA and CGA)>TGA>GGA as determined by in vivo screening results.

[0394] TG-ZFD-028 “QSHT” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AGA, CGA, TGA, and GGA.

EXAMPLE 38

TG-ZFD-029 “QSHV”

[0395] TG-ZFD-029 “QSHV” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECDHCGKSFSQSSHLNVHKRTH (SEQ ID NO:113). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTGATCACTGTGGAAAATCCTTTAGCCAGAGCTCTCATCTGAATGTG CACAAAAGAACTCAC-3′ (SEQ ID NO:112).

[0396] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-029 “QSHV” demonstrates recognition specificity for the 3-bp target sequence CGA, AGA, and TGA. Its binding site preference is CGA>AGA>TGA as determined by in vivo screening results.

[0397] TG-ZFD-029 “QSHV” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence CGA, AGA, and TGA.

EXAMPLE 39

TG-ZFD-030 “QSNI”

[0398] TG-ZFD-030 “QSNI” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YMCSECGRGFSQKSNLIIHQRTH (SEQ ID NO: 115). It is encoded by the human nucleic acid sequence: 5′-TACATGTGCAGTGAGTGTGGGCGAGGCTTCAGCCAGAAGTCAAACCTCATCAT ACACCAGAGGACACAC-3′ (SEQ ID NO: 114).

[0399] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-030 “QSNI” demonstrates recognition specificity for the 3-bp target sequence AAA and CAA as determined by in vivo screening results.

[0400] TG-ZFD-030 “QSNI” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AAA or CAA.

EXAMPLE 40

TG-ZFD-031 “QSNR3”

[0401] TG-ZFD-031 “QSNR3” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECEKCGKAFNQSSNLTRHKKSH (SEQ ID NO: 117). It is encoded by the human nucleic acid sequence: 5′-TATGAATGTGAAAAATGTGGCAAAGCTTTTAACCAGTCCTCAAATCTTACTAG ACATAAGAAAAGTCAT-3′ (SEQ ID NO: 116).

[0402] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-031 “QSNR3” demonstrates recognition specificity for the 3-bp target sequence GAA as determined by in vivo screening results.

[0403] TG-ZFD-031 “QSNR3” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAA.

EXAMPLE 41

TG-ZFD-032 “QSSR3”

[0404] TG-ZFD-032 “QSSR3” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECNECGKFFSQSSSLIRHRRSH (SEQ ID NO: 119). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGCAATGAATGTGGGAAGTTTTTTAGCCAGAGCTCCAGCCTCATTAG ACATAGGAGAAGTCAC-3′ (SEQ ID NO: 118).

[0405] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-032 “QSSR3” demonstrates recognition specificity for the 3-bp target sequence GTA and GCA. Its binding site preference is GTA>GCA as determined by in vivo screening results.

[0406] TG-ZFD-032 “QSSR3” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GTA or GCA.

EXAMPLE 42

TG-ZFD-033 “QTHQ”

[0407] TG-ZFD-033 “QTHQ” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECHDCGKSFRQSTHLTQHRRIH (SEQ ID NO: 121). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTCACGATTGCGGAAAGTCCTTTAGGCAGAGCACCCACCTCACTCA GCACCGGAGGATCCAC-3′ (SEQ ID NO:120).

[0408] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-033 “QTHQ” demonstrates recognition specificity for the 3-bp target sequence AGA, TGA, and CGA. Its binding site preference is AGA>(TGA and CGA) as determined by in vivo screening results.

[0409] TG-ZFD-033 “QTHQ” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence AGA, TGA, and CGA.

EXAMPLE 43

TG-ZFD-034 “QTHR1”

[0410] TG-ZFD-034 “QTHR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECHDCGKSFRQSTHLTRHRRIH (SEQ ID NO: 123). It is encoded by the human nucleic acid sequence: 5′-TATGAGTGTCACGATTGCGGAAAGTCCTTTAGGCAGAGCACCCACCTCACTCG GCACCGGAGGATCCAC-3′ (SEQ ID NO:122).

[0411] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-034 “QTHR1” demonstrates recognition specificity for the 3-bp target sequence GGA, GAA, and AGA. Its binding site preference is GGA>(GAA and AGA) as determined by in vivo screening results.

[0412] TG-ZFD-034 “QTHR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA, GAA, and AGA.

EXAMPLE 44

TG-ZFD-035 “QTHR2”

[0413] TG-ZFD-035 “QTHR2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: HKCLECGKCFSQNTHLTRHQRT (SEQ ID NO:125). It is encoded by the human nucleic acid sequence: 5′-CACAAGTGCCTTGAATGTGGGAAATGCTTCAGTCAGAACACCCATCTGACTCG CCACCAACGCACCCAC-3′ (SEQ ID NO:124).

[0414] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-035 “QTHR2” demonstrates recognition specificity for the 3-bp target sequence GGA as determined by in vivo screening results.

[0415] TG-ZFD-035 “QTHR2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGA.

EXAMPLE 45

TG-ZFD-036 “RDER2”

[0416] TG-ZFD-036 “RDER2” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YHCDWDGCGWKFARSDELTRHYRKH (SEQ ID NO: 127). It is encoded by the human nucleic acid sequence: 5′-TACCACTGTGACTGGGACGGCTGTGGATGGAAATTCGCCCGCTCAGATGAACT GACCAGGCACTACCGTAAACAC-3′ (SEQ ID NO:126).

[0417] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-036 “RDER2” demonstrates recognition specificity for the 3-bp target sequence GCG and GTG. Its binding site preference is GCG>GTG as determined by in vivo screening results.

[0418] TG-ZFD-036 “RDER2” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG and GTG.

EXAMPLE 46

TG-ZFD-037 “RDER3”

[0419] TG-ZFD-037 “RDER3” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YRCSWEGCEWRFARSDELTRHFRKH (SEQ ID NO: 129). It is encoded by the human nucleic acid sequence: 5′-TACAGATGCTCATGGGAAGGGTGTGAGTGGCGTTTTGCAAGAAGTGATGAGTT AACCAGGCACTTCCGAAAGCAC-3′ (SEQ ID NO:128).

[0420] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-037 “RDER3” demonstrates recognition specificity for the 3-bp target sequence GCG and GTG as determined by in vivo screening results.

[0421] TG-ZFD-037 “RDER3” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG and GTG.

EXAMPLE 47

TG-ZFD-038 “RDER4”

[0422] TG-ZFD-038 “RDER4” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FSCSWKGCERRFARSDELSRHRRTH (SEQ ID NO: 131). It is encoded by the human nucleic acid sequence: 5′-TTCAGCTGTAGCTGGAAAGGTTGTGAAAGGAGGTTTGCCCGTTCTGATGAACT GTCCAGACACAGGCGAACCCAC-3′ (SEQ ID NO: 130).

[0423] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-038 “RDER4” demonstrates recognition specificity for the 3-bp target sequence GCG and GTG as determined by in vivo screening results.

[0424] TG-ZFD-038 “RDER4” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG and GTG.

EXAMPLE 48

TG-ZFD-039 “RDER5”

[0425] TG-ZFD-039 “RDER5” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FACSWQDCNKKFARSDELARHYRTH (SEQ ID NO:133). It is encoded by the human nucleic acid sequence: 5′-TTCGCCTGCAGCTGGCAGGACTGCAACAAGAAGTTCGCGCGCTCCGACGAGC TGGCGCGGCACTACCGCACACAC-3′ (SEQ ID NO:132).

[0426] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-039 “RDER5” demonstrates recognition specificity for the 3-bp target sequence GCG as determined by in vivo screening results.

[0427] TG-ZFD-039 “RDER5” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG.

EXAMPLE 49

TG-ZFD-040 “RDER6”

[0428] TG-ZFD-040 “RDER6” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YHCNWDGCGWKFARSDELTRHYRKH (SEQ ID NO:135). It is encoded by the human nucleic acid sequence: 5′-TACCACTGCAACTGGGACGGCTGCGGCTGGAAGTTTGCGCGCTCAGACGAGCT CACGCGCCACTACCGAAAGCAC-3′ (SEQ ID NO: 134).

[0429] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-040 “RDER6” demonstrates recognition specificity for the 3-bp target sequence GCG and GTG. Its binding site preference is GCG>GTG as determined by in vivo screening results.

[0430] TG-ZFD-040 “RDER6” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GCG and GTG.

EXAMPLE 50

TG-ZFD-041 “RDHR1”

[0431] TG-ZFD-041 “RDHR1” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FLCQYCAQRFGRKDHLTRHMKKSH (SEQ ID NO: 137). It is encoded by the human nucleic acid sequence: 5′-TTCCTCTGTCAGTATTGTGCACAGAGATTTGGGCGAAAGGATCACCTGACTCG ACATATGAAGAAGAGTCAC-3′ (SEQ ID NO:136).

[0432] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-041 “RDHR1” demonstrates recognition specificity for the 3-bp target sequence GAG and GGG as determined by in vivo screening results.

[0433] TG-ZFD-041 “RDHR1” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAG and GGG.

EXAMPLE 51

TG-ZFD-043 “RDHT”

[0434] TG-ZFD-043 “RDHT” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FQCKTCQRKFSRSDHLKTHTRTH (SEQ ID NO: 141). It is encoded by the human nucleic acid sequence: 5′-TTCCAGTGTAAAACTTGTCAGCGAAAGTTCTCCCGGTCCGACCACCTGAAGAC CCACACCAGGACTCAT-3′ (SEQ ID NO:140).

[0435] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-043 “RDHT” demonstrates recognition specificity for the 3-bp target sequence TGG, AGG, CGG, and GGG as determined by in vivo screening results.

[0436] TG-ZFD-043 “RDHT” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence TGG, AGG, CGG, and GGG.

EXAMPLE 52

TG-ZFD-044 “RDKI”

[0437] TG-ZFD-044 “RDKI” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FACEVCGVRFTRNDKLKIHMRKH (SEQ ID NO: 143). It is encoded by the human nucleic acid sequence: 5′-TTTGCCTGCGAGGTCTGCGGTGTTCGATTCACCAGGAACGACAAGCTGAAGAT CCACATGCGGAAGCAC-3′ (SEQ ID NO:142).

[0438] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-044 “RDKI” demonstrates recognition specificity for the 3-bp target sequence GGG as determined by in vivo screening results.

[0439] TG-ZFD-044 “RDKI” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGG.

EXAMPLE 53

TG-ZFD-045 “RDKR”

[0440] TG-ZFD-045 “RDKR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YVCDVEGCTWKFARSDKLNRHKKRH (SEQ ID NO: 145). It is encoded by the human nucleic acid sequence: 5′-TATGTATGCGATGTAGAGGGATGTACGTGGAAATTTGCCCGCTCAGATAAGCT CAACAGACACAAGAAAAGGCAC-3′ (SEQ ID NO:144).

[0441] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-045 “RDKR” demonstrates recognition specificity for the 3-bp target sequence GGG and AGG. Its binding site preference is GGG>AGG as determined by in vivo screening results.

[0442] TG-ZFD-045 “RDKR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GGG and AGG.

EXAMPLE 54

TG-ZFD-046 “RSNR”

[0443] TG-ZFD-046 “RSNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YICRKCGRGFSRKSNLIRHQRTH (SEQ ID NO:147). It is encoded by the human nucleic acid sequence: 5′-TATATTTGCAGAAAGTGTGGACGGGGCTTTAGTCGGAAGTCCAACCTTATCAG ACATCAGAGGACACAC-3′ (SEQ ID NO:146).

[0444] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-046 “RSNR” demonstrates recognition specificity for the 3-bp target sequence GAG and GTG. Its binding site preference is GAG>GTG as determined by in vivo screening results.

[0445] TG-ZFD-046 “RSNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAG and GTG.

EXAMPLE 55

TG-ZFD-047 “RTNR”

[0446] TG-ZFD-047 “RTNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YLCSECDKCFSRSTNLIRHRRTH (SEQ ID NO: 149). It is encoded by the human nucleic acid sequence: 5′-TATCTATGTAGTGAGTGTGACAAATGCTTCAGTAGAAGTACAAACCTCATAAG GCATCGAAGAACTCAC-3′ (SEQ ID NO:148).

[0447] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-047 “RTNR” demonstrates recognition specificity for the 3-bp target sequence GAG as determined by in vivo screening results.

[0448] TG-ZFD-047 “RTNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA site containing the sequence GAG.

EXAMPLE 56

TG-ZFD-048 “HSSR”

[0449] TG-ZFD-048 “HSSR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FKCPVCGKAFRHSSSLVRHQRTH (SEQ ID NO:173). It is encoded by the human nucleic acid sequence: 5′-TTCAAGTGCCCAGTGTGCGGCAAGGCCTTCCGGCATAGCTCCTCGCTGGTGCG GCACCAGCGCACGCAC-3′ (SEQ ID NO:174).

[0450] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-048 “HSSR” demonstrates recognition specificity for the 3-bp target sequence GTT, as determined by in vivo screening results.

[0451] TG-ZFD-048 “HSSR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA containing the sequence GTT.

EXAMPLE 57

TG-ZFD-049 “ISNR”

[0452] TG-ZFD-049 “ISNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YRCKYCDRSFSISSNLQRHVRNIH (SEQ ID NO:175). It is encoded by the human nucleic acid sequence: 5′-TACAGGTGTAAGTACTGCGACCGCTCCTTCAGCATCTCTTCGAACCTCCAGCG GCACGTCCGGAACATCCAC-3′ (SEQ ID NO: 176).

[0453] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-049 “ISNR” demonstrates recognition specificity for the 3-bp target sequences GAA, GAT, and GAC, as determined by in vivo screening results. Its binding site preference is GAA>GAT>GAC, as determined by in vivo screening results.

[0454] TG-ZFD-049 “ISNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA containing the sequence GAA, GAT or GAC.

EXAMPLE 58

TG-ZFD-050 “KSNR”

[0455] TG-ZFD-050 “KSNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YGCHLCGKAFSKSSNLRRHEMIH (SEQ ID NO:177). It is encoded by the human nucleic acid sequence: 5′-TATGGATGTCATCTATGTGGGAAAGCCTTCAGTAAAAGTTCTAACCTTAGACG ACATGAGATGATTCAC-3′ (SEQ ID NO:178).

[0456] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-050 “KSNR” demonstrates recognition specificity for the 3-bp target sequence GAG, as determined by in vivo screening results.

[0457] TG-ZFD-050 “KSNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence GAG.

EXAMPLE 59

TG-ZFD-051 “QSNK”

[0458] TG-ZFD-051 “QSNK” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YKCEECGKAFTQSSNLTKHKKIH (SEQ ID NO:179). It is encoded by the human nucleic acid sequence: 5′-TACAAGTGTGAAGAATGTGGCAAAGCTTTTACCCAATCCTCAAACCTTACTAA ACATAAGAAAATTCAT-3′ (SEQ ID NO: 180).

[0459] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-051 “QSNK” demonstrates recognition specificity for the 3-bp target sequences AAA, GAA, and TAA, as determined by in vivo screening results. Its binding site preference is GAA>TAA>AAA, as determined by in vivo screening results.

[0460] TG-ZFD-051 “QSNK” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA containing the sequence GAA, TAA or AAA.

EXAMPLE 60

TG-ZFD-052 “QSNT”

[0461] TG-ZFD-052 “QSNT” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECVQCGKGFTQSSNLITHQRVH (SEQ ID NO:181). It is encoded by the human nucleic acid sequence: 5′-TACGAGTGTGTGCAGTGTGGGAAAGGTTTCACCCAGAGCTCCAACCTCATCAC ACATCAAAGAGTTCAC-3′ (SEQ ID NO:182).

[0462] As a polypeptide fusion to fingers 1 and 2 of Zif268, TG-ZFD-052 “QSNT” demonstrates recognition specificity for the 3-bp target sequence AAA, as determined by in vivo screening results. Its binding site preference is AAA, as determined by in vivo screening results.

[0463] TG-ZFD-052 “QSNT” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence AAA.

EXAMPLE 61

TG-ZFD-053 “VSNV”

[0464] TG-ZFD-053 “VSNV” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECDHCGKAFSVSSNLNVHRRIH (SEQ ID NO: 183). It is encoded by the human nucleic acid sequence: 5′-TATGAATGCGATCACTGTGGGAAAGCCTTCAGCGTCAGCTCCAACCTGAACGT GCACAGAAGGATCCAC-3′ (SEQ ID NO:184).

[0465] As a polypeptide fusion to finger 1 and 2 of Zif268, TG-ZFD-053 “VSNV” demonstrates recognition specificity for the 3-bp target sequences AAT, CAT, and TAT, as determined by in vivo screening results. Its binding site preference is AAT>CAT>TAT, as determined by in vivo screening results.

[0466] TG-ZFD-053 “VSNV” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domains, e.g., for the purpose of recognizing a DNA containing the sequence AAT, CAT or TAT.

EXAMPLE 62

TG-ZFD-054 “DSCR”

[0467] TG-ZFD-054 “DSCR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YTCSDCGKAFRDKSCLNRHRRTH (SEQ ID NO: 185). It is encoded by the human nucleic acid sequence: 5′-TACACATGCAGTGACTGTGGGAAAGCTTTCAGAGATAAATCATGTCTCAACAG ACATCGGAGAACTCAT-3′ (SEQ ID NO:186)

[0468] As a polypeptide fusion to finger 1 and 2 of Zif268, TG-ZFD-054 “DSCR” demonstrates recognition specificity for the 3-bp target sequence GCC as determined by in vivo screening results.

[0469] TG-ZFD-054 “DSCR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence GCC.

EXAMPLE 63

TG-ZFD-055 “ISNV”

[0470] TG-ZFD-055 “ISNV” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YECDHCGKAFSIGSNLNVHRRIH (SEQ ID NO: 187). It is encoded by the human nucleic acid sequence: 5′-TACGAATGCGATCACTGTGGGAAGGCCTTCAGCATAGGCTCCAACCTGAATGT GCACAGGCGGATCCAT-3′ (SEQ ID NO:188)

[0471] As a polypeptide fusion to finger 1 and 2 of Zif268, TG-ZFD-055 “ISNV” demonstrates recognition specificity for the 3-bp target sequence AAT as determined by in vivo screening results.

[0472] TG-ZFD-055 “ISNV” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence AAT.

EXAMPLE 64

TG-ZFD-056 “WSNR”

[0473] TG-ZFD-056 “WSNR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: YRCEECGKAFRWPSNLTRHKRIH (SEQ ID NO: 189). It is encoded by the human nucleic acid sequence: 5′-TACAGATGTGAGGAATGTGGCAAAGCCTTTAGGTGGCCCTCAAACCTTACTAG ACATAAGAGAATTCAC-3′ (SEQ ID NO: 190)

[0474] As a polypeptide fusion to finger 1 and 2 of Zif268, TG-ZFD-056 “WSNR” demonstrates recognition specificity for the 3-bp target sequence GGT, and GGA as determined by in vivo screening results. Its binding site preference is GGT>GGA as determined by in vivo screening results.

[0475] TG-ZFD-056 “WSNR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence GGT or GGA.

EXAMPLE 65

TG-ZFD-057 “DSAR”

[0476] TG-ZFD-057 “DSAR” was identified by in vivo screening from human genomic sequence. Its amino acid sequence is: FMCTWSYCGKRFTDRSALARHKRTH (SEQ ID NO:191). It is encoded by the human nucleic acid sequence: 5′-TACTCCTGTGGCATTTGTGGCAAATCCTTCTCTGACTCCAGTGCCAAAAGGAG ACACTGCATTCTACAC-3′ (SEQ ID NO:192)

[0477] As a polypeptide fusion to finger 1 and 2 of Zif268, TG-ZFD-057 “DSAR” demonstrates recognition specificity for the 3-bp target sequence GTC as determined by in vivo screening results.

[0478] TG-ZFD-057 “DSAR” can be used as a module to construct a chimeric DNA binding protein comprising multiple zinc finger domain, e.g., for the purpose of recognizing a DNA containing the sequence GTC.

[0479] The afore-mentioned zinc finger domains and their specificities are summarized in the following Tables.

TABLE 3
Binding site Name of ZFD (SEQ ID NO:)
AAA          QSNI (115), QSNV1 (51), QSNV2 (53), QSNV3 (55), QSNV4 (57)
ACA          QSTV (31)
AGA          QSHR1 (37), QSHR5 (45), QSHT (111), QSHV (113), QTHQ (121),
             QTHR1 (123)
AGG          RDHT (141), RDKR (145)
CAA          QSNI (51), QSNV1 (51), QSNV2 (53)
CGA          QTHQ (121), QSHR5 (45), QSHT (111), QSHV (113)
CGG          RDHT (141)
GAA          CSNR1 (23), CSNR2 (35), QGNR (107), QSHR1 (37), QSHR3 (41),
             QSHR4 (43), QSHR5 (45), QSNR1 (47), QSNR2 (49), QSNR3 (117),
             QTHRT1 (123)
GAC          CSNR1 (23), CSNR2 (35), HSNK (25), SSNR (27)
GAG          CSNR1 (23), CSNR2 (35), RDER1 (29), RDHR1 (137), RSNR (147),
             RTNR (149), SSNR (27), QFNR (105),
GCA          QSSR1 (59), QSSR3 (119), QSTR (63)
GCG          RDER1 (29), RDER2 (127), REDR3 (129), RDER4 (131), RDER5 (133),
             RDER6 (135), VSTR (33)
GCT          VSTR (33)
GGA          QAHR (103), QSHR1 (37), QSHR2 (39), QSHR3 (41), QSHR4 (43),
             QSHR5 (45), QSHT (111), QTHR1 (123), QTHR2 (125)
GGG          RDKI (143), RDHR1 (137), RDHT (141), RDKR (143), RSHR (65),
GTA          QSSR1 (59), QSSR2 (61), QSSR3 (119), QSTR (63), VSSR (67)
GTG          RSNR (147), RDER1 (29), RDER2 (127), RDER3 (129), RDER4 (131),
             RDER6 (135), VSSR (67)
GTT          VSSR (67)
TGA          QSHT (111), QSHV (113), QTHQ (121)
TGG          RDHT (141)

[0480]

TABLE 4A
Binding site Name of ZFD (SEQ ID NO:)
AAA          QSNK(179), QSNT(181)
AAT          VSNV(183)
CAT          VSNV(183)
GAA          ISNR(175), QSNK(179)
GAC          ISNR(175)
GAG          KSNR(177)
GAT          ISNR(175)
GTT          HSSR(173)
TAA          QSNK(179)
TAT          VSNV(183)

[0481]

TABLE 4B
Binding site Name of ZFD (SEQ ID NO:)
AAT          ISNV(187)
GCC          DSCR(185)
GGT          WSNR(189)
GGA          WSNR(189)
GTC          DSAR(191)

[0482]

TABLE 5
Name of		Polypeptide	Nucleic Acid**
ZFD	Binding site	SEQ ID NO:	SEQ ID NO:
CSNR1	GAA > GAC> GAG	23	22
HSNK	GAC	25	24
SSNR	GAG > GAC	27	26
RDER1	GCG > GTG, GAG	29	28
QSTV	ACA	31	30
VSTR	GCT > GCG	33	32
CSNR2	GAA > GAC> GAG	35	34
QSHR1	GGA > GAA> AGA	37	36
QSHR2	GGA	39	38
QSHR3	GGA > GAA	41	40
QSHR4	GGA > GAA	43	42
QSHR5	GGA > AGA> GAA > CGA	45	44
QSNR1	GAA	47	46
QSNR2	GAA	49	48
QSNV1	AAA > CAA	51	50
QSNV2	AAA > CAA	53	52
QSNV3	AAA	55	54
QSNV4	AAA	57	56
QSSR1	GTA > GCA	59	58
QSSR2	GTA	61	60
QSTR	GTA > GCA	63	62
RSHR	GGG	65	64
VSSR	GTT > GTG > GTA	67	66
QAHR	GGA	103	102
QFNR	GAG	105	104
QGNR	GAA	107	106
QSHT	AGA, CGA > TGA > GGA	111	110
QSHV	CGA > AGA > TGA	113	112
QSNI	AAA, CAA	115	114
QSNR3	GAA	117	116
QSSR3	GTA > GCA	119	118
QTHQ	AGA > CGA, TGA	121	120
QTHR1	GGA > GAA, AGA	123	122
QTHR2	GGA	125	124
RDER2	GCG > GTG	127	126
RDER3	GCG > GTG	129	128
RDER4	GCG > GTG	131	130
RDER5	GCG	133	132
RDER6	GCG > GTG	135	134
RDHR1	GAG, GGG	137	136
RDHT	TGG, AGG, CGG, GGG	141	140
RDKI	GGG	143	142
RDKR	GGG > AGG	145	144
RSNR	GAG > GTG	147	146
RTNR	GAG	149	148
**The indicated nucleic acid SEQ ID refers to a nucleic acid that encodes the zinc finger domain.

[0483]

TABLE 6
Name of		Polypeptide	Nucleic Acid**
ZFD	Binding site	SEQ ID NO:	SEQ ID NO:
HSSR	GTT	173	174
ISNR	GAA > GAT > GAC	175	176
KSNR	GAG	177	178
QSNK	GAA > TAA > AAA	179	180
QSNT	AAA	181	182
VSNV	AAT > CAT > TAT	183	184
**The indicated nucleic acid SEQ ID refers to a nucleic acid that encodes the zinc finger domain.

[0484]

	TABLE 7
	Name of		Polypeptide	Nucleic Acid**
	ZFD	Binding site	SEQ ID NO:	SEQ ID NO:
	DSCR	GCC	185	186
	ISNV	AAT	187	188
	WSNR	GGT > GGA	189	190
	DSAR	GTC	191	192
	**The indicated nucleic acid SEQ ID refers to a nucleic acid that encodes the zinc finger domain.

EXAMPLE 66

Construction of Individual Three-Finger Proteins

[0485] The vector P3 was used to express chimeric zinc finger proteins in mammalian cells. P3 was constructed by modification of the pcDNA3 vector (Invitrogen, San Diego Calif.). A synthetic oligonucleotide duplex having compatible overhangs was ligated into the pcDNA3 vector digested with HindIII and XhoI. The duplex contains nucleic acid that encodes the hemagglutinin (HA) tag and a nuclear localization signal. The duplex also includes BamHI, EcoRI and NotI and BglII restriction site sites and a stop codon (FIG. 11A). Further, the XmaI site in SV40 origin of the resulting vector was destroyed by digestion with XmaI, filling in the overhanging ends of the digested restriction site, and religation of the ends.

[0486] To construct a zinc finger protein that includes three particular zinc finger domains, a nucleic acid encoding the first zinc finger was ligated into the P3 vector. Nucleic acids encoding the second and third zinc finger domains were ligated together using Dynabeads® and MPC-S (Dynal) as follows. Nucleic acids encoding the second and third zinc finger domains were synthesized using forward primers that contain an XmaI site and reverse primers that contain AgeI and NotI sites. The forward primer of the second zinc finger domain was biotinylated. The nucleic acid encoding the second zinc finger domain was digested with AgeI and ligated to XmaI digested nucleic acid encoding the third zinc finger domain. After ligation for one hour at room temperature, the ligation sample was bound to Dynabeads® M-280 streptavidin (Dynal) for 15 minutes at room temperature. The beads were washed three times with TE buffer (10 mM Tris.HCl 0.1 mM EDTA, pH 8.0). The attached ligation sample was digested with XmaI and NotI for three hours at 37° C. Nucleic acid released by the XmaI and NotI digestion was purified using the PCR purification kit (Qiagen) and ligated to the P3 vector that included the nucleic acid encoding the first zinc finger. Products of this final ligation were transformed in E. coli. Clones containing the correct size insert in the P3 vector were identified. The nucleic acid encoding the resultant three-finger ZFP was confirmed by DNA sequencing.

EXAMPLE 67

Construction of a Library of Three-Finger Proteins

[0487] FIG. 11B depicts one method of constructing a diverse three finger library. First, nucleic acid encoding each zinc finger domain was cloned into the P3 vector to form “single finger” vectors. Equal amounts of each “single finger” vector were combined to form a pool. The pool was separately digested with two sets of enzymes; AgeI and XhoI, and XmaI and XhoI. After phosphatase treatment for 30 min, digested vector nucleic acid from the AgeI and XhoI digested pool were ligated to the nucleic acid segments released from the vector by the XmaI and XhoI digestion. These segments each encode a single zinc finger domain. The ligation of the digested vector nucleic acids to the nucleic acid segments forms vectors encoding two zinc finger domains. After transformation into E. coli, the ligation products yielded approximately 1.4×104 transformants, thereby forming a two-finger library. The size of the insert region of the two-finger library was verified by colony PCR analysis of 40 colonies. The correct size insert was present in 95% of the library.

[0488] Subsequently, the 2-finger library was digested with AgeI and XhoI. The digested vector which retains nucleic acid sequences encoding two zinc finger domains was ligated to the pool of one-finger fragment prepared above by digestion with XmaI and XhoI. The products of this ligation were transformed into E. coli to yield about 2.4×105 independent transformants. Verification of the inset region indicated that library members were predominantly correctly constructed, i.e., they each encoded three zinc finger domains.

EXAMPLE 68

In vivo Assays for Three-Finger Proteins

[0489] Kim and Pabo ((1997) J Biol Chem 272:29795-29800) demonstrated that the Zif268 protein efficiently repressed VP 16-activated transcription of a target gene when the Zif268 protein was bound near the transcription start site of a target gene. It was hypothesized that such a bound zinc finger protein would inhibit the binding of the basal transcription machinery such as the RNA polymerase II complex to the promoter or the binding of TFIID to the transcription start site or TATA box.

[0490] A similar in vivo repression assay was used to determine if the new three-finger proteins were functional in vivo. The assay utilized a luciferase reporter construct in which a target site is located at a position comparable to the position of the Zif268 site in the construct of Kim and Pabo, supra.

[0491] The luciferase reporter plasmids were constructed from pΔS-modi, a modified version of pGL3-TATA/Inr (Kim and Pabo, supra). These reporters utilize firefly luciferase as the reporter protein. The SacI site in upstream of the TATA box was deleted from pΔS-modi. A new SacI site was inserted following the transcription initiation site. An oligomer containing a specific 9 base pairs of binding site of each ZFP replaced 14 base pairs located after 12 bases downstream of the transcription initiation site in pΔS-modi by digestion of SacI and HindIII. The resulting reporter plasmid was named as p1G-ZFP ID (The ZFP ID is determined according to the binding site of the specific reporter). The sequences of pΔS-modi and p1G are set forth in FIG. 12.

[0492] The in vivo activity assay for a particular three-finger protein was carried out as follows. HEK 293 cells were transfected with four plasmids: 14 ng of a plasmid expressing the particular three-finger protein; 14 ng of the reporter plasmid described above; 70 ng of a plasmid that expresses GAL4-VP 16; and 1.4 ng of a plasmid that expresses Renillar luciferase. The GAL4-VP 16 activates transcription of the minimal synthetic promoter in the reporter so that the repression effected by a particular three-finger protein could be clearly detected and compared to other three-finger proteins. The plasmid expressing Renillar luciferase provides a control of transfection efficiency.

[0493] Lipofectamine (Gibco-BRL) was used for the transfection procedures. Cells were transfected at 30-50% confluency in wells of a 96 well plate. The cells were incubated for two days prior to harvesting for the luciferase assay. Then luciferase activities were measured using the Dual-Luciferase™ Reporter Assay System (Promega). The observed firefly luciferase activity was normalized using the observed level of Renilla luciferase. The extent of repression or “fold-repression” was calculated by dividing a value for normalized reporter expression in the absence of a zinc finger protein by a value for normalized reporter expression in the presence of the zinc finger protein.

[0494] Zinc finger proteins were classified as satisfying a high stringency cut-off value if they repressed transcription at least 2-fold in the transfection assay or as satisfying a low stringency cut-off value if they repressed between 1.5 and 2-fold in the transfection assay.

EXAMPLE 69

Binding Assay Result of ZFPs with Their Specific Reporter

[0495] Gel shift assays were used to correlate activity observed in the in vivo assays to binding affinity. A good correlation was observed between the dissociation constants measured by gel shift assays and the level of transcriptional repression in the transfection assays described above. Table 8 relates the binding affinity of Zif268 for a variety of DNA sites and the corresponding in vivo repression data using the transfection assay above.

[0496] In general, zinc finger proteins exhibiting more than 2-fold repression (that is, 50% repression) in the transfection assays showed a dissociation constant of less than 1 nM as determined by gel shift assays.

TABLE 8
In vivo and in vitro DNA-binding activities of Zif268.
		Dissociation	Fold repression in
	Target	Constant (nM)	human cells
	sequence	for Zif268 binding	expressing Zif268
	GCT TGG GCG	2.1 ± 0.3	1.5 ± 0.1
	GCG TGG GCG	0.024 ± 0.004	28 ± 1
	GAG TGG GCG	0.17 ± 0.04	5.9 ± 0.1
	GAG CGG GCG	2.3 ± 0.9	1.6 ± 0.0
	GAC TGG GCG	4.9 ± 0.6	1.2 ± 0.1
	ACA TGG GCG	1.3 ± 0.3	1.3 ± 0.1

EXAMPLE 70

Characterization of Three-Finger Proteins

[0497] Two types of “three-finger” chimeric zinc finger proteins were constructed. One type includes chimeric proteins that are composed exclusively of human zinc finger domain that are identical to naturally-occurring zinc finger domains. The other type includes chimeric proteins that include zinc finger domains that are not identical to a naturally-occurring zinc finger domain. The latter zinc finger domains were identified by in vitro mutagenesis of a naturally-occurring zinc finger domain followed by phage display selection. Such domains have avoided the scrutiny of natural evolution.

[0498] The component zinc finger domains are listed in Table 9. A total of 36 zinc finger domains, 18 human zinc finger domains and 18 mutated zinc finger domains, were used to assemble a set of test three-finger proteins. The mutated zinc finger domains have been reported in Choo and Klug. (1994) Proc. Natl. Acad. Sci. USA 91:11168-11172; Desjarlais and Berg (1994) Proc. Natl. Acad. Sci. USA. 91:11099-11103; Dreier et al. (2001) J. Biol. Chem. 276:29466-29478; Dreier et al. (2000) J Mol Biol. 303:489-502; Fairall et al. (1993) Nature 366:483-487; Greisman and Pabo. (1997) Science. 275:657-661; Kim and Pabo (1997) J. Biol. Chem. 272:29795-29800; and Segal et al. (1999) Proc. Natl. Acad. Sci. USA 96:2758-2763.

TABLE 9
Some Exemplary Domains for Construction of Three-Fingers ZFP
Domain		SEQ ID NO	target
name	Source	or reference	sites
CSNR1	human	23	GAA,
			GAC,
			GAG
HSNK	human	25	GAC
ISNR	human	175	GAA,
			GAT,
			GAC
QSHR2	human	39	GGA
QSHR3	human	41	GGA,
			GAA
QSHT	human	111	NGA
QSNR1	human	47	GAA
QSNR3	human	117	GAA
QSNV2	human	53	AAA,
			CAA
QSSR1	human	59	GTA,
			GCA
QTHQ	human	121	AGA,
			CGA,
			TGA
RDHT	human	141	NGG
RDER1	human	29	GCG,
			GTG
RSHR	human	65	GGG
RSNR	human	147	GAG,
			GTG
VSNV	human	183	AAT
VSSR	human	67	GTT,
			GTG,
			GTA
VSTR	human	33	GCT
DGAR	mutated/phage display	PNAS, Segal, D.J. et al.	GTC
		(1999)
DGHR	mutated/phage display	PNAS, Segal, D.J. et al.	GGC
		(1999)
DGNR	mutated/phage display	PNAS, Segal, D.J. et al.	GAC
		(1999)
DGNV	mutated/phage display	J.B.C., Dreier, B. et al. (2001)	AAC
DRDR	mutated/phage display	PNAS, Segal, D.J. et al.	GCC
		(1999)
GRER	mutated/phage display	J.B.C., Dreier, B. et al. (2001)	GCC
NDTR	mutated/phage display	PNAS, Choo & Klug, (1994)	GTT
QAHR	mutated/phage display	PNAS, Segal, D.J. et al.	GGA
		(1999)
QGDR	mutated/phage display	PNAS, Segal, D.J. et al.	GCA,
		(1999)	GCC,
			GCT
QGTR	mutated/phage display	Science, Greisman, H.A. &	ACA
		Pabo, C. (1997)
QSDR	mutated/phage display	PNAS, Desjarlais, J.R. &	GCT
		Berg, J.M. (1994)
QSNR	mutated/phage display	PNAS, Segal, D.J. et al.	GAA
		(1999)
QSSR	mutated/phage display	PNAS, Segal, D.J. et al.	GTA
		(1999)
RDKR	mutated/phage display	J.B.C., Dreier, B. et al. (2001)	GGG
RDNR	mutated/phage display	PNAS, Segal, D.J. et al.	GAG
		(1999)
RDTN	mutated/phage display	J.B.C., Dreier, B. et al. (2001)	AAG
TDKR	mutated/phage display	PNAS, Segal, D.J. et al.	GGG,
		(1999)	GGT
TGNR	mutated/phage display	PNAS, Segal, D.J. et al.	GAT,
		(1999)	GAA
N in the target site can be any of A, C, G, and T.

[0499] Nucleic acids encoding the 36 domains were individually subcloned into P3 vector digested with EcoRI and NotI, and the resulting plasmids were used as starting material for the chimeric zinc finger protein construction.

[0500] Nucleic acids encoding chimeric 3-finger proteins were prepared by two different methods.

[0501] In the first method, nucleic acids encoding all the zinc finger domains were randomly mixed, as described in Example 68, and 3-finger constructs were randomly picked for further analysis. Each construct was sequenced to determine the component zinc finger domains in the polypeptide that it encodes. Subsequently, target DNA sequences were synthesized for each randomly assorted 3-finger protein. Target DNA sequences were based on the expected preferred target site. The targets were cloned into the luciferase reporter vector described above. This approach is referred to as “zinc finger protein-first” approach.

[0502] In the second method, nucleic acid encoding chimeric 3-finger proteins were assembled based on a given target DNA sequences, as described in Example 66. A computer algorithm was used to a match recognition sites of zinc finger domains and target DNA sequences. Promoter sequences of known genes were used as the input target DNA sequences. The promoter sequences were scanned to identify segments that are nine nucleotides in length and that are acceptable target sites for recognition by chimeric 3-finger proteins given the available collection of zinc finger domains. Once identified, a nucleic acid was constructed that encoded the chimeric 3-finger proteins. This approach is referred to as “target site-first” approach.

[0503] Zinc finger domains that include an aspartate residue at position 2 of the base contacting residues were analyzed with special consideration. Such zinc finger domains include RDER1, RDHT, RDNR, RDKR, RDTN, TDKR, and NDTR. The X-ray co-crystal structure of Zif268 bound to DNA showed that an aspartate at position 2 can form a hydrogen bond with a base outside of the 3-basepair subsite recognized by zinc fingers. As a result, the RDER finger containing an aspartate residue at position 2 prefers the 4-basepair site: 5′-GCG (G/T)-3′. The computer algorithm accounted for this additional specificity. Similarly, randomly-assembled 3-finger proteins that include a finger having aspartate at position 2 and that violate this rule for the 4-bp site were excluded in other analyses described herein.

[0504] A total of 153 three-finger chimeric proteins were constructed from both the “zinc finger protein-first” and the “target site-first” approaches. These proteins were tested using the transient cotransfection assay described in Example 68. The results are set forth in Table 10.

TABLE 10
Zinc finger proteins and their DNA-binding activity
	Domain Name		Fold
	1	2	3	Target composite sequence	repression
1	RSNR	RDHT	RSNR	5′-GAG AGG GAG C-3′ (SEQ ID NO: 199)	8.1
2	CSNR1	RSHR	RDHT	5′-TGG GGG GAC A-3′ (SEQ ID NO: 200)	4.5
3	RDHT	QSNV2	QSSR1	5′-GCA CAA TGG-3′	4.0
4	RSHR	RDER1	RDER1	5′-GCG GCG GGG C-3′ (SEQ ID NO: 201)	3.8
5	QSHR3	QAHR*	QSSR*	5′-GTA GGA GGA T-3′ (SEQ ID NO: 202)	3.7
6	RSHR	RDER1	RDHT	5′-AGG GCG GGG C-3′ (SEQ ID NO: 203)	3.6
7	RDHT	QSNV2	RSHR	5′-GGG AAA CGG G-3′ (SEQ ID NO: 204)	3.6
8	RSNR	QSHR2	QSSR1	5′-GTA GGA GAG T-3′ (SEQ ID NO: 205)	3.3
9	QSDR*	RDHT	QSHR3	5′-GGA AGG GCT T-3′ (SEQ ID NO: 206)	3.3
10	RDHT	RSHR	QSHR2	5′-GGA GGG TGG-3′	3.1
11	QSHT	RSHR	RDHT	5′-TGG GGG TGA-3′	3.0
12	QSSR1	QSNV2	RSNR	5′-GAG CAA GTA G-3′ (SEQ ID NO: 207)	2.9
13	QSHR2	RDER1	RSNR	5′-GAG GTG GGA G-3′ (SEQ ID NO: 208)	2.8
14	DGHR*	QSNR1	RDHT	5′-GTA GGC GCC-3′	2.6
15	VSNV	CSNR1	RSNR	5′-GAG GAC AAT G-3′ (SEQ ID NO: 209)	2.5
16	QSHR2	RDER1	RSHR	5′-GGG GCG GGA T-3′ (SEQ ID NO: 210)	2.3
17	VSSR	QGDR*	RDHT	5′-GGG GCA GTT-3′	2.3
18	RDER1	QSSR1	QSHT	5′-CGA GCA GCG-3′	2.2
19	RDER1	VSSR	QSHT	5′-CGA GTT GCG-3′	2.1
20	QSNR3	QSHR2	RSNR	5′-GAG GGA GAA G-3′ (SEQ ID NO: 211)	2.1
21	RDHT	QSHT	RSNR	5′-GGA GAG AGA-3′	2.1
22	RSNR	VSSR	RSHR	5′-GGG GTT GAG-3′	2.1
23	RDHT	RSNR	QSNR3	5′-GAA GAG AGG T-3′ (SEQ ID NO: 212)	2.1
24	CSNR1	QSHT	RSNR	5′-GAG TGA GAC C-3′ (SEQ ID NO: 213)	2.1
25	QSNR3	RDER1	RSNR	5′-GAG GCG GAA A3′ (SEQ ID NO: 214)	2.1
26	QSNR3	QSNV2	RSHR	5′-GGG AAA GAA C-3′ (SEQ ID NO: 215)	2.0
27	RSHR	RDER1	RSHR	5′-GGG GTG GGG-3′	2.0
28	VSSR	QSNR3	RDER1	5′-GCG GAA GTT C-3′ (SEQ ID NO: 216)	2.0
29	QSNR3	RDHT	RSNR	5′-GAG TGG GAA A-3′ (SEQ ID NO: 217)	2.0
30	RSHR	RSHR	QSHR2	5′-GGA GGG GGG C-3′ (SEQ ID NO: 218)	2.0
31	ISNR	RSNR	RDHT	5′-TGG GAG GAT C-3′ (SEQ ID NO: 219)	2.0
32	QSNV2	RSNR	RDHT	5′-GGG GAG AAA-3′	1.9
33	QSNV2	RSHR	RDER1	5′-GTG GGG AAA A-3′ (SEQ ID NO: 220)	1.9
34	VSSR	HSNK	RSNR	5′-GAG GAC GTG-3′	1.9
35	VSSR	QSHT	RSHR	5′-GGG TGA GTG-3′	1.9
36	RSNR	VSSR	RSNR	5′-GAG GTT GAG G-3′ (SEQ ID NO: 221)	1.8
37	QAHR*	QSNR	QTHQ	5′-AGA GAA GGA G-3′ (SEQ ID NO: 222)	1.8
38	RSNR	ISNR	QSHT	5′-TGA GAT GAG C-3′ (SEQ ID NO: 223)	1.8
39	VSTR	RSNR	QSHR2	5′-GGA GAG GCT C-3′ (SEQ ID NO: 224)	1.8
40	ISNR	VSTR	RDHT	5′-AGG GCT GAT T-3′ (SEQ ID NO: 225)	1.8
41	QSNR3	RSNR	RSHR	5′-GGG GAG GAA A-3′ (SEQ ID NO: 226)	1.7
42	RDHT	QSHR2	QSHT	5′-AGA GGA AGG T-3′ (SEQ ID NO: 227)	1.7
43	QSSR1	QSNR3	QSHR2	5′-GGA GAA GTA G-3′ (SEQ ID NO: 228)	1.7
44	RDHT	DGHR*	TDKR*	5′-GGT GGC AGG T-3′ (SEQ ID NO: 229)	1.7
45	HSNK	QSNV2	VSSR	5′-GTT CAA GAC-3′	1.7
46	HSNK	QSHT	RSNR	5′-GAG AGA GAC-3′	1.7
47	RSHR	QSHR2	VSTR	5′-GCT GGA GGG G-3′ (SEQ ID NO: 230)	1.7
48	RDHT	RSHR	RDER1	5′-GCG GGG AGG G-3′ (SEQ ID NO: 231)	1.6
49	RSHR	QSNV2	QSHT	5′-AGA AAA GGG-3′	1.6
50	RSHR	RDER1	QSNV2	5′-AAA GTG GGG A-3′ (SEQ ID NO: 232)	1.6
51	VSNV	QSNV2	QSHT	5′-AGA AAA AAT A-3′ (SEQ ID NO: 233)	1.6
52	QSHR2	QSHT	RSNR	5′-GAG TGA GGA-3′	1.6
53	QSHR2	RDHT	CSNR1	5′-GAC AGG GGA G-3′ (SEQ ID NO: 234)	1.6
54	QSHT	VSSR	RSHR	5′-TGA GTT GGG A-3′ (SEQ ID NO: 235)	1.6
55	QSNV2	QSHR2	QSNR3	5′-GAA GGA AAA T-3′ (SEQ ID NO: 236)	1.6
56	RSNR	VSTR	RSHR	5′-GGG GCT GAG G-3′ (SEQ ID NO: 237)	1.5
57	QSHR2	CSNR1	QSHT	5′-TGA GAC GGA G-3′ (SEQ ID NO: 238)	1.5
58	VSNV	QSHR2	VSTR	5′-GCT GGA AAT T-3′ (SEQ ID NO: 239)	1.5
59	DGAR*	DGNR*	RDKR*	5′-GGG GAC GTC-3′	1.5
60	QSNR3	QSSR1	QSNV2	5′-CAA GTA GAA G-3′ (SEQ ID NO: 240)	1.5
61	QSNR3	RDER1	RSNR	5′-GAG GCG GAA A-3′ (SEQ ID NO: 241)	1.5
62	RDER1	QSSR1	VSTR	5′-GCT GCA GCG T-3′ (SEQ ID NO: 242)	1.5
63	QSHR3	DGHR*	RDHT	5′-GGG GGC GGA-3′	1.5
64	VSSR	RSHR	ISNR	5′-GAT GGG GTT T-3′ (SEQ ID N0: 243)	1.5
65	RSNR	RDER1	RSHR	5′-GGG GCG GAG-3′	1.5
66	RSNR	RDER1	QSNR3	5′-GAA GCG GAG G-3′ (SEQ ID NO: 244)	1.4
67	QSHR3	QSNV2	DGHR*	5′-GGC AAA GGA-3′	1.4
68	QSNV2	QSNR3	QSSR1	5′-GTA GAA AAA-3′	1.4
69	QSNR3	RDER1	RDER1	5′-GTG GCG GAA G-3′ (SEQ ID NO: 245)	1.4
70	QSNV2	QSDR*	QSSR1	5′-GTA GCT AAA-3′	1.4
71	QSNV2	QSHR2	QSNV2	5′-AAA GGA AAA G-3′ (SEQ ID NO: 246)	1.4
72	QSNV2	VSSR	RDHT	5′-CGG GTT AAA A-3′ (SEQ ID NO: 247)	1.4
73	QSHR3	QTHQ	QSDR*	5′-GCT AGA GGA-3′	1.4
74	RSHR	VSTR	QSSR1	5′-GTA GCT GGG A-3′ (SEQ ID NO: 248)	1.4
75	RDER1	QSNV2	QSHR2	5′-GGA CAA GCG G-3′ (SEQ ID NO: 249)	1.3
76	QSNV2	QSHT	QSNV2	5′-AAA AGA AAA A-3′ (SEQ ID NO: 250)	1.3
77	QSHR2	QSHR2	QSSR1	5′-GTA GGA GGA T-3′ (SEQ ID NO: 202)	1.3
78	QSNR3	QSSR1	QSHT	5′-AGA GTA GAA T-3′ (SEQ ID NO: 251)	1.3
79	QSNV2	QSSR1	QSNV2	5′-AAA GTA AAA A-3′ (SEQ ID NO: 252)	1.3
80	QSHR2	RSNR	RDHT	5′-AGG GAG GGA G-3′ (SEQ ID NO: 253)	1.3
81	RSNR	VSNV	QSNV2	5′-AAA AAT GAG C-3′ (SEQ ID NO: 254)	1.3
82	QSHT	QSNR3	RDHT	5′-CGG GAA AGA A-3′ (SEQ ID NO: 255)	1.3
83	QTHQ	QGDR*	QSSR*	5′-GTA GCA AGA C-3′ (SEQ ID NO: 256)	1.3
84	QSNV2	QSSR1	VSNV	5′-AAT GTA AAA A-3′ (SEQ ID NO: 257)	1.3
85	RDKR*	QAHR*	RDHT	5′-CGG GGA GGG G-3′ (SEQ ID NO: 258)	1.3
86	QSNR*	QSNR*	QAHR*	5′-TTC TTC TCC-3′	1.3
87	DGNR*	RSNR	QSSR1	5′-GTA GAG GAC-3′	1.2
88	CSNR1	QSHT	QSNV2	5′-CAA AGA GAC T-3′ (SEQ ID NO: 259)	1.2
89	RDER1	ISNR	QSNR3	5′-GAA GAT GCG T-3′ (SEQ ID NO: 260)	1.2
90	RDHT	QSSR1	QSHT	5′-CGA GCA TGG G-3′ (SEQ ID NO: 261)	1.2
91	RDHT	QGTR*	QGTR*	5′-ACA ACA GGG G-3′ (SEQ ID NO: 262)	1.20
92	RSHR	RSHR	VSSR	5′-GTT GGG GGG C-3′ (SEQ ID NO. 263)	1.2
93	RDER1	RSNR	RDHT	5′-AGG GAG GTG T-3′ (SEQ ID NO: 264)	1.2
94	RSHR	CSNR1	QSHT	5′-TGA GAC GGG G-3′ (SEQ ID NO. 265)	1.2
95	QSHR2	VSSR	QSNR3	5′-GAA GTT GGA A-3′ (SEQ ID NO: 266)	1.2
96	QSNR3	QSNV2	QSHT	5′-AGA AAA GAA A-3′ (SEQ ID NO: 267)	1.2
97	QSNV2	QSHT	CSNR1	5′-GAC TGA CAA T-3′ (SEQ ID NO: 268)	1.2
98	TGNR*	RDNR*	QSDR*	5′-GCT GAG GAT G-3′ (SEQ ID NO: 269)	1.2
99	QSNV2	RSNR	RSHR	5′-GGG GAG AAA T-3′ (SEQ ID NO: 270)	1.2
100	QSNR3	QSHT	QSHT	5′-TGA TGA GAA A-3′ (SEQ ID NO: 271)	1.2
101	HSNK	QSHR2	QSSR1	5′-GCA GGA GAC T-3′ (SEQ ID NO. 272)	1.2
102	TGNR*	QAHR*	RDHT	5′-TGG GGA GAT T-3′ (SEQ ID NO. 273)	1.1
102	TGNR*	QAHR*	RDHT	5′-TGG GGA GAT T-3′ (SEQ ID NO: 274)	1.1
103	RDHT	QSNR3	RDER1	5′-GCG GAA TGG A-3′ (SEQ ID NO: 275)	1.1
104	QSHR3	RDHT	DGAR*	5′-GTC TGG GGA C-3′ (SEQ ID NO: 276)	1.1
105	RDER1	RSHR	RSNR	5′-GAG GGG GCG T-3′ (SEQ ID NO: 277)	1.1
106	VSTR	VSTR	QSSR1	5′-GAC GCT GCT T-3′ (SEQ ID NO: 278)	1.1
107	TGNR*	QAHR*	QAHR*	5′-ATC TCC TCC-3′	1.1
108	DGHR*	QGDR*	RDKR*	5′-GGG GCA GGC G-3′ (SEQ ID NO: 279)	1.1
109	RSHR	RSHR	TGNR*	5′-GAT GGG GGG-3′	1.1
110	QSNV2	QSNV2	QSNV2	5′-AAA AAA AAA G-3′ (SEQ ID NO: 280)	1.1
111	RSNR	QSHT	QSHR2	5′-GGA AGA GAG G-3′ (SEQ ID NO: 281)	1.1
112	QSNV2	RSHR	QSNV2	5′-CAA GGG AAA A-3′ (SEQ ID NO. 282)	1.1
113	QGDR*	TGNR*	TDKR*	5′-GGT GAT GCA C-3 (SEQ ID NO: 283)	1.1
114	RDER1	DGAR*	RDTN*	5′-AAG GTC GCG G-3′ (SEQ ID NO: 284)	1.0
115	QAHR*	QSDR*	RDKR*	5′-GGG GCT GGA G-3′ (SEQ ID NO: 285)	1.0
116	VSSR	TDKR*	RDHT	5′-GGG GGG GTT-3′	1.0
117	QSSR*	TDKR*	RDKR*	5′-GGG GGT GTA C-3′ (SEQ ID NO: 286)	1.0
118	QSDR*	TGNR*	TDKR*	5′-GGT GAT GCT C-3′ (SEQ ID NO: 287)	1.0
119	CSNR1	QSHT	VSSR	5′-GTT TGA GAC A-3′ (SEQ ID NO. 288)	1.0
120	RSNR	QSHR3	DGHR*	5′-GGC GGA GAG-3′	1.0
121	VSNV	QSNV2	VSTR	5′-GCT AAA AAT C-3′ (SEQ ID NO: 289)	1.0
122	QSDR*	QAHR*	QTHQ	5′-AGA GGA GCT T-3′ (SEQ ID NO: 290)	1.0
123	RSHR	ISNR	QSHT	5′-TGA GAT GGG G-3′ (SEQ ID NO. 291)	1.0
124	QSNR*	QAHR*	RDKR*	5′-TTC TCC CCC-3′	0.9
125	DGHR*	RDHT	QSDR*	5′-GCT TGG GGC T-3′ (SEQ ID NO: 292)	0.9
126	RDER1	QGDR	VSSR	5′-GTT GGG GCG G-3′ (SEQ ID NO: 293)	0.9
127	QSDR*	QSDR*	QAHR*	5′-GGA GCT GCT T-3′ (SEQ ID NO: 294)	0.9
128	DGHR*	RSNR	DGNV*	5′-AAC GAG GGC-3′	0.9
129	QSHR3	QGDR*	TGNR*	5′-GAT GCA GGA C-3′ (SEQ ID NO: 295)	0.9
130	QSNR1	DRDR*	TGNR*	5′-GAT GCC GAA-3′	0.9
131	DGAR*	RDHT	DGHR*	5′-GGC CGG GTC G-3′ (SEQ ID NO: 296)	0.9
132	TDKR*	TDKR*	TGNR*	5′-GAT GGT GGT T-3′ (SEQ ID NO: 297)	0.9
133	NDTR*	QSNR*	QAHR*	5′-GGA GAA GTT-3′	0.9
134	TGNR*	QGTR*	QSDR*	5′-GCT ACA GAT-3′	0.8
135	RDER1	TDKR*	DRDR*	5′-GCC GGG GCG G-3′ (SEQ ID NO: 298)	0.8
136	QSNR1	VSSR	DGNV*	5′-AAC GTT GAA-3′	0.8
137	DGAR*	QSSR*	GRER*	5′-GCC GTA GTC-3′	0.8
138	CSNR1	RSHR	VSTR	5′-GCT GGG GAC T-3′ (SEQ ID NO: 299)	0.8
139	QSSR*	QSDR*	QSSR*	5′-GTA GCT GTA A-3′ (SEQ ID NO: 300)	0.8
140	QSNV2	RSNR	QSSR1	5′-GTA GAG AAA-3′	0.8
141	TDKR*	DGHR*	RDKR*	5′-GGG GGC GGT T-3′ (SEQ ID NO: 301)	0.8
142	TGNR*	QSDR*	TDKR*	5′-GGT GCT GAT T-3′ (SEQ ID NO: 302)	0.8
143	DRDR*	DGHR*	QSSR1	5′-GTA GGC GCC-3′	0.8
144	QAHR*	QSSR*	QGDR*	5′-GCA GTA GGA G-3′ (SEQ ID NO: 303)	0.8
145	QSHT	RSNR	QSDR*	5′-GCT GAG AGA-3′	0.8
146	DGNV*	QGDR*	DGNV*	5′-AAC GCA AAC-3′	0.7
147	QGDR*	TDKR*	DGAR*	5′-GTC GGG GCA-3′	0.7
148	TDKR*	QSNR1	DGNR*	5′-GAC GAA GGG G-3′ (SEQ ID NO: 304)	0.7
149	QSNR*	QGDR*	NDTR*	5′-GTT GCT GAA-3′	0.7
150	QSNR*	RDKR*	DGHR*	5′-GGC GGG GAA-3′	0.7
151	DGNV*	QGDR*	DGNR*	5′-GAC GCA AAC-3′	0.7
152	QSDR*	DGNR*	DGNR*	5′-GAC GAC GCT T-3′ (SEQ ID NO: 305)	0.7
153	CSNR1	TGNR*	DGNR*	5′-GAC GAT GAA-3′	0.6
*Domains followed by the “*” symbol are zinc finger domains obtained by mutagenesis. The domains not so indicated are human zinc finger domains described herein. The target composite sequences were designed by juxtaposing individual target sites of each domain.

[0505] The distribution of results relative to the high and low stringency criteria are tabulated in Tables 11 and 12. As shown in Table 11, 31 of 153 chimeric zinc finger proteins demonstrated greater than 2-fold repression, the high stringency criterion (RF≧2; RF=fold repression). Table 12 demonstrates that, of the proteins constructed entirely from naturally-occurring human zinc finger domains, 28.1% (27 of 96) exceeded the high stringency criterion and 59.4% exceeded the low stringency criterion (RF≧1.5). Of the proteins constructed from two naturally-occurring zinc finger domains and one mutated domain, 33.3% exceeded the high stringency criterion, and only 20% exceeded the low stringency criterion.

[0506] In contrast, of the 17 proteins constructed from one human domain and two mutated domains, only one protein (5.9%) exceeded the high stringency criterion. and only two proteins (11.8%) exceeded the low stringency criterion. Strikingly, no zinc finger proteins composed exclusively of mutated domains satisfied the high stringency criterion in the repression assay. Only one such protein (4%) satisfied the low stringency criterion. These results indicate that naturally-occurring human zinc finger domains are in general much better building blocks for the construction of new DNA-binding proteins than mutated domains.

TABLE 11
No of Tested	No. of Active ZFPs (B)	B/A (%)
ZFPs (A)	RF > 1.5	RF > 2.0	RF > 1.5	RF > 2.0
153	65	31	42.5	20.3

[0507]

TABLE 12
Compositions of ZFPs	No. of Tested	No. of Active ZFPs (B)	B/A (%)
Human D	Mutated D	ZFPs (A)	RF > 1.5	RF > 2.0	RF > 1.5	RF > 2.0
3	0	96	57	27	59.4	28.1
2	1	15	5	3	33.3	20
1	2	17	2	1	11.8	5.9
0	3	25	1	0	4.0	0

[0508] A number of embodiments of the invention have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the invention. Accordingly, other embodiments are within the scope of the following claims.

Claims

1. A library comprising a plurality of polypeptides, each polypeptide comprising a first and a second zinc finger domain, wherein (1) the first and second zinc finger domains of each polypeptide are each identical to a zinc finger domain from a naturally occurring protein and either (i) do not occur in the same naturally occurring protein or (ii) occur in the same naturally occurring protein in a different configuration than in the polypeptide, (2) the first zinc finger domain varies among polypeptides of the plurality, and (3) the second zinc finger domain varies among polypeptides of the plurality.

2. A library comprising a plurality of polypeptides, each polypeptide comprising a first and a second zinc finger domain, wherein (1) the first and second zinc finger domains of each polypeptide are each identical to a zinc finger domain from a naturally occurring protein and do not occur in the same naturally occurring protein, (2) the first zinc finger domain varies among polypeptides of the plurality, and (3) the second zinc finger domain varies among polypeptides of the plurality.

3. The library of claim 1, wherein each polypeptide of the plurality binds to a target DNA site with a dissociation constant (Kd) of less than 5 nM.

4. The library of claim 2, wherein each polypeptide of the plurality binds to a predetermined site.

5. The library of claim 2 wherein the plurality contains at least 80% of the members of the library.

6. The library of claim 2, wherein the first zinc finger domain of at least one polypeptide of the plurality is selected from the zinc finger domains listed in any of Tables 5, 6, and 7.

7. The library of claim 6 wherein the first zinc finger domain of each polypeptide of the plurality is selected from the zinc finger domains listed in any of Tables 5, 6, and 7.

8. The library of claim 6, wherein the first and second zinc finger domains of at least one polypeptide of the plurality are selected from the zinc finger domains listed in any of Tables 5, 6, and 7.

9. The library of claim 2 wherein the naturally occurring protein is a eukaryotic protein.

10. The library of claim 9 wherein the naturally occurring protein is a mammalian protein.

11. The library of claim 10 wherein the naturally occurring protein is a human protein.

12. The library of claim 2, wherein each polypeptide of the plurality further comprises a third zinc finger domain.

13. The library of claim 2, wherein the third zinc finger domain is a domain of a naturally occurring protein.

14. The library of claim 12, wherein the third zinc finger domain differs from a domain of a naturally occurring protein by insertion, deletion, or substitution of at least one but no more than six amino acids.

15. The library of claim 2, wherein each polypeptide of the plurality further comprises a transcriptional regulatory domain.

16. The library of claim 2, wherein the plurality comprises at least 100 different polypeptides.

17. A library comprising a plurality of nucleic acids, each nucleic acid of the plurality encoding a polypeptide comprising a first and a second zinc finger domain, wherein (1) the first and second zinc finger domains of the polypeptide encoded by each nucleic acid of the plurality are each identical to zinc finger domains from naturally occurring proteins and either (i) do not occur in the same naturally occurring protein or (ii) occur in the same naturally occurring protein in a different configuration than in the polypeptide, (2) the first zinc finger domain varies among nucleic acids of the plurality, and (3) the second zinc finger domain varies among nucleic acids of the plurality.

18. The library of claim 17, wherein each polynucleotide resides within a cell.

19. The library of claim 18, wherein the cell is a eukaryotic cell.

20. The library of claim 19, wherein the cell is a yeast cell.

21. The library of claim 18, wherein the cell contains a heterologous reporter construct comprising a reporter gene operably linked to a promoter.

22. A method of producing a plurality of chimeric nucleic acids, the method comprising: (a) providing a set of nucleic acids, each nucleic acid of the set comprising a sequence encoding a zinc finger domain from a naturally occurring protein; and (b) joining each nucleic acid of the set to one or more other nucleic acids of the set to form a plurality of chimeric nucleic acids.

23. The method of claim 22 wherein the set comprises at least two sequences that encode zinc finger domains from different naturally occurring proteins.

24. The method of claim 22 wherein the set also comprises at least two sequences that encode zinc finger domains from the same naturally occurring proteins.

25. The method of claim 22 wherein step (a) comprises amplifying a collection of polynucleotides encoding zinc finger domains from genomic DNA, a messenger RNA (mRNA) mixture, or a complementary DNA (cDNA) mixture using an oligonucleotide primer that anneals to sequences that encode a conserved domain boundary.

26. The method of claim 22 wherein step (a) comprises: (i) selecting a plurality of zinc finger domains, each domain having specificity for a sequence within a target site of interest; and (ii) providing a plurality of polynucleotides, each polynucleotide encoding at least one of the selected zinc finger domains, thereby providing the set of polynucleotides.

27. The method of claim 26 wherein the plurality of zinc finger domains are selected by querying a database that includes information relating zinc finger domains to their respective binding sites.

28. A method of generating an artificial zinc finger polypeptide that specifically binds to a target DNA site, the method comprising: providing the polypeptide library of claim 1;contacting the target DNA site with the polypeptides of the library; and identifying one or more polypeptides that specifically bind to the target DNA site.

29. The method of claim 28, wherein the polypeptides of the library are immobilized on a solid support.

30. The method of claim 28, wherein each polypeptide of the library is displayed on the surface of a virus or viral particle.

31. A method of profiling a test nucleic acid, the method comprising; contacting the test nucleic acid with the polypeptides of the library of claim 1;evaluating a binding interaction between the test nucleic acid and each polypeptide of the library; and determining a profile of the test nucleic acid from results of the evaluating, the profile comprising information about the evaluated binding interactions between the test nucleic acid and each polypeptide of the library.

32. A method of identifying a nucleic acid encoding a polypeptide that recognizes a target DNA site, the method comprising: providing a plurality of nucleic acids, each nucleic acid of the plurality encoding a polypeptide comprising a first and a second zinc finger domain, wherein the first and second zinc finger domains of the polypeptide encoded by each nucleic acid of the plurality are identical to zinc finger domains from different naturally occurring mammalian proteins, the first zinc finger domain varies among nucleic acids of the plurality, and the second zinc finger domain varies among nucleic acids of the plurality; providing cells containing a reporter gene operably linked to a target DNA site; expressing the plurality of nucleic acids in the cells; identifying a cell having altered expression of the reporter gene relative to the level of expression in the absence of a polypeptide that recognizes the target DNA site level; and identifying a nucleic acid expressed in the cell, the nucleic acid being a nucleic acid of the plurality, thereby identifying a nucleic acid encoding a polypeptide that recognizes the target DNA site.

33. The method of claim 32, wherein the given level is the level of reporter gene expression in a reference cell that includes a reference nucleic acid.

34. A method of identifying a nucleic acid encoding a zinc finger polypeptide that specifically recognizes a target DNA site, the method comprising: providing the library of polynucleotides of claim 17;providing cells containing a reporter gene operably linked to a target DNA site; expressing the plurality of polynucleotides in the cells; identifying a cell having altered expression of the reporter gene relative to the level of expression in the absence of a polypeptide that recognizes the target DNA site level; and identifying a polynucleotide expressed in the cell, the polynucleotide being a polynucleotide of the plurality, thereby identifying a polynucleotide encoding a polypeptide that specifically recognizes the target DNA site.

35. The method of claim 34, further comprising the step of modifying the amino acid sequence of the identified zinc finger polypeptide without altering the binding specificity of the zinc finger polypeptide for the target DNA site.

36. The method of claim 34, wherein the target site comprises at least six predetermined nucleotides.

37. The method of claim 34, wherein the cells are yeast cells.

38. The method of claim 34, further comprising the step of introducing the polynucleotides into each of the cells.

39. The method of claim 34, further comprising the step of fusing the cells containing the reporter gene to cell that includes the polynucleotides of the library.

40. A polypeptide comprising a first and a second zinc finger domain, wherein the first and second zinc finger domains are each from naturally occurring proteins and are selected from the zinc finger domains of Tables 5, 6, and 7.

41. A polypeptide of claim 40 that further comprises a third zinc finger domain, wherein the set of three zinc finger domains is listed in a row of Table 10.

42. A nucleic acid sequence comprising a polynucleotide that encodes the polypeptide of claim 40.

43. A nucleic acid sequence comprising a polynucleotide that encodes the polypeptide of claim 41.

44. A purified polypeptide comprising an amino acid sequence selected from the group consisting of: Xa-X-Cys-X2-5-Cys-X3-Xa-X-His-X-Ser-Ser-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 167), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 168), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Lys-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:169), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Lys-His-X3-5-His (SEQ ID NO:170), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO:171), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Val-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO: 172), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Cys-Xb-X-Arg-His-X3-5-His (SEQ ID NO:193), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO: 194), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Trp-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:195), and Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Ala-Xb-X-Arg-His-X3-5-His (SEQ ID NO:196), wherein Xa is phenylalanine or tyrosine, and Xb is a hydrophobic residue.

45. The purified polypeptide of claim 44 wherein the polypeptide comprises an amino acid sequence selected from the group consisting of: SEQ ID NO:173, 175, 177, 179, 181, 183, 185, 187, 189, and 191.

46. A purified polypeptide comprising between two and ten segments, each segment having an amino acid sequence selected from the group consisting of: Xa-X-Cys-X2-5-Cys-X3-Xa-X-His-X-Ser-Ser-Xb-X-Arg-His-X3-5-His (SEQ ID NO:167), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 168), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Lys-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:169), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Lys-His-X3-5-His (SEQ ID NO:170), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO:171), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Val-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO: 172), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Cys-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 193), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ile-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO:194), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Trp-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:195), and Xa-X-Cys-X2-5-Cys-X3-Xa-X-Asp-X-Ser-Ala-Xb-X-Arg-His-X3-5-His (SEQ ID NO: 196), wherein Xa is phenylalanine or tyrosine, and Xb is a hydrophobic residue.

47. The purified polypeptide of claim 44 further comprising a second amino acid sequence selected from the group consisting of: Xa-X-Cys-X2-5-Cys-X3-Xa-X-Cys-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:68), Xa-X-Cys-X2-5-Cys-X3-Xa-X-His-X-Ser-Asn-Xb-X-Lys-His-X3-5-His (SEQ ID NO:69), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Ser-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:70), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Thr-Xb-X-Val-His-X3-5-His (SEQ ID NO:71), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Val-X-Ser-Xc-Xb-X-Arg-His-X3-5-His (SEQ ID NO:72), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:73), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Val-His-X3-5-His (SEQ ID NO:74), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Xc-Xb-X-Arg-His-X3-5-His (SEQ ID NO:75), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ala-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:150), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Phe-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:151), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO:152), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-His-Xb-X-Val-His-X3-5-His (SEQ ID NO:153), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Ile-His-X3-5-His (SEQ ID NO:154), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:155), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Thr-His-Xb-X-Gln-His-X3-5-His (SEQ ID NO:156), Cys-X2-5-Cys-X3-Xa-X-Gln-X-Thr-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:157), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-Lys-Xb-X-Ile-His-X3-5-His (SEQ ID NO:158), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Ser-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:159), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Gln-X-Gly-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:161), Xa-X-Cys-X2-5-Cys-X3-Xa-Arg-X-Asp-Glu-Xb-X-Arg-His-X3-5-His (SEQ ID NO:162), Xa-X-Cys-X2-5-CYS-X3-Xa-X-Arg-X-Asp-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:163), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-His-Xb-X-Thr-His-X3-5-His (SEQ ID NO:164), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Asp-Lys-Xb-X-Arg-His-X3-5-His (SEQ ID NO:165), Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Ser-His-Xb-X-Arg-His-X3-5-His (SEQ ID NO:166), and Xa-X-Cys-X2-5-Cys-X3-Xa-X-Arg-X-Thr-Asn-Xb-X-Arg-His-X3-5-His (SEQ ID NO:160), wherein Xa is phenylalanine or tyrosine, and Xb is a hydrophobic residue.

48. The polypeptide of claim 44 wherein the amino acid sequence is a segment of a naturally occurring protein.

49. A nucleic acid comprising a sequence encoding the polypeptide of claim 44.

50. A nucleic acid comprising a sequence encoding the polypeptide of claim 45.

51. A nucleic acid comprising a sequence encoding the polypeptide of claim 46.

52. A nucleic acid comprising a sequence encoding the polypeptide of claim 47.