DNA-binding proteins of the zinc-finger class

Abstract

The invention is directed to the design of DNA-binding proteins (DBP's) with capabilities of binding to any predetermined target double-stranded DNA sequence. Disclosed are the rules for design of the proteins; an algorithm for screening for the optimal DBP's; a computer system employing the rules and the algorithm; general formulae encompassing the proteins; and methods of use of the proteins.

Description

BACKGROUND OF THE INVENTION

A superfamily of eukaryotic genes encoding potential nucleic-acid-binding proteins contains zinc-finger (ZF) domains of the Cys 2 -His 2 (C 2 H 2 ) class. Proteins that have these characteristic structural features play a key role in the regulation of gene expression[1-4]. Sequence comparisons, mutational analyses, and a recent crystallographic investigation have revealed that each finger domain, as a rule, interacts with the major groove of B-form DNA through contacts with some or all three base pairs within a DNA triplet. These base-specific interactions are mediated through amino acid (AA) side chains at specific positions in the a-helical region [5-10] of the protein domain.

Although the AA sequences of more than 1,300 ZF motifs have been identified, the exact DNA-binding sites are known only for a few proteins. The available information on DNA contact regions concerns mainly guanine-cytosine-rich strands [5-9] and fewer adenine-thymine-rich sites [11,12]. On the basis of experimental data, the first proposals for rules relating ZF sequences to preferred DNA-binding sites have been made [13,14]. However, no general rules for ZF protein-DNA recognition have been proposed. This is likely due to the fact that neither computer modeling [2,3,5] nor crystallographic analysis [7] have provided enough information on the overall structural variety in the ZF-DNA contact region.

Using physical atomic-molecular models to characterize the steric conditions in the specific contact positions for different ZF-DNA interactions, an objective of the work leading to the present invention was to determine a set of general rules for ZF-DNA recognition for the C 2 H 2 class of ZF domains. Once this objective had been reached, the work of the invention plan was to develop an algorithm, and a computer system using the algorithm, to design effective zinc-finger DNA-binding polypeptides. The achievement of these goals represents a major advance of knowledge in the field, knowledge characterized by the disclosures of Rebar, et. al. and Beerli, et. al. [15,16]. These two disclosures are concerned with the selection, using the phage display system, of specific zinc fingers with new DNA-binding specificities. On the other hand, the present disclosure is concerned with the design of DNA-binding proteins for any given DNA sequence.

SUMMARY OF THE INVENTION

The invention is directed to the design and specification of DNA-binding proteins binding via C 2 H 2 zinc-finger motifs (DBP's or, individually, a DBP). On the basis of the studies described herein, general rules for optimizing such binding have been determined, and a formula describing the class of DBP's having optimal DNA-binding properties has been constructed. Furthermore, a program has been developed, based on the rules, which affords the design of DBP's with such high binding affinity for any given DNA sequence. Lastly, rules have been determined for the design of DBP's which, while not having optimal binding, do have significant and useful DNA-binding properties.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts the alignment of ZF domains in various known DBP's. TFIIIA fingers 1-9 are shown as SEQ ID NOS: 207-215, respectively, in the Sequence Listing; Xenopus Xfin finger 31 is shown as SEQ ID NO: 216; the ADRI finger is shown as SEQ ID NO: 217; MKR2 fingers 1-9 are shown as SEQ ID NOS: 218-226, respectively; and Kruppel fingers 1-5 are shown as SEQ ID NOS: 227-231, respectively.

FIG. 2 is a schematic representation of the interaction between a target DNA triplet and a single ZF domain.

FIG. 3 is a schematic representation of the interaction between a target DNA string of 9 bases and a three-domain DBP.

FIG. 4 is a block flow diagram of the computer system by which the instant DBP design process is implemented.

FIG. 5 is a block flow diagram wherein the Computer Program block (2) of FIG. 4 is further broken down.

FIG. 6 is a block flow diagram wherein the Process Genome into Blocking Fragment Files block (2) of FIG. 5 is further broken down.

FIG. 7 is a block flow diagram wherein the Design DBP's for a Genome block (3) of FIG. 5 is further broken down.

FIG. 8 is a block flow diagram wherein block (22) of FIG. 7 is further broken down.

FIG. 9 is a block flow diagram wherein block (24) of FIG. 7 is further broken down.

FIG. 10 shows the distribution of binding strengths of acceptable 9-finger DBP's across the yeast genes analyzed.

FIG. 11 shows the values of the binding energies of the acceptable 9-finger DBP's found for the yeast genes analyzed.

FIG. 12 shows the distribution of DBP subsite (spurious) binding energies across the yeast genes analyzed.

FIG. 13 shows, in nonlogarithmic fashion, the distribution depicted in FIG. 12 .

FIG. 14 shows the ratios of binding energy to subsite (spurious) binding energy, across the yeast genes analyzed, for the acceptable 9-finger DBP's.

FIG. 15 shows the values of the spurious binding energies for each of the 27-base-pair (bp) frames of the 300-bp promoter region of yeast gene YAR073.

FIG. 16 shows the ratios of binding energy to subsite (spurious) binding energy for each of the 27-base-pair (bp) frames of the 300-bp promoter region of yeast gene YAR073.

FIG. 17 shows the distribution of sizes of acceptable DBP's across the C. elegans genes analyzed.

FIG. 18 shows the ratios of binding energy to subsite (spurious) binding energy, across the C. elegans genes analyzed, for the acceptable DBP's.

DETAILED DESCRIPTION OF THE INVENTION

The general rules governing the binding of C 2 H 2 ZF motifs to DNA were developed by using a combination of the database analysis of the homologies between 1,851 possible ZF domains and physical molecular modeling of the interaction of a DBP model with a DNA model containing all 64 possible base-pair triplets. The DBP model approximates the size and shape of a half-gallon jug of milk. The DNA model is approximately four feet long and one foot in diameter. The axis of the DNA model is horizontal and can be rotated to observe each of the 64 base-pair triplets. By moving the DBP model in and out with respect to the DNA model one can observe the amino acid and nucleic acid contacts.

Although the following description details the scientific precedents of this invention, the completeness of the rule set governing the DBP-DNA interaction could have only been obtained by the continual, derivative interplay of data base analysis and physical modeling during the invention period. Observations as to the conservation and variability of amino acids at various places in the ZF motif were embodied, first, by constructing a physical model of the ZF motif and, then, by physically modeling the interaction of a specific DBP with a designated DNA bp triplet. The physical modeling indicated patterns of amino acid and nucleic acid interaction which led to further analysis of the database. Iterations of this interplay between database analysis and physical modeling enabled conceptual refinement and expansion of the nature of contact patterns. As these patterns emerged, systematic variation of the amino acids in the ZF motif was undertaken for each of the 64 base-pair triplets. The physical modeling of the interaction between a DBP and DNA was efficient because alternative amino acids could be easily introduced into the ZF motif and the resulting protein physically modeled against the DNA. Hydrogen bonding, and water and hydrophobic contacts could then be modeled, clearly determined and counted very quickly. From this physical modeling a general set of rules was developed which incorporates criteria for the design of DBP's that specifically interact with DNA.

The utility of ZF sequence analysis and alignment is illustrated by FIG. 1 . The TFIIIA protein is widely used as a model for ZF proteins both in terms of physical measurement and modification and theoretical data analysis. For each of the nine zinc-finger domains the TFIIIA amino acid sequence in this figure has been aligned so that the zinc-binding amino acids, the two cysteines (CYS) and the two histidines (HIS), are aligned in four columns. In order to achieve this alignment dashes must be inserted into the sequence at various places to provide for domains which have additional amino acids. The same type of alignment has been done for ZF protein MKR2 and the Kruppel proteins. The MKR2 sequence alignment is very compact; there is no need for any insertions, since all of its ZF domains are of the same size. Compared to TFIIIA, MKR2 acts as a much more uniform model for studying the interaction of the amino acids of the protein with the bases of the specific double-stranded DNA. To arrive at the present invention, MKR2 has been used exclusively as the sequence basis for deducing the general rules which govern DBP-DNA interactions.

The crystallographic analysis of a complex containing three ZFs from ZF protein Zif268 and a consensus DNA-binding site helped identify the localization of ZF-B-DNA recognition sub-sites [7]. Because the mutagenesis and sequence investigation results are in accordance with crystal structure data, it is reasonable to expect that the same contact regions also participate in the interaction of other ZF-DNA complexes [5,6,8-10]. Thus, it has been assumed that the following ZF components of a ZF protein play a key role in the anti-parallel DNA reading process: 1) the AA immediately preceding the a-helical region of the protein; 2) the third residue within the a-helical region, i.e., that immediately preceding constant leucine; and, 3) the sixth residue of this region, i.e., that immediately preceding invariant histidine.

These components are indicated below as Z 3 , Z 2 and Z 1 , respectively, in the generalized ZF sequence (a-helical and b-structural regions are underlined) given in Formula I:

wherein X is any amino acid; X 2-4 is a peptide 2 to 4 amino acids in length; X 3-5 is a peptide 3 to 5 amino acids in length; X 0-2 is a peptide 0 to 2 amino acids in length and C, D, E, F, G, H, K, L, P, R, S, T and Y designate specific amino acids according to the standard single-letter code. Pairs of letters separated by “/” indicate that the position can be filled by either of the two specific amino acids designated.

Keeping in mind the above formula, one can envision the formation of antiparallel, trinucleotide-peptide complexes with three (first, second and third) contact positions as follows:

5′—N 1 —N 2 —N 3 —3′

COOH—Z 1 —Z 2 —Z 3 —NH 2

The crystallographic investigation of the Zif268-DNA complex also gave indications of the way the contact groups interact. Pavletich and Pabo [7] concluded that Zif268 forms 11 critical hydrogen bonds (H-bonds) with the bases of the coding DNA strand in the major groove. Two arginine residues in the first contact positions (see the designations of positions above) make H-bonds with the N7 and O6 atoms of the guanine. Three arginine residues hydrogen bond in the same way with guanine in the third contact position. In addition, each arginine residue in this position forms lateral H-bond, salt bridge interactions with carboxylate groups of aspartic acid occurring as the second residue in the a-helix. The N6 atom of the histidine residue in the middle contact position of the second ZF of Zif268 donates an H-bond to the N7 or O6 atom of guanine. The role of arginine and histidine residues in the interaction with guanine in ZF polypeptide-DNA complexes is confirmed by experiments of directed mutagenesis [5,6,9,14]. The crystallographic investigations of DNA-binding domains of lambda and phage 434 repressors, complexed with corresponding operator sites, revealed that guanine can also be H-bonded by lysine, asparagine, glutamine and serine residues [17,18]. No doubt, the remaining polar AA's—threonine and tyrosine—are able to form analogous bonds with guanine.

In fingers 1 and 3 of the Zif268-DNA complex, the second (middle) critical position is occupied by a glutamic acid that does not contact the cytosine at the corresponding region in the DNA [7]. However, ZF protein-DNA binding assays have shown that in natural binding sites this interaction does occur with both glutamic acid and aspartic acid [5,6,9,14,19]. Desjarlais and Berg [14] proposed an H-bonding formula for the interaction between cytosine and aspartic acid. The authors emphasized that the preference for aspartic or glutamic acid in the interaction with cytosine depends on the presence of glutamine or arginine in the third contact position (Z 3 ), and serine or aspartic acid in the second position (Z 2 ). The mutagenesis experiments of Nardelli et al. [5] reveal that cytosine can interact with a glutamine residue. This may also be true for asparagine, which has similar polar groups. Cytosine should also be capable of making an H-bond with the hydroxyl oxygen atom in serine and threonine residues.

Thymine in the Zif268-DNA complex does not seem to participate in the recognition process. However, the crystal structure investigations of the lambda repressor, DNA-binding-domain DNA and engrailed homeodomain-DNA complexes, as well as ZF protein-DNA binding assays, demonstrate that thymine can make both hydrophobic contacts with non-polar residues (alanine, leucine, isoleucine, valine) and H-bonds with polar AA's (lysine, arginine, glutamine) [8,11,14,17,20].

The X-ray crystallographic studies of lambda and phage 434 repressor, DNA-binding domain complexes with corresponding operator sites revealed that an adenine base forms two H-bonds to glutamine: 1) the amide NH 2 -group of the glutamine side chain donates an H-bond to the N7-atom of adenine and 2) the amide O-atom accepts an H-bond from the N6 atom [17,18]. Similar H-bonds have been found between adenine and asparagine residues in the two homeodomain complexes [20,21]. ZF protein-DNA binding assays also indicate, that in ZF contact positions, adenine makes strong interactions with both glutamine and asparagine [8,11,12,14]. Considering that glutamic and aspartic acid carboxylic groups have O-atoms capable of accepting H-bonds as do glutamine and asparagine amide O-atoms, one may suppose that adenine can form a single H-bond with both glutamic and aspartic acid. Indeed, Letovsky and Dynan [19] have shown in a directed mutagenesis investigation that transcription factor Sp1, containing a glutamic acid residue in the central contact position of the ZF, binds only 3-fold more weakly to the adenine-substituted variant (-GAG-) than to the wild consensus recognition site (-GCG-). In addition, Desjarlais and Berg [14] and Berg [8] think it probable that adenine can (like guanine in the Zif268-DNA complex) make one H-bond to a histidine residue. It is likely that not only histidine but also other polar amino acids (arginine, lysine, tyrosine, serine and threonine) are capable of forming an H-bond to atom N7 of adenine.

A database of potential ZF protein domains, containing 1,851 entries, has been assembled. This database was used computationally to observe the homologies between the ZF domains.

Several years ago Seeman et al. [22] concluded that a single H-bond is inadequate for uniquely identifying any particular base pair, as this leads to numerous degeneracies. They proposed that fidelity of recognition may be achieved using two H-bonds, as occurs in the major groove when asparagine or glutamine binds to adenine, and arginine binds to guanine.

On the basis of the above-given results, it was reasonable to test, using the models described herein, base recognition at the ZF contact positions of the following AA's:

1) guanine—R, H, K, Y, Q, N, S, T;

2) cytosine—E, D, Q, N, S, T;

3) thymine—I, L, V, A, R, H, K, Y, Q, N, S, T;

4) adenine—Q, N, E, D, H, R, K, Y, S, T

Plastic space-filling atomic-molecular and ionic models [23,24] have been used to build ZF-DNA complex imitations. These molecular models were chosen due to the extraordinary firmness of their connectors, their convenient scale (1 cm=1 Å=0.1 nm) and their improved theoretical parameters which were very suitable for the modeling of macromolecules. New modules of tetrahedral carbon atoms, with bond angles 100° and 105°, dihedral oxygen atoms (120°) and tetrahedral phosphorus atoms (102° and 118°), maintained the exact modeling of deoxyribose puckering and sugar-phosphate chain conformation in the B-DNA model. Peptide bonds in the DBP models were imitated by the fixing, to each other, of special modules of carbon atoms (bond angles 116°, 120.5° and 123.5°) and nitrogen atoms (122° and 119°). The zinc ion was represented in the model by a sphere (R=0.85 cm) fixed tetrahedrally to N and S atom modules of ZF histidine and cysteine residues. A long horizontal 34-base B-form DNA model with laterally-fixed DBP models was used for docking experiments.

In the first stage of the subject investigation, the models of Zif268 fingers 1, 2 and 3 were assembled, and the general spatial orientation of the ZF-B-DNA complex was observed. In the second stage, the steric fitness of all 64 nucleotide triplets to the different combinations of the above-mentioned AA's in the critical positions of the ZF-DNA complex was modeled.

A plastic molecular model of the Zif268 peptide-DNA complex was assembled on the basis of crystallographic data [7]. After the imitating of ZF-DNA backbone contacts and H-bonds between AA and bases in the major groove, it was confirmed that the overall arrangement of Zif268 is antiparallel to the DNA strand. The most steady ZF-DNA, nonspecific interaction seems to be the H-bond between a phosphodiester oxygen atom and the first invariant histidine residue fixed to the Zn 2+ ion. A conserved arginine on the second b strand also contacts phosphodiester oxygen atoms on the primary DNA strand. However, fingers 2 and 3 of Zif268 contact equivalent phosphates with respect to the 3-bp sub-sites, whereas the finger-1 H-bond is shifted by one nucleotide. Another four ZF-DNA backbone contacts made by arginine and serine residues are even more irregular in relation to the ZF modular structure.

All 11 critical H-bonds found in the Zif268-DNA crystal complex have been observed in the plastic models. As expected, the threonine residue in the first contact position of the second finger was too far from thymine to make an H-bond. However, differing from the results of crystal structure analysis, the model investigation clearly indicated the possibility of hydrogen bonding between a glutamic acid residue and cytosine in the second contact position of fingers 1 and 3.

It is noteworthy that, of the six guanine-AA contacts in recognition positions observed in the Zif268-DNA crystal structure, five were made with arginine and only one with histidine. It is even more interesting that this histidine-guanine interaction was the only one in the central-specific position. Considering the smaller size of histidine in comparison with arginine, it may be supposed that the middle position has steric constraints prohibiting contact between guanine and the larger arginine residue, although, due to its capability of forming two H-bonds, the latter pairing should be energetically favored.

To investigate the spatial conditions in different recognition positions, a B-DNA model was built which contained, in the primary strand, 1) the triplet GGG, and 2) models of ZF α-helical protein fragments (including the AA immediately preceding the a-helix) with a) side groups of the first Zn-binding histidine and b) groups for critical AA triplets R 1 R 2 R 3 and R 1 H 2 R 3 . The models of a-helical fragments were fixed to the B-DNA model by an imitation of an H-bond joining a phosphodiester oxygen atom with a histidine residue. Specific base-AA contacts were then tested in these complexes. It was elucidated that only the complex GGG-RiH 2 R 3 contains the contact groups in positions corresponding to the distances of critical H-bonds found in the Zif268-DNA crystal structure. The complex GGG-R 1 R 2 R 3 is sterically unfavorable; molecular modeling reveals that, although in the outer contact positions guanine and arginine can be joined by two H-bonds, in the middle position such a pair cannot be included due to the limited space.

Observations derived from the physical models confirmed the supposition of steric constraints for some AA-base contacts in the central contact position. In the case of the complex G 1 G 2 G 3 —R 1 H 2 R 3 , the following approximate distances from guanine N7 and O6 atoms to the C a atoms of corresponding AA's have been determined: G 1 N7—R 1 =7 Å, G 1 O6—R 1 =8 Å, G 2 N7—H 2 =5.5 Å, G 2 O6 H 2 =6.5 Å, G 3 N7—R 3 =8 Å and G 3 O6—R 3 =7 Å.

Using the models, the investigation of B-DNA and a-helix basic structure elucidated the molecular basis for steric constraints in the second ZF-DNA recognition position. Joining, by a straight line, the analogous atomic groups (for example, N7 atoms of guanine) of the first and third base in the DNA triplet in the major groove results in the corresponding group of the middle (second) base being distanced from this line by about 1.5 Å. Similarly, joining the C α atoms of the AA's in the first and third contact positions of the ZF by such a line results in the C α atom in the middle position also being at a distance of about 1.5 Å. Thus, the space allowed for a critical AA in the middle contact position is compressed from both sides approximately 1.5 Å.

Analysis of the above-given data on the ZF-DNA backbone contacts, as well as observations derived from the models, led to the conclusion that there are considerable differences in spatial conditions between first and third ZF-DNA recognition positions. In the first position the C α atom of the AA is distanced about 6.5 Å from the phosphodiester oxygen atom where the ZF protein is fixed to the DNA backbone by the invariant histidine residue. Due to the steady fixing of this ZF α-helical part by histidine, the freedom of conformational rearrangements in the first contact position is limited: the C α atom, with corresponding side chain, can be moved 2-3 Å “up and down” in the plane of the base where it is localized in the primary DNA strand or, alternatively, 1-2 Å perpendicularly to this plane.

On the other hand, the fixing of the N-terminal end of the ZF α-helical region to the DNA backbone seems to be rather loose and variable, therefore allowing relatively large rearrangements for the C α atom and the corresponding AA in the third contact position. The latter contact position is favored by the fact that the C α atom in this position is more distant from the main fixation place (about 10.5 Å from the phosphodiester atom bound to the histidine residue), and the corresponding AA in this position is not a part of the α-helix. The most important finding is that, due to the above-described circumstances, the critical AA in the third contact site can apparently occupy very different positions in the corresponding bp plane. This means this residue may, in certain complexes, be very close to the base of the complementary DNA strand. One of the reasons for the appearance of such a geometrical configuration is that the typical, right-handed helical twist of B-DNA makes the complementary base on the nucleic acid second strand in the third contact site even more accessible than the main base on the primary chain. Molecular modeling clearly shows that in the third, and also partially in the second contact position, this DNA strand is capable of participating in the ZF-nucleic acid recognition process. In the Zif268-DNA crystal complex, the α-helix of each ZF domain, which is bound only to the DNA primary strand, is tipped at about a 45° angle with respect to the plane of the base pairs [7]. In cases wherein the second DNA strand, via critical H-bonds involving the third and second contact positions, is involved in the reading process, the direction of the α-helix axis should be even more perpendicular to the base pair plane.

Thus, this more detailed investigation of ZF-DNA-complex imitations, through use of physical molecular models, shows that steric conditions in each of the three contact regions are different. These steric conditions are reflected in the ZF-DNA recognition rules.

On the basis of information obtained above, which yielded a general observation of steric conditions in the ZF-DNA recognition process, an extensive model study of various AA-base combinations in the critical contact positions was undertaken. The results of this investigation are presented both as the ZF-DNA reading code and main rules for recognition (Tables 1, 2 and 3). The rules are in good accordance with crystallographic, directed mutagenesis, DNA-binding and sequence analysis data.

With reference to the sequence of Formula I and the 2-dimensional structure diagram in FIG. 2 (which provides a schematic representation of a zinc-finger domain and its interaction with a DNA strand), the studies confirmed the identity of the three critical contact positions in a given zinc-finger domain as follows:

1) between the first nucleotide in the triplet and the first AA preceding the constant histidine at the COOH end of the α-helix;

2) between the second nucleotide in the triplet and the fourth AA preceding the constant histidine at the COOH end of the α-helix; and,

3) between the third nucleotide in the triplet and the seventh AA preceding the constant histidine at the COOH end of the α-helix.

Steric conditions in the three contact sites of the ZF-DNA recognition complexes are different. The first contact position is relatively large and strictly fixed, which enables the binding of a longer AA to bases on the primary DNA strand with sufficient specificity and affinity. The second position is compressed and can accommodate smaller AA's with somewhat lower specificity and affinity. The third position allows considerable conformational rearrangements including the contacts with the complementary DNA strand.

In Table 1, for each nucleotide of a given DNA triplet on the primary strand, both main (Column A) and alternative (Column B) base-binding AA's are presented. Both specificity and affinity were considered in including a residue in Column A. As was proposed already by Seeman et al. [22], the fidelity of recognition is better maintained, in the case of purine bases (guanine and adenine), because they occupy a greater portion of the major groove and offer more hydrogen bonding sites than the pyrimidines. Therefore, the strongest AA interactions appeared to be those of arginine, glutamine and asparagine, each binding by two H-bonds to either guanine or adenine. The affinities of aspartic acid, glutamic acid, asparagine and glutamine were frequently enhanced by the formation of water bridges between carboxylate or amide oxygen atoms and DNA backbone, phosphodiester oxygen atoms. Although van der Waals interactions are relatively weak, they can play a certain role in recognition of the thymine methyl group by hydrophobic AA's (alanine, valine, leucine and isoleucine).

As indicated in Table 1, in many ZF-DNA complexes the base recognition in the nucleotide triplet of the primary DNA strand occurs not entirely via the primary strand, but by binding simultaneously to both the primary and complementary strands, or even exclusively to the complementary strand. Without “help” from the complementary DNA strand, the binding of critical AA's to nucleotides of the primary DNA chain would be too weak, in the case of several triplets, to realize the recognition process. All possible AA replacements were tested for strength of interaction in the Z 1 -Z 3 positions. Domains with fewer than 2 hydrogen bonds on the primary strand were considered to be unstable.

Table 2 presents the ZF AA triplets having the highest affinity for interaction with corresponding DNA triplets. These ZF triplets contain only the main residues presented in Column A of Table 1. Table 2 also presents the binding energy components (H-bonds, water bridges, van der Waals interactions) maintaining the ZF-DNA recognition process in specific contact regions.

As can be seen from Table 2, the participation of the complementary DNA strand in the process of ZF binding, combined with the number of interactions (H-bonds, water bridges and van der Waals interactions) possible in the three contact regions, when optimal combinations are used, makes it possible to show that a complex formation with all 64 DNA triplets can be achieved. Table 2 shows that the maximal number of H-bonds, the strongest of the three types of interactions, is obtained when the first nucleotide of the triplet is guanine or adenine.

In nucleotide triplets wherein the number of H-bonds possible is less than maximal, the deficiency is often partially compensated by a significant amount of water-bridging between critical AA's and the sugar-phosphate backbone.

Even in cases wherein the first nucleotide of the triplet is thymine, and the number of the H-bonds is lowest, 1) the formation of two ES-bonds between the AA in the Z 3 position, and the adenine and complementary thymine in the third contact position, and 2) probably, a single H-bond between thymine and serine or threonine in the second contact position, means that even TTN triplets can bind a ZF protein with sufficient affinity.

In any event, to obtain DBP's of the greatest effectiveness, attention should be paid to having the strongest interactions in the flanking contact points (1 and 3). If weaker combinations must be used, they would have less effect if positioned in the center contact point (2). It is important to note, however, that even weak binding in the contact points is important for establishing specificity.

Table 3 presents the main ZF AA triplets of Table 2, as well as the alternative AA's (shown in Column B of Table 1) which would be also expected to provide effective binding to the respective bases of a given DNA triplet. Table 3 also presents the binding energy components (H-bonds, water bridges, van der Waals interactions) maintaining the ZF-DNA recognition process in specific contact regions.

TABLE 1-Z1
	Z1	Z1	Hydrogen	Water	Hydrophobic
Codon	Column A	Column B	Bonds	Contacts	Contacts
AAC	Q=	E*/R 1 -K 1 -N 1 =/D 1 */(H-/Y-/S-/T-)	6	0	0
AAG	Q=	E*/R-/K-	6	0	0
AAT	Q=	R-/K-/E*	6	0	0
ACC	Q=	E*/K 1 -	6	0	0
ACT	Q=	E-/R 1 -/K 1 -	6	0	0
GAA	R=	K-/H 1 -/Y 1 -/Q 1 -	6	0	0
GAC	R=	K-/H 1 -/Y 1 -	6	0	0
GAG	R=	H-/K-/Y-/Q-	6	0	0
GAT	R=	H-/K-/Y-/Q*	6	0	0
CCC	R=	H-/K-/Q-/N-/(Y-/S-/T-)	0	0
GCT	R=	H-/K-/Y-/Q-	6	0	0
ACA	Q=	R-/K-/N-/E-/D-	5	1	0
ACG	Q=	R-/K-/N-/E*/D-	5	1	0
AGA	Q=	E*/R 1 -/K 1 -	5	1	0
AGG	Q=	E*/R 1 -/K 1 -	5	1	0
CAA	E*	Q*/N 1 */D 1 */R 2 -/K 2 -/Y 2 -/S 2 -/T 2 -	5	1	0
CAG	E*	Q*/N*/D*/R 2 -/K 2 -	5	1	0
CAT	E*	Q*/R 2 -/K 2 -/(D*/N*/S-/T-/Y 2 -)	5	1	0
CCC	E*	Q*/N 1 */D 1 */R 2 =/K 2 -/Q 2 */N 2 *	5	1	0
CCT	E*	Q*/R 2 -/K 2 -	5	1	0
GCA	R=	K-/Q-/(H-/Y-/N-/S-/T-)	5	1	0
CCG	R=	H-/K-/Y-/Q-/N-/S-/T-	5	1	0
CGA	R=	H-/K-/Q*/N*/Y 1 -	5	1
AAA	R-/K-		5	0	0
AGC	Q=	R-/K-/E*	5	0	0
AGT	Q=	E*/R 1 -/K 1 -	5	0	0
GGG	R=	K-/Q*/(H-/Y-/N-)	5	0	0
GGG	R=	H-/K-/Y-/Q*N-)	5	0	0
GGT	R=	H-/K-/Y-/Q-/N-	5	0	0
CAC	E*	Q*/R 2 -/K 2 -	4	2	0
CCA	E*	Q*/R 2 -/K 2 -	4	2	0
CCG	E*	Q*/N*/D*/R 2 =/K 2 -	4	2	0
CGA	E*	Q*/N*/D*/R 2 =/K 2 -	4	2	0
CGC	E*	Q*/N*/D*/R 2 -/K 2 -/Y 2 -/Q 2 -/(S-/T-)	4	1	0
CGG	E*	Q*/N*/D*/R 2 -/K 2 -/Q 3 =	4	1	0
CGT	E*	Q*/D 1 */R 2 =/K 2 -/Q 2 -	4	1	0
CTA	E*	Q*	3	1	1
CTC	E*	Q*/N 1 -/D 1 -/R 2 =/K 2 -/Q 2 -/N 2 -	3	1	1
CTG	E*	Q*/N*/D*/R 2 -/K 2 -	3	1	1
CTT	E*	Q*/N*/D*/R 2 -/K 2 -/Q 3 =	3	1	1
TCA	I#/L#	R-/K-/Q*	3	1	1
TCG	I#/L#	R-/K-/Q*	3	1	1
TGA	I#/L#	R-/K-/Q*	3	1	1
TAC	I#/L#/V#	R-/K-/Q*	3	0	1
TGC	I#/L 1 #/V 1 #	R-/K-/H 1 -/Q 1 */N 1 */S 1 -/T 1 -	3	0	1
TCG	I#/L#	R-/K-/Q*	3	0	1
TGT	I#	R-/H-/K-/Q*/N*/L#	3	0	1
TTA	I#/L#	R-/K-/Q*/N*	2	0	2
TTC	I#/L#/V#	R-/K-/Q*/N*	2	0	2
TTG	I#/L#	R-/K-/Y-/Q*	2	0	2
TTT	I#/L#	R-/K-/Q*/N*/V 1 #	2	0	2
ATA	Q=	E*/R 1 -/K 1 -	4	0	1
ATC	Q=	N-/E*/D*/R 1 -/K 1 -	4	0	1
ATG	Q=	R-/K-/E-/(H-)	4	0	1
ATT	Q=	E*/R 1 -/K 1 -	4	0	1
GTA	R=	H-/K-/Y-/Q-	4	0	1
GTC	R=	H-/K-/Y-/Q*	4	0	1
GTG	R=	K-/Q-/H 1 -	4	0	1
GTT	R=	H-/K-/Q-/N-/Y 1 -	4	0	1
TAA	I#/L#	R-/K-/Q-/V 1 #	4	0	1
TAG	I#/L#	R-/K-/Q-	4	0	1
TAT	I#/L#/V#	R-/K-/Y-/Q-/N-	4	0	1
TCC	I#/L#	R-/H-/K-/Q*/N*/V#/A#	4	0	1
TCT	I 1 #/L 1 #	R-/H-(K-/Q*	4	0	1
where / separates alternative amino acids
where X without subscript has all its interactions with the primary strand
where X 1 has some interactions with the primary strand and some interactions with the complementary strand
where X 2 has interaction with the complementary strand
where X 3 has interactions with both the primary and complementary strands
where - is one hydrogen bond between the animo acid and the base
where = is two hydrogen bonds between the amino acid and the base
where is one hydrogen bond via a water bridge between the amino acid and the phosphodiester oxygen atom of the backbone
where # is one or more van der Waals contacts between the amino acid and the base
where amino acids in ( ) have interaction with the base of the primary strand where one of two other possible protein-DNA recognition interactions is absent

TABLE 1-Z2
CGC	H 1 -	Q*/N*/S-/T-/K 1 -/(R 1 =/Y-)	4	1	0
CGG	H-	K-/Q*/N*/R 1 -/(Y-)	4	1	0
CCT	H-	Q*/N*/R 1 -/K 1 -/(Y-)	4	1	0
ATA	I#/L#/V#/A#	S-/T-/K 1 -/Q 1 */N 1 */(R-/H-/Y-)	4	0	1
ATC	I#/L#	N*/S-/T-/V-/R 1 -/H 1 -/K 1 -/Y 1 -/Q 1 */R 2 -/K 2 -/Q 2 =/N 2 =/E 2 */D 2 *	4	0	1
ATG	I#/L#/V#	S-/T-/E 2 -/D 2 -/Q 3 =/N 2 =/(R-/H-/K-/Y-)	4	0	1
ATT	I#/L#/V#	R-/H-/K-/Y-/Q*/N*/S-/T-	4	0	1
GTA	I#/L#/V#/A#	Q*/N*/S-/T-/R 2 -/H 1 -/K 1 -/E 2 */D 2 */Q 3 =/N 3 =/(Y-)	4	0	1
GTC	I#/L#	N-/S-/T-/V-/R 1 -/H 1 -/K 1 -/Q 1 *	4	0	1
GTG	I#/L#/V#	Q*/N*/S-/T-/H 1 -/K 1 -	4	0	1
GTT	I#/L#/V#	Q*/N*/S-/T-/K 1 -/(R-/H-/Y-/A-)	4	0	1
TAA	N=	D*/R 1 -/H 1 -/K 1 -/Y 1 -/Q 1 =/E 1 -	4	0	1
TAG	N=	Q=/E*/D*/R 1 -/K 1 -/K 2 -	4	0	1
TAT	N=	K-/Q=/N=/E*/D*/S-/T-/H 2 -/H 2 -/K 2 -/Q 3 =/N 3 =/(R-/Y-)	4	0	1
TCC	Q 3 =/E*	Q*/N*/D*/S-/T-/R 2 -/H 2 -/K 2 /Y 2 -/Q 2 -/N 2 -	4	0	1
TCT	N 3 =/D*	Q*/N*/D*/S-/T-/R 2 -/H 2 -/K 2 /Y 2 -/Q 2 *	4	0	1
CTA	I#/L#/V#/A#	S-/T-/Q 1 =/N 1 =(H-/K-)	3	1	1
CTC	I#/L#	S-/T-/V-/R 1 -/H 1 -/K 1 -/Y 1 -/Q 1 */N 1 *	3	1	1
CTG	I#/L#/V#	N*/S-/T-/K 1 -/Q 1 *	3	1	1
CTT	I#/L#	Q*/N*/S-/T-/V#/R 1 -/H 1 -/K 1 -/E 2 -/D 2 -/Q 2 =/N 3 =/(Y-)	3	1	1
TCA	D*	Q*/N*/E*/S-/T-/R 2 =/H 2 -/K 2 -/Y 2 -/Q 3 =(N 2 =	3	1	1
TCG	D*	Q*/N*/E*/S-/T-/R 2 =/H 2 -/K 2 -/Y 2 -/S 2 -/T 2 -/Q 3 =(N 2 =	3	1	1
TGA	N*	Q*/S-/T-/H 1 -/K 1 -/(R-/Y-)	3	1	1
TAC	N=	D-/H 1 -/K 1 -/Q 1 =/E 1 */k 2 /(R-/Y-)	3	0	1
TGC	H 1 -	Q*/N*/S-/T-/R 1 =/K 1 -/Y 1 -	3	0	1
TGG	H-	R-/K-/Q*/N*/Y 1 -	3	0	1
TGT	H 1 -	N*/S-/T-/K 1 -/Y 1 -/Q 1 */(R=)	3	0	1
TTA	I#/L#/V#/A#	S-/T-/R 1 -/H 1 /K 1 -/Y 1 -/E 2 -/D 2 -/Q 3 =/N 3 =	2	0	2
TTC	I#/L#	N*/S-/T-V-/A-/R 1 /H 1 -/K 1 -/Y 1 -/K 2 -/Q 3 =/N 3 =	2	0	2
TTG	I#/L#/V#	N*/S-/T-/H 1 -/K 1 -/Q 1 *	2	0	2
TTT	I#/L#/V#	Q*/N*/S-/T-/A-/H 1 -/K 1 -/(R-/Y-)	2	0	2
AAC	Q 1 =	N=/D*/S-/T-/R 1 -/K 1 -/E 1 */(H-/Y-)	6	0	0
AAG	Q=/N=	R-/H-/K-/E*/D*/K 2 0	6	0	0
AAT	N=	K-/Q=/E*/D*/R 1 -/H Q -/K 2 -/Q 3 =/N 3 =	6	0	0
ACC	Q 3 =/E*	D*/S-/T-/N 3 =/(K 2 -)	6	0	0
ACT	N 3 =/D*	Q*/N*/E*/S-/T-/K 2 -/Q 3 =	6	0	0
GAA	N=	D*/R 1 -/H 1 -/K 1 -/Y 1 /Q 1 =/E 1 */K 2 -	6	0	0
GAC	N=	D*/R 1 -/H 1 -/K 1 -/Y 1 /Q 1 =/E 1 */K 2 -	6	0	0
GAG	N=	Q=/E*/D*/R 1 -/H 1 -/K 1 -/7 1 -/K 2 -	6	0	0
GAT	Q=/N=	K-/E*/D*/K 2 -/(R-/H-/Y-)	6	0	0
GCC	Q 3 =/E*	Q*/N*/D*/S-/T-R 2 /H 2 -/K 2 -/Q 2 -/N 2 -/S 2 -/T 2 -	6	0	0
GCT	N 3 =/D*	Q-/N-/E-/S-/T-/H 2 -/K 2 -/N 2 */Q 3 =/(R 2 =/Y 2 -)	6	0	0
ACA	D*	Q*/N*/E*/S-/T-K 2 -	5	1	0
ACG	E*/D*	Q*/N*/S-/T-/R 2 -/H 2 /K 2 -/Y 2 -/Q 3 =/N 3 =	5	1	0
AGA	N*	R 1 -/H 1 -/K 1 -/Y 1 -/Q 1 *	5	1	0
AGG	Q*/N*	R 1 */H 1 */K 1 -	5	1	0
CAA	N=	D*/S-/T-/R 1 -/H 1 -/K 1 -/Y 1 -/Q 1 =/E 1 *	5	1	0
CAG	Q=	N=/E*/D*/R 1 -/K 1 -/K 2 -/Q 3 =	5	1	0
CAT	Q 1 =/N=	D-/S-/T-/R 1 -/H 1 -/K 1 -/Y 1 -/E 1 =/K 2 -/Q 3 =N 3 =	5	1	0
CCC	Q 2 =/E 1 *	N*/D*/S-/T-/H 2 -/K 2 -/N 3 =/(Y 2 -)	5	1	0
CCT	N 3 =/D*	Q*/N*/E*/S-/T-/H 2 -/K 2 -/Y A -/Q 3 =/N 2 =	5	1	0
GCA	D*	Q*/N*/E*/S-/T-/R 2 -/H 2 -/K 2 -/Y 2 -/Q 3 =/N 3 =	5	1	0
GCG	E*/D*	Q*/N*/S-/T-/K 2 -/Q 3 =/N 3 =/(H 2 -)	5	1	0
GGA	N*	Q*/S-/T-/K 1 -/(R-/Y-/H-)	5	1	0
AAA	N=	D*/R 1 /H 1 /K 1 /Y 1 /Q 1 =/E 1 *	5	0	0
AGC	H 1 -	Q*/N*/S-/T-/R 1 -/K 1 -/(R=/Y-)	5	0	0
AGT	H 1 -	Q*/N*/S-/T-/R 1 -/K 1 -	5	0	0
GGC	H 1 -	N*/S-/T-/K 1 -/(R-/K-/7-/Q*)	5	0	0
GGG	H-	K-/Q*/N*/S-/T-/Y 1 -/(R-)	5	0	0
GGT	H-	Q*/N*/S-/T-/R 1 -/K 1 -	5	0	0
CAC	N=	D*/R 1 -/K 1 -/Q 1 =/E 1 *	4	2	0
CCA	D*	N*/S-/T-/Q 1 */E 1 */K 2 -/N 3 =	4	2	0
CCG	D*	Q*/N*/E*/S-/T-/K 2 -/Q 3 =/N 3 /(R-/H-/Y-)	4	2	0
CGA	N*	Q*/S-/T-/R 1 =/H 1 -/K 1 -/(Y-)	4	2	0
where / separates alternative amino acids
where X without subscript has all its interactions with the primary strand
where X 1 has some interactions with the primary strand and some interactions with the complementary strand
where X 2 has interaction with the complementary strand
where X 3 has interactions with both the primary and complementary strands
where - is one hydrogen bond between the animo acid and the base
where = is two hydrogen bonds between the amino acid and the base
where is one hydrogen bond via a water bridge between the amino acid and the phosphodiester oxygen atom of the backbone
where # is one or more van der Waals contacts between the amino acid and the base
where amino acids in ( ) have interaction with the base of the primary strand where one of two other possible protein-DNA recognition interactions is absent

TABLE 1-Z3
	Z3	Z3	Hydrogen	Water	Hydrophobic
Codon	Column A	Column B	Bonds	Contacts	Contacts
AAC	Q=	E*/R 1 -K 1 -N 1 =/D 1 */(H-/Y-/S-/T-)	6	0	0
AAG	Q=	E*/R-/K-	6	0	0
AAT	Q=	R-/K-/E*	6	0	0
ACC	Q=	E*/K 1 -	6	0	0
ACT	Q=	E-/R 1 -/K 1 -	6	0	0
GAA	R=	K-/H 1 -/Y 1 -/Q 1 -	6	0	0
GAC	R=	K-/H 1 -/Y 1 -	6	0	0
GAG	R=	H-/K-/Y-/Q-	6	0	0
GAT	R=	H-/K-/Y-/Q*	6	0	0
CCC	R=	H-/K-/Q-/N-/(Y-/S-/T-)	0	0
GCT	R=	H-/K-/Y-/Q-	6	0	0
ACA	Q=	R-/K-/N-/E-/D-	5	1	0
ACG	Q=	R-/K-/N-/E*/D-	5	1	0
AGA	Q=	E*/R 1 -/K 1 -	5	1	0
AGG	Q=	E*/R 1 -/K 1 -	5	1	0
CAA	E*	Q*/N 1 */D 1 */R 2 -/K 2 -/Y 2 -/S 2 -/T 2 -	5	1	0
CAG	E*	Q*/N*/D*/R 2 -/K 2 -	5	1	0
CAT	E*	Q*/R 2 -/K 2 -/(D*/N*/S-/T-/Y 2 -)	5	1	0
CCC	E*	Q*/N 1 */D 1 */R 2 =/K 2 -/Q 2 */N 2 *	5	1	0
CCT	E*	Q*/R 2 -/K 2 -	5	1	0
GCA	R=	K-/Q-/(H-/Y-/N-/S-/T-)	5	1	0
CCG	R=	H-/K-/Y-/Q-/N-/S-/T-	5	1	0
CGA	R=	H-/K-/Q*/N*/Y 1 -	5	1
AAA	R-/K-		5	0	0
AGC	Q=	R-/K-/E*	5	0	0
AGT	Q=	E*/R 1 -/K 1 -	5	0	0
GGG	R=	K-/Q*/(H-/Y-/N-)	5	0	0
GGG	R=	H-/K-/Y-/Q*N-)	5	0	0
GGT	R=	H-/K-/Y-/Q-/N-	5	0	0
CAC	E*	Q*/R 2 -/K 2 -	4	2	0
CCA	E*	Q*/R 2 -/K 2 -	4	2	0
CCG	E*	Q*/N*/D*/R 2 =/K 2 -	4	2	0
CGA	E*	Q*/N*/D*/R 2 =/K 2 -	4	2	0
CGC	E*	Q*/N*/D*/R 2 -/K 2 -/Y 2 -/Q 2 -/(S-/T-)	4	1	0
CGG	E*	Q*/N*/D*/R 2 -/K 2 -/Q 3 =	4	1	0
CGT	E*	Q*/D 1 */R 2 =/K 2 -/Q 2 -	4	1	0
CTA	E*	Q*	3	1	1
CTC	E*	Q*/N 1 -/D 1 -/R 2 =/K 2 -/Q 2 -/N 2 -	3	1	1
CTG	E*	Q*/N*/D*/R 2 -/K 2 -	3	1	1
CTT	E*	Q*/N*/D*/R 2 -/K 2 -/Q 3 =	3	1	1
TCA	I#/L#	R-/K-/Q*	3	1	1
TCG	I#/L#	R-/K-/Q*	3	1	1
TGA	I#/L#	R-/K-/Q*	3	1	1
TAC	I#/L#/V#	R-/K-/Q*	3	0	1
TGC	I#/L 1 #/V 1 #	R-/K-/H 1 -/Q 1 */N 1 */S 1 -/T 1 -	3	0	1
TCG	I#/L#	R-/K-/Q*	3	0	1
TGT	I#	R-/H-/K-/Q*/N*/L#	3	0	1
TTA	I#/L#	R-/K-/Q*/N*	2	0	2
TTC	I#/L#/V#	R-/K-/Q*/N*	2	0	2
TTG	I#/L#	R-/K-/Y-/Q*	2	0	2
TTT	I#/L#	R-/K-/Q*/N*/V 1 #	2	0	2
ATA	Q=	E*/R 1 -/K 1 -	4	0	1
ATC	Q=	N-/E*/D*/R 1 -/K 1 -	4	0	1
ATG	Q=	R-/K-/E-/(H-)	4	0	1
ATT	Q=	E*/R 1 -/K 1 -	4	0	1
GTA	R=	H-/K-/Y-/Q-	4	0	1
GTC	R=	H-/K-/Y-/Q*	4	0	1
GTG	R=	K-/Q-/H 1 -	4	0	1
GTT	R=	H-/K-/Q-/N-/Y 1 -	4	0	1
TAA	I#/L#	R-/K-/Q-/V 1 #	4	0	1
TAG	I#/L#	R-/K-/Q-	4	0	1
TAT	I#/L#/V#	R-/K-/Y-/Q-/N-	4	0	1
TCC	I#/L#	R-/H-/K-/Q*/N*/V#/A#	4	0	1
TCT	I 1 #/L 1 #	R-/H-(K-/Q*	4	0	1
where / separates alternative amino acids
where X without subscript has all its interactions with the primary strand
where X 1 has some interactions with the primary strand and some interactions with the complementary strand
where X 2 has interaction with the complementary strand
where X 3 has interactions with both the primary and complementary strands
where - is one hydrogen bond between the animo acid and the base
where = is two hydrogen bonds between the amino acid and the base
where is one hydrogen bond via a water bridge between the amino acid and the phosphodiester oxygen atom of the backbone
where # is one or more van der Waals contacts between the amino acid and the base
where amino acids in ( ) have interaction with the base of the primary strand where one of two other possible protein-DNA recognition interactions is absent

TABLE 2
	Z1	Z2	Z3	Hydrogen	Water	Hydrophobic
Codon	Column A	Column A	Column A	Bonds	Contacts	Contacts
AAC	Q	Q	R	6	0	0
AAG	Q	N/Q	R	6	0	0
AAT	Q	N	Q	6	0	0
ACC	Q	E/Q	R	6	0	0
ACT	Q	D/N	Q	6	0	0
GAA	R	N	Q	6	0	0
GAC	R	N	E/Q	6	0	0
GAG	R	N	R	6	0	0
GAT	R	N/Q	Q	6	0	0
GCC	R	E/Q	R	6	0	0
GCT	R	D/N	Q	6	0	0
ACA	Q	D	Q	5	1	0
ACG	Q	D/E	R	5	1	0
AGA	Q	N	Q	5	1	0
AGG	Q	N/Q	R	5	1	0
CAA	E	N	Q	5	1	0
CAG	E	Q	R	5	1	0
CAT	E	N/Q	N/Q	5	1	0
CCC	E	E/Q	R	5	1	0
CCT	E	D/N	Q	5	1	0
GCA	R	D	Q	5	1	0
GCG	R	D/E	R	5	1	0
GGA	R	N	Q	5	1	0
AAA	K/R	N	Q	5	0	0
AGC	Q	H	R	5	0	0
AGT	Q	H	Q	5	0	0
GGC	R	H	R	5	0	0
GGG	R	H	R	5	0	0
GGT	R	H	N/Q	5	0	0
CAC	E	N	E	4	2	0
CCA	E	D	Q	4	2	0
CCG	E	D	R	4	2	0
CGA	E	N	Q	4	2	0
CGC	E	H	R	4	1	0
CGG	E	H	R	4	1	0
CGT	E	H	N/Q	4	1	0
ATA	Q	A/I/L/V	Q	4	0	1
ATC	Q	I/L	E/R	4	0	1
ATG	Q	I/L/V	R	4	0	1
ATT	Q	I/L/V	Q	4	0	1
GTA	R	A/I/L/V	Q	4	0	1
GTC	R	I/L	E/R	4	0	1
GTG	R	I/L/V	R	4	0	1
GTT	R	I/L/V	Q	4	0	1
TAA	I/L	N	Q	4	0	1
TAG	I/L	N	R	4	0	1
TAT	I/L/V	N	Q	4	0	1
TCC	I/L	E/Q	R	4	0	1
TCT	I/L	D/N	N/Q	4	0	1
CTA	E	A/I/L/V	Q	3	1	1
CTC	E	I/L	E/R	3	1	1
CTG	E	I/L/V	R	3	1	1
CTT	E	I/L	Q	3	1	1
TCA	I/L	D	Q	3	1	1
TCG	I/L	D	R	3	1	1
TGA	I/L	N	Q	3	1	1
TAC	I/L/V	N	E	3	0	1
TGC	I/L/V	H	R	3	0	1
TGG	I/L	H	R	3	0	1
TGT	I	H	Q	3	0	1
TTA	I/L	A/I/L/V	Q	2	0	2
TTC	I/L/V	I/L	E/R	2	0	2
TTG	I/L	I/L/V	R	2	0	2
TTT	I/L	I/L/V	Q	2	0	2
where / separates alternative amino acids

TABLE 3
	Z1		Z2		Z3		Hydro-	Water	Hydro-
Co-	Column	Z1	Column	Z2	Column	Z3	gen	Con-	phobic
don	A	Column B	A	Column B	A	Column B	Bonds	tacts	Contacts
AAC	Q	D/E/H/K/N/R/S/T/Y	Q	D/E/H/K/N/R/S/T/Y	R	D/E/H/K/N/Q/Y	6	0	0
AAG	Q	E/K/R	N/Q	D/E/H/K/R	R	D/E/H/K/N/Q/S/T/Y	6	0	0
AAT	Q	E/K/R	N	D/E/H/K/N/Q/R	Q	D/E/H/K/N/Q/R/Y	6	0	0
ACC	Q	E/K	E/Q	D/K/N/S/T	R	E/K/N/Q/S/T	6	0	0
ACT	Q	E/K/R	D/N	E/K/N/Q/S/T	Q	D/E/H/K/N/Q/R/Y	6	0	0
GAA	R	H/K/Q/Y	N	D/E/H/K/Q/R/Y	Q	E/H/K/Q/R/Y	6	0	0
GAC	R	H/K/Y	N	D/E/H/K/Q/R/Y	E/Q	H/K/N/Q/R/S/T/Y	6	0	0
GAG	R	H/K/Q/Y	N	D/E/H/K/Q/R/Y	R	D/E/K/N/Q/S/T	6	0	0
GAT	R	H/K/Q/Y	N/Q	D/E/H/K/R/Y	Q	D/E/H/I/K/N/Q/R/Y	6	0	0
GCC	R	H/K/N/Q/S/T/Y	E/Q	D/H/K/N/Q/R/S/T	R	D/E/H/K/N/Q/S/T/Y	6	0	0
GCT	R	H/K/Q/Y	D/N	E/H/K/N/Q/R/S/T/Y	Q	D/E/H/K/N/Q/R/S/T/Y	6	0	0
ACA	Q	D/E/K/N/R	D	E/K/N/Q/S/T	o	D/E/H/I/K/L/N/Q/R/S/T/V/Y	5	1	0
ACG	Q	D/E/K/N/R	D/E	H/K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/S/T/Y	5	1	0
AGA	Q	E/K/R	N	H/K/Q/R/Y	Q	A/E/H/I/K/L/N/Q/R/V/Y	5	1	0
AGG	Q	E/K/R	N/Q	H/K/R	R	D/E/K/N/Q/Y	5	1	0
CAA	E	D/K/N/Q/R/S/T/Y	N	DfE/H/K/Q/R/S/T/Y	Q	E/H/K/Q/R/Y	5	1	0
CAG	E	D/K/N/Q/R	Q	D/E/K/N/Q/R	R	D/E/H/K/N/Q/S/T/Y	5	1	0
CAT	E	D/K/N/Q/R/S/T/Y	N/Q	D/E/H/K/N/Q/R/S/T/Y	N/Q	D/E/H/K/Q/R/Y	5	1	0
CCC	E	D/K/N/Q/R	E/Q	D/H/K/N/S/T/Y	R	E/H/KfN/Q/S/T/Y	5	1	0
CCT	E	K/Q/R	D/N	E/H/K/N/Q/S/T	Q	E/H/K/N/Q/R/S/T/Y	5	1	0
GCA	R	H/K/N/Q/S/T/Y	D	E/H/K/N/Q/R/S/T/Y	Q	A/E/H/I/K/L/N/Q/R/S/T/V/Y	5	1	0
GCG	R	H/K/N/Q/S/T/Y	D/E	H/K/N/Q/S/T	R	D/E/H/K/N/Q/S/T/Y	5	1	0
GGA	R	H/K/N/Q/Y	N	H/K/Q/R/S/T/Y	Q	A/D/E/H/I/K/L/N/Q/R/V/Y	5	1	0
AAA	K/R		N	D/E/H/K/Q/R/Y	Q	D/E/H/I/K/L/N/Q/R/Y	5	0	0
AGC	Q	E/K/R	H	K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/Y	5	0	0
AGT	Q	E/K/R	H	K/N/Q/R/S/T	Q	D/E/H/I/K/L/N/Q/R/S/T/Y	5	0	0
GGC	R	H/K/N/Q/Y	H	K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/S/T/Y	5	0	0
GGG	R	H/K/N/Q/Y	H	K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/S/T/Y	5	0	0
GGT	R	H/K/N/Q/Y	H	K/N/Q/R/S/T	N/Q	D/E/K/N/Q/R/S/T	5	0	0
CAC	E	K/Q/R	N	D/E/K/Q/R	E	H/K/Q/R/Y	4	2	0
CCA	E	K/Q/R	D	E/K/N/Q/S/T	Q	A/E/H/I/K/L/N/Q/R/S/T/V/Y	4	2	0
CCG	E	D/K/N/Q/R	D	E/H/K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q	4	2	0
CGA	E	D/K/N/Q/R	N	H/K/Q/R/S/T/Y	Q	A/D/E/H/I/K/L/N/Q/R/S/T/V/Y	4	2	0
CGC	E	D/K/N/Q/R/S/T/Y	H	K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/Y	4	1	0
CGG	E	D/K/N/Q/R	H	K/N/Q/R/Y	R	D/E/H/K/N/Q/S/T/Y	4	1	0
CGT	E	D/K/Q/R	H	K/N/Q/R/Y	N/Q	D/E/H/K/N/Q/R/Y	4	1	0
ATA	Q	E/K/R	A/I/L/V	H/K/N/Q/R/S/T/Y	Q	E/H/I/K/L/O/R/V/Y	4	0	1
ATC	Q	D/E/K/N/R	I/L	D/E/H/K/N/Q/R/S/T/V/Y	E/R	H/K/N/Q/R/Y	4	0	1
ATG	Q	E/H/K/R	I/L/V	D/E/H/K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/Y	4	0	1
ATT	Q	E/K/R	I/L/V	H/K/N/Q/R/S/T/Y	Q	D/E/H/K/N/Q/R/S/T/Y	4	0	1
GTA	R	H/K/Q/Y	A/I/L/V	D/E/H/K/N/Q/R/S/T/Y	Q	A/D/E/H/I/K/L/N/Q/R/S/T/V/Y	4	0	1
GTC	R	H/K/Q/Y	I/L	H/K/N/Q/R/S/T/V	E/R	H/K/N/Q/S/T/Y	4	0	1
GTG	R	H/K/Q	E/L/V	H/K/N/Q/S/T	R	D/E/H/K/N/Q/S/T/Y	4	0	1
GTT	R	H/K/N/Q/Y	I/L/V	A/H/K/N/Q/R/S/T/Y	Q	D/E/H/I/K/L/N/Q/R/V/Y	4	0	1
TAA	I/L	K/O/R/V	N	D/E/H/K/Q/R/Y	Q	A/E/H/I/K/L/Q/R/V/Y	4	0	1
TAG	I/L	K/Q/R	N	D/E/K/Q/R	R	D/E/H/K/N/O/Y	4	0	1
TAT	E/L/V	K/N/Q/R/Y	N	D/E/H/K/N/Q/R/S/T/Y	Q	D/E/H/I/K/L/N/O/R/S/T/V/Y	4	0	1
TCC	E/L	A/H/*K/N/Q/R/V	E/Q	D/H/K/N/Q/R/S/T/Y	R	E/H/K/N/Q/S/T/Y	4	0	1
TCT	I/L	H(K/Q/R	D/N	E/H/K/N/Q/R/S/T/Y	N/Q	D/E/H/K/Q/R/Y	4	0	1
CTA	E	Q	A/I/L/V	H/K/N/Q/S/T	Q	A/E/I/K/L/N/Q/R/S/T/V	3	1	1
CTC	E	D/K/N/Q/R	I/L	H/K/N/Q/R/S/T/V/Y	E/R	D/H/*K/N/Q/Y	3	1	1
CTG	E	D/K/N/Q/R	I/L/V	K/N/Q/S/T	R	D/E/K/N/Q/Y	3	1	1
CTT	E	D/K/N/Q/R	I/L	D/E/H/K/N/Q/R/S/T/V/Y	Q	D/E/H/K/N/Q/R/Y	3	1	1
TCA	I/L	K/Q/R	D	E/H/K/N/Q/R/S/T/Y	Q	A/E/H/I/K/L/N/Q/R/S/T/V/Y	3	1	1
TCG	E/L	K/O/R	D	E/H/K/N/Q/R/S/T/Y	R	D/E/H/K/N/Q/S/T/Y	3	1	1
TGA	E/L	K(Q/R	N	H/K/Q/R/S/T/Y	Q	D/E/H/K/N1O/R/Y	3	1	1
TAC	I/L/V	K/Q/R	N	D/E/H/K/Q/R/Y	E	H/K/N/Q/R/Y	3	0	1
TGC	E/L/V	H/K/N/Q/R/S/T	H	K/N/Q/R/S/T/Y	R	D/E/H/K/N/O/Y	3	0	1
TGG	I/L	K/Q/R	H	K/N/Q/R/Y	R	D/E/H/K/N/Q/S/T/Y	3	0	1
TGT	I	H/K/L/N/Q/R	H	K/N/Q/R/S/T/Y	Q	E/H/E/K/L/N/Q/R/Y	3	0	1
TTA	I/L	K/N/Q/R	A/I/L/V	D/E/H/K/N/O/R/S/T/Y	Q	A/E/H/I/K/L/N/R/S/T/V/Y	2	0	2
TTC	E/L/V	K/N/Q/R	I/L	A/H/K/N/Q/R/S/T/V/Y	E/R	D/H/K/N/Q/S/T/Y	2	0	2
TTG	I/L	K/Q/R/Y	I/L/V	H/K/N/Q/S/T	R	D/E/H/K/N/Q/Y	2	0	2
TTT	I/L	K/N/Q/R/V	I/L/V	A/H/K/N/Q/R/S/T/Y	Q	D/E/H/K/N/Q/R/Y	2	0	2
where / separates alternative amino acids

The results of the molecular modeling analysis of various ZF a-helix complexes with the 64 different DNA triplets (Tables 1, 2 and 3), and the findings of spatial peculiarities in the three contact positions, are reflected in the ZF-DNA recognition rules. On the basis of the rules set forth in Tables 1, 2 and 3, DBP's with optimal binding affinity for any target DNA sequence can be designed. The “Column A” designations, i.e., the “A Rules,” in Tables 1-3, show the amino acids with optimal binding for a given codon (triplet). The “Column B” designations, i.e., the “B rules,” in Tables 1 and 3, show the amino acids with secondary, but still significant, binding affinity for a given triplet.

The column A rules range from the strongest triplet recognition with six H-bonds, zero water contracts and zero hydrophobic contacts with an evaluated energy of (5×6)+(2×0)+(×0)=30 to two hydrogen bonds, zero water contacts and two hydrophobic contacts with an evaluated energy of (5×2)+(2×0)+(1×2)=12. The Column A rules ordinarily have a choice of just one or two amino acids in positions Z 1 , Z 2 and Z 3 . The column B rules, by comparison, have from three possible amino acids in each of the Z 1 , Z 2 and Z 3 positions to as many as eighteen amino acids in different contacting arrangements in each of the Z 1 , Z 2 and Z 3 positions. In the evaluation of the column B energies, there are a large number different groupings of three amino acids in positions Z 1 , Z 2 and Z 3 . The minimum energy is three hydrogen bonds, zero water contacts and zero hydrophobic contacts with an evaluated energy of (5×3)+(2×0)+(1×0)=15. The maximum energy evaluation for these combinations is, on average, three hydrogen bonds and either two water contacts or two hydrophobic contacts, with an evaluated energy of from (5×3)+(2×2)+(1×0)=19 down to (5×3)+(2×0)+(1×2)=17. Thus, the column B rules have a narrower energy range (i.e., from 19 down to 15) than do the column A rules, which have an energy range from 30 down to 12. The narrow energy range for the column B rules means that the 64 different rules do not distinguish on the basis of energy as well as the 64 column A rules.

For example, as set forth in Table 2, a DBP which binds optimally to the DNA base triplet guanine-cytosine-cytosine (GCC) is one wherein the portion of the protein responsible for the binding to the triplet is a ZF domain within which is contained a segment having the sequence Z 3 XXZ 2 LXZ 1 H (SEQ ID NO: 2), wherein Z 1 is an arginine which interacts with position 1 of the DNA triplet; Z 2 is a glutamine or a glutamic acid which interacts with position 2 of the DNA triplet; Z 3 is an arginine which interacts with position 3 of the DNA triplet; X is an arbitrary amino acid; L is leucine and H is histidine.

As set forth in Table 1 or 3 (see the “column B” entries for the Z 1 , Z 2 , and Z 3 positions for a given codon), a DBP which effectively, if not optimally, binds to the DNA base triplet guanine-cytosine-cytosine (GCC) is one wherein the portion of the protein responsible for the binding to the triplet is a ZF domain within which is contained a segment having the sequence Z 3 XXZ 2 LXZ 1 H (SEQ ID NO: 2), wherein Z 1 is an amino acid selected from the group consisting of histidine, lysine, glutamine, asparagine, tyrosine, serine and threonine which interacts with position 1 of the DNA triplet; Z 2 is an amino acid selected from the group consisting of glutamine, asparagine, aspartic acid, serine, threonine, arginine, histidine, and lysine which interacts with position 2 of the DNA triplet; Z 3 is an amino acid selected from the group consisting of glutamine, asparagine, glutamic acid, aspartic acid, histidine, lysine, tyrosine, serine and threonine which interacts with position 3 of the DNA triplet; X is an arbitrary amino acid; L is leucine and H is histidine.

It will be appreciated, of course, that DBP's of intermediate affinity, i.e., ones wherein the Z 1 , Z 2 and Z 3 contact amino acids are selected according to a combination of the “A” and “B Rules,” can be designed. For example, in the segment Z 3 XXZ 2 LXZ 1 H (SEQ ID NO: 2) within a ZF domain for binding to the triplet GCC, Z 1 could be an arginine; Z 2 could be a glutamnine or a glutamic acid; and Z 3 could be selected from the group consisting of glutamine, asparagine, glutamic acid, aspartic acid, histidine, lysine, tyrosine, serine and threonine.

The basic building block for such proteins is denoted by the formula:

NH 2 —ZiF c —COOH,

where ZiF c is a ZF domain of the form

Y/FXCX 2-4 CG/D K/RXFXZ 3 XXZ 2 LXZ 1 HX 3-5 H   (sites 1-20 of SEQ ID NO: 1),

where

Z 1 , Z 2 and Z 3 are amino acids chosen from Table 1, 2 or 3 to correspond to the three bases of the DNA triplet, and the remaining components of the formula are as described earlier in the description of Formula I.

In the preferred embodiment of the invention, a zinc-finger domain for binding to a given DNA triplet is designed by selection of the appropriate AA's in Table 2 or in column A of Table 1 or Table 3. In another embodiment of the invention, the ZF domain is designed by selection from among the AA's set forth for a given DNA triplet in column B of Table 1 or 3.

One such domain is required for each triplet of the target sequence; for a target string of only 3 bases, the above formula defines the protein.

If the target string of DNA is 6 bases, the DBP design is extended as follows:

NH 2 —ZiF 1 —{linker}—ZiF 2 —COOH

where ZiF 1 and ZiF 2 are ZF domains designed, as shown above for ZiFC, to bind to the first and second triplets of the six bases, and (linker) is an amino acid sequence conforming to the pattern

T/S G/E X 0-2 E K/R P   (sites 21-26 of SEQ ID NO: 1),

again wherein the components are as defined previously in Formula I.

If 1) the target string of DNA contains 9, 12, or a higher multiple of 3 bases; 2) it is required to design a DBP for 3n+3 bases; and 3) the DBP for the first 3n bases is given by the sequence:

NH 2 —ZiF 1 —{linker}—ZiF 2 —{linker}— . . . —{linker}—ZiFn—COOH

then the DBP design is extended recursively and the required DBP is specified by the sequence:

NH 2 —ZiF 1 —{linker}—ZiF 2 —{linker}— . . .

. . . —{linker}—ZiF n —{linker}—ZiF n+1 ——COOH

where ZiF n+1 is a ZF domain designed, as shown above for ZiFC, to bind with the n th +1 triplet of the target sequence of base pairs.

FIG. 3 provides a schematic representation of a ZF protein wherein n=3, i.e., one which has 3 ZF domains (i.e., n=3) connected by linker sequences and is designed to bind to a target DNA string of 9 (3n) bases.

The above rules enable ready determination of the optimal amino acid(s) for binding to any given DNA triplet and thus the identification and positioning of the 3 amino acids in a ZF domain which would be the ideal component of a DBP for binding to the DNA triplet.

The application of the rules can then be extended to design of a DBP containing a set number, n d , of ZF domains, which DPB binds to a target stretch of 3n d nucleotides within a given DNA sequence. The target 3n d stretch of nucleotides, and the collection and order of n d domains in the DBP, are such that the binding energy for the DPB and target DNA sequence is the highest possible for any pairing of a DBP containing the set number, n d , of ZF domains with any stretch of 3n d nucleotides within the entire DNA molecule being screened.

Accordingly, the embodiment of the invention of primary importance is a method for designing such a DBP for a DNA sequence of any length. The method employs the rules disclosed above in combination with a means of screening and ranking all possible segments of 3n d nucleotides within the sequence by their affinities for DBP's containing n d ZF domains to determine a unique DBP with the desired properties.

More particularly, the invention is directed to a method for designing a DBP, with multiple ZF domains connected by linker sequences, that binds selectively to a target DNA sequence within a given gene, each of said ZF domains having the formula

A 1 XCX 2-4 CA 2 A 3 XFXZ 3 XXZ 2 LXZ 1 HX 3-5 H   (SEQ ID NO: 3)

and each of said linkers having the formula

A 4 A 5 X 0-2 EA 6 P   (SEQ ID NO: 4),

wherein

(i) X is any amino acid; (ii) X 2-4 is a peptide from 2 to 4 amino acids in length; (iii) X 3-5 is a peptide from 3 to 5 amino acids in length; (iv) X 0-2 is a peptide from 0 to 2 amino acids in length; (iv) A 1 is selected from the group consisting of phenylalanine and tyrosine; (v) A 2 is selected from the group consisting of glycine and aspartic acid; (vi) A 3 is selected from the group consisting of lysine and arginine; (vii) A 4 is selected from the group consisting of threonine and serine; (viii) A 5 is selected from the group consisting glycine and glutamic acid; (ix) A 6 is selected from the group consisting of lysine and arginine; (x) C is cysteine; (xi) F is phenylalanine; (xii) L is leucine; (xiii) H is histidine; (xiv) E is glutamic acid; (xv) P is proline; and (xvi) Z 1 , Z 2 and Z 3 are the base-contacting amino acids, comprising the steps of:

(a) setting a genome to be screened;

(b) selecting the target DNA sequence in the genome for binding;

(c) setting the number of zinc-finger domains to n d ;

(d) dividing the target DNA sequence into nucleotide blocks wherein each block contains n z nucleotides using a first routine where n z is determined using the following relationship:

n z =3n d ;

(e) assigning base-contacting amino acids at Z 1 , Z 2 and Z 3 to each ZF domain, according to the A Rules and /or B Rules set forth in Tables 1-3, of a DBP which binds to the first nucleotide block from step (d) as numbered from the first 5′ nucleotide of the target gene sequence to generate a block-specific DBP and calculating the binding energy, Binding Energy block, of each ZF domain of each such block-specific DBP as the product of the binding energies, Binding Energy domain, of all zinc-finger domains of the polypeptide, each determined using the formula:

Binding Energy domain, =(5×the number of hydrogen bonds)+(2×the number of H 2 O contacts)+(the number of hydrophobic contacts);

(f) subdividing the DBP from step (d) into blocks using a second routine to generate a subdivided DBP having three ZF domains;

(g) screening the subdivided DBP from step (f) against the genome using a third routine to determine the number of binding sites in the genome for each subdivided DBP in the genome and assigning a binding energy for each such site using the following formula:

Binding Energy site n =(5×the number of hydrogen bonds)+(2×the number of H 2 O contacts)+(the number of hydrophobic contacts);

(h) calculating a ratio of binding energy, R b , using a fourth routine for each nucleotide-block-specific DBP from step (e) using the following formula:

R b =Binding Energy block /the sum of all Binding Energy site n 's for all subdivided DBP's from step (g);

(i) repeating steps (f) through (h) for each subdivided DBP wherein n d ≧4;

(j) repeating steps (d) through (i) for each nucleotide block in the target DNA sequence containing n z nucleotides;

(k) rank-ordering R b numerical values obtained from step (h); and

(l) selecting a DBP with an acceptable R b value.

Preferred embodiments of this aspect of the invention are:

1) the design method as set forth above wherein the DBP R b numerical value is the highest numerical value for all DBP's in step (h) that bind to the target DNA sequence.

2) the method above wherein the DBP R b numerical value determined in step (h) is at least 10,000.

3) the method above wherein the number of ZF domains, n d , is nine.

4) the method above wherein the rules for assigning base-contacting amino acids at Z 1 , Z 2 and Z 3 for each nucleotide block in step (e) are selected from rule set A.

The invention is further directed to a computer system for designing a DBP, with multiple ZF domains connected by linker sequences, that binds selectively to a target DNA sequence within a given gene, each of said ZF domains having the formula

A 1 XCX 2-4 CA 2 A 3 XFXZ 3 XXZ 2 LXZ 1 HX 3-5 H   (SEQ ID NO: 3)

and each of said linkers having the formula

A 4 A 5 X 0-2 EA 6 P   (SEQ ID NO: 4),

wherein

(i) X is any amino acid; (ii) X 2-4 is a peptide from 2 to 4 amino acids in length; (iii) X 3-5 is a peptide from 3 to 5 amino acids in length; (iv) X 0-2 is a peptide from 0 to 2 amino acids in length; (iv) A 1 is selected from the group consisting of phenylalanine and tyrosine; (v) A 2 is selected from the group consisting of glycine and aspartic acid; (vi) A 3 is selected from the group consisting of lysine and arginine; (vii) A 4 is selected from the group consisting of threonine and serine; (viii) A 5 is selected from the group consisting glycine and glutamic acid; (ix) A 6 is selected from the group consisting of lysine and arginine, (x) C is cysteine; (xi) F is phenylalanine; (xii) L is leucine; (xiii) H is histidine; (xiv) E is glutamic acid; (xv) P is proline; and (xvi) Z 1 , Z 2 and Z 3 are the base-contacting amino acids, comprising the steps of:

(a) setting a genome to be screened;

(b) selecting the target DNA sequence in the genome for binding;

(c) setting the number of ZF finger domains to n d ;

(d) dividing the target DNA sequence into nucleotide blocks wherein each block contains n z nucleotides using a first routine where n z is determined using the following relationship:

n z =3n d ;

(e) assigning base-contacting amino acids at Z 1 , Z 2 and Z 3 to each ZF domain, according to the A Rules and/or B Rules set forth in Tables 1-3, of a DBP which binds to the first nucleotide block from step (d) as numbered from the first 5′ nucleotide of the target gene sequence to generate a block-specific DBP and calculating the binding energy, Binding Energy block, of each ZF domain of each such block-specific DBP as the product of the binding energies, Binding Energy domain, of all domains of the DBP, each determined using the formula:

Binding Energy domain =(5×the number of hydrogen bonds)+(2×the number of H 2 O contacts)+(the number of hydrophobic contacts);

(f) subdividing the DBP from step (d) into blocks using a second routine to generate a subdivided DBP having three ZF domains;

(g) screening the subdivided DBP from step (f) against the genome using a third routine to determine the number of binding sites in the genome for each subdivided DBP in the genome and assigning a binding energy for each such site using the following formula:

Binding Energy site n =(5×the number of hydrogen bonds)+(2×the number of H 2 O contacts)+(the number of hydrophobic contacts);

(h) calculating a ratio of binding energy, R b , using a fourth routine for each nucleotide block-specific DBP from step (e) using the following formula:

R b =Binding Energy block /the sum of all Binding Energy site n 'S for all subdivided DBP's from step (g);

(i) repeating steps (f) through (h) for each subdivided DBP wherein n d ≧4;

(j) repeating steps (d) through (i) for each nucleotide block in the target DNA sequence containing n z nucleotides;

(k) rank-ordering R b numerical values obtained from step (h);

(l) selecting a DBP with an acceptable R b value.

According to the instant invention, R b , as defined in (h) above for both the design method and computer system, has a lower limit of 10,000. Preferably R b is greater than 10 6 .

Preferred embodiments of this aspect of the invention are:

1) the computer system as set forth above wherein the DBP R b numerical value is the highest numerical value for all DBP's in step (h) that bind to the target DNA sequence.

2) the computer system above wherein the DBP R b numerical value determined in step (h) is at least 10,000.

3) the computer system above wherein the number of ZF domains, n d , is nine.

4) the computer system above wherein the rules for assigning base-contacting amino acids at Z 1 , Z 2 and Z 3 for each nucleotide block in step (e) are selected from rule set A.

The method and computer system of the instant invention are further illustrated by the block flow diagrams of FIGS. 4-9 .

FIG. 4 shows the components of the computer system on which the DBP design process is implemented. A Central Processor Digital Computer (1) of any manufacture is provided with a Computer Program (2) written by the inventors. This Computer Program (2) reads a series of files described as DNA-Triple Energy Rules (6), Genome Descriptors (9), Genomic DNA Sequence (10) and Gene Features (5). The Central Processor (1) transforms this information into the DBP Blocking Fragment Files (7) and the Optimal DBP Designs for Genome (8).

FIG. 5 shows that the Computer Program (2) in FIG. 4 has two portions. The genomic data is first transformed by the Process Genome into Blocking Fragment Files function (2). These files are then used by the Design DBP's for a Genome function (3).

The Process Genome into Blocking Fragment Files block (2) of FIG. 5 is represented in greater detail in FIG. 6 . For every n d from 11 down to 3 the Genome Descriptors file (12) and the Genome DNA Sequence file (32) are read and transformed into the Unsorted Fragment File (7). This same Unsorted Fragment File (14) is transformed by the Sort function (13) provided by the computer manufacturer into the Sorted Fragment file (15). The same Sorted Fragment File (30) is read and transformed eventually into the DBP-Size Blocking File (22).

The Design DBP's for a Genome block (3) of FIG. 5 is represented in greater detail in FIG. 7 . The Genome Descriptors file (3), the Gene Features file (7), the Genome DNA Sequence file (9) and the DBP-Size Blocking Files (37) corresponding to the n d 's from 11 down to 3 are read and used to transform the genomic DNA first into genes and then into a file of the Optimal DBP Designs for a Genome (38). The transformation and design process is done for all the genes in a genome.

The “Determine if Current-Sub-Window is in Current-Blocking-File” block (22) in FIG. 7 is expanded in greater detail in FIG. 8 .

The “Calculate Binding-Energy-of-Blocking-Fragment” block (24) in FIG. 7 is expanded in greater detail in FIG. 9 .

By applying the algorithm to a variety of DBP's of varying n d , it was experimentally determined that a value for n d of 9 is the best starting point in the algorithm, i.e., the process should begin with the search for 9-finger DBP's. This can be better understood in terms of the selection criterion, R b , used in evaluating various DBP's. In short DBP's, e.g., ones wherein n d =4 or 5, Binding Energy block, which increases geometrically as the product of all Binding Energy domain 's, is significantly lower, and Binding Energy site n values are relatively large. However, as n d increases, the numerator of R b increases dramatically, while, it has been observed, the denominator, representing “background” or “noise,” does not significantly change. Thus, the case of n d =9 provides assurance of high affinity and specificity of binding without also bringing on the possibility of undue computational needs.

However, it should also be emphasized that the present invention is not limited to the design of DBP's wherein n d ≦9. For that matter, it will also be appreciated that, while n d =9 has been found to be the best starting point, the best DBP for a given situation may turn out to be one wherein n d <9, the length of the target DNA sequence notwithstanding. The concept of the invention can be applied to the design of DBP's of any length as required.

In any event, for a given DNA sequence of N nucleotides, there are N-27, 9-finger DBP sequences. Each of these can be ordered in terms of strength of binding by evaluating the energy function for each 3-nucleotide segment as set forth in part (e) of the design method disclosed above.

In initial computational experiments, a selectable sequence could have no 8, 7, 6, 5, and 4-finger subsites; however, with the present system, only the sum of the subsite binding energies need be minimized. As a result, it does not matter whether the subsite binding energy comes from 3-finger subsites, 4-finger subsites or even (in principle) larger subsites. This simple change from logical exclusion to energetic exclusion has been mandated not so much by examination of the yeast genome, but more by examination of the worm genome.

The central portion of the instant algorithm is, in the case of finding an acceptable n d -finger site (e.g., a 27-base segment for a 9-finger DBP), the search against all other n d -finger sites in the entire genome to see if there are any similar sites. If such turns out to be the case, the DBP with the highest R b value is selected. Furthermore, the algorithm checks to see if there are any equivalent 8-finger, 7-finger, 6-finger, 5-finger and 4-finger subsites in the whole genome for a given 9-finger site. In the event no acceptable 9-finger site is found, the algorithm then searches for a suitable 8-finger site. If necessary, the search is continued for a 7-finger site and so on, until an acceptable DBP binding site is found.

Within the search for a 9-finger DBP, the algorithm looks at all 27-base sequences, which are called “frames.” Each frame is evaluated to determine its interaction with DNA and the interaction of all other subframes down to 3-finger subsites. The number of instances of each frame and subframe in the genome has been recorded during the genome processing phase of the execution of the software. The sequence of the frame or subframe is evaluated as a product of the binding energy of each ZF. Each ZF domain recognizes three DNA bases. The underlying DNA sequence that a ZF recognizes determines how many hydrogen bonds, water contacts and hydrophobic contact exist between the ZF and the DNA.

The way the algorithm detects whether a given n,-base site occurs in other places in the genome is by looking in a B-tree for the site. The whole genome is processed for each of the n d -finger sites. The algorithm contains means for sorting and merging the myriad fragments and, in the end, there is produced an ordered list of all the blocking fragments for all the different finger sizes.

EXAMPLE 1

The following is given as an example of how the search for, and design of, a DBP is typically carried out. It involves screening for 9-finger DBP's (i.e., n d =9) to bind to a target DNA sequence of 100 nucleotides (i.e, N=100). The sequence is screened, beginning with position 1, for every 27-nucleotide sequence, i.e., 1-27, 2-28, 3-29 etc., in the entire 100-nucleotide sequence. Once this has been done, the 9-fingers are broken down into 3-finger sections, i.e., 1-3, 2-4, 3-5 etc. The algorithm scans and looks for relative strengths of binding. The idea is to maximize the ratio of DBP binding to subsite binding, R b , thus eliminating those 9-mers interacting with the greatest numbers of subsites.

The algorithm of the present invention was applied to the genomes of S. cerevisiae and C. elegans as illustrated by the following examples:

EXAMPLE 2

The algorithm has been applied to the screening of the yeast genome. Two chromosomes of yeast, containing 110 and 447 genes, respectively, have been processed. For each gene the algorithm selected the n d -finger sequence with the lowest sum of subsite binding energies. In yeast the number of 3-finger blocking fragments is almost maximal (i.e., 4 9 , versus 4 12 maximal). In the worm genome (see Example 3), the 3-finger blocking sequences are absolutely maximal. In yeast the 4-finger blocking sequences are large in number but the population of 5-finger blocking sequences is relatively small. In worm the 4-finger blocking sequences are larger in number than the 5-finger blocking sequences, but the latter are larger in number relative to yeast. In going in the future from worm to human, one can expect that the 4-finger blocking sequences might come close to saturation (i.e. close to 4 12 ) The algorithmic analysis was performed for 2 of the 16 chromosomes of yeast. The 557 cenes in the first two chromosomes seem to present a realistic picture of properties of all the chromosomes in the yeast genome. Sample calculations have been run on the whole yeast genome but these results are not different from those produced by calculating the properties of just two chromosomes' worth of genes. The results of the analysis of 100 yeast genes, typical of the findings throughout the analysis of the yeast genome, are presented in Table 4.

The power of the algorithm is further demonstrated in the results displayed in FIGS. 10-14 . The figures display results obtained for all 557 genes of the two yeast chromosomes on which the studies were focused.

The strength of each acceptable 9-finger DBP can be calculated. FIG. 10 shows that the strengths of binding of all the acceptable 9-finger DBP's are uniformly distributed. If this curve were bowed down, then the stronger frames would be more preferred. If this curve were bowed up, then the weaker frames would be preferred.

FIG. 11 shows that the binding energies (Binding Energy block 's) of the acceptable 9-finger DBP's are uniformly distributed between 10 11 and 10 13 binding units.

FIG. 12 shows that the distribution of the sum of the spurious subsite binding energies (Binding Energy site 's) is itself uniform in the range of 10 6 to 10 8 binding units.

FIG. 13 is a nonlogarithmic version of FIG. 12 . It shows that most of the acceptable 9-finger DBP's have spurious subsite binding energies of less than 5×10 6 .

FIG. 14 , produced by taking the ratios of the FIG. 11 values to those of FIG. 12 , is a graph of the R b 's for the 9-finger DBP's. This chart shows that the ratio of the DBP binding strength of the acceptable 9-finger DBP's to the sum of the binding energies of the spurious subsite interactions varies from 10 4 to 10 6 .

The analytical tools of the present invention were also employed in the further analysis of a single yeast gene, YAR073, in particular the 300-bp region of the promoter immediately upstream of the coding region. The full sums of the subsite binding energies (SBE's) for each 27-base frame in this portion of the gene were determined; the results are depicted graphically in FIG. 15 . The primary binding energies (BE's) were also determined, and a correlation was found between the SBE values and the values of the ratios of BE:SBE (R b ). Still further (FIG. 16 ), it was seen that the peaks of the plot of the R b values correspond to the footprints of the transcription factors of the same gene (determined in a separate study).

EXAMPLE 3

Application of the algorithm according to the instant invention to 100 genes in C. elegans showed that the system can be applied as successfully to C. elegans as to S. cerevisiae . The results of analysis of the 100 C. elegans genes are presented in Table 5.

In FIG. 17 , it can be seen that, for one of the analyzed C. elegans genes, only a 5-finger DBP could be designed. For another gene, only a 7-finger DBP could be designed. These two genes, 2 and 32, are not seen in Table 5, since it presents results of the analysis only for those genes (98 out of 100) for which a 9-mer could be designed. In any event, the results depicted in FIG. 17 are in keeping with the expectation for analysis of the entire C. elegans genome namely, that the distribution of 5- through 9-finger DBP's is somewhat different than in S. cerevisiae.

FIG. 18 represents the same analysis for the C. elegans genes as was depicted in FIG. 14 for S. cerevisiae genes. FIG. 18 shows a similar R b value distribution to that seen in FIG. 14 .

Examples 2 and 3 demonstrate the applicability of the instant invention to the design of DBP's for the genomes of two widely disparate organisms. The various results of the application of the algorithm to the yeast genome, in particular, and also to the worm genome, show the power of the algorithmic tool and demonstrate its foundation in reality, i.e., that it does not merely provide a random and/or theoretical analysis. It is to be expected, on the basis of these analyses, that the inventive algorithm can be extended to the design of DBP's for any desired segment of the genome of any organism of interest, including that of a human.

Although the instant algorithm involves a search against the entire genome of an organism, the results of the present studies strongly indicate that lack of complete knowledge of the genome of a given organism would not constitute an impediment to application of the present invention to the design of DBP's for that organism. One would expect to be able to use the knowledge of block sequences obtained in the studies presented herein on S. cerevisiae (a unicellular organism) and C. elegans (a multicellular organism) to form valid estimates of allowable sequences for the systems of higher eukaryotes.

For example, the present studies on yeast and worm indicate that the genomic “noise,” in this context the spurious binding site energies, is relatively constant, and this can be projected to higher, more complex organisms as well. In other words, one would expect from the demonstrated combinatorics of DNA sequences to be able to extrapolate, or extend, the present algorithm to the analysis of more complex genomes, however much is known of the specific sequences therein, with the object of designing effective DBP's. Furthermore, as the entire genomes of larger organisms, e.g., D. melanogaster , become known, they will provide further keys to the analysis of the genomes of higher organisms, including humans.

A DBP as specified above may be built by using standard protein synthesis techniques; or, employing the standard genetic code, may be used as the basis for specifying and constructing a gene whose expression is the DBP.

Proteins so designed can be used in any application requiring accurate and tight binding to a DNA target sequence. For example, a DBP, according to the instant invention, can be coupled with a DNA endonuclease activity. When the resultant molecule binds to the target DNA, said DNA can be cut at a fixed displacement from the DBP binding site.

Similarly, in instances in which the target DNA sequence is a promoter, one can produce a promoter-specific DBP which, when bound, will act to alter (i.e., enhance, attenuate or even terminate) expression of a given gene or, alternatively, genes under control of that promoter.

As another application, a DBP could be designed to bind specific DNA sequences when attached to solid supports. Such solid supports could include styrene beads, acrylamide well-plates or glass substrates.

In order to realize the specific applications mentioned above, as well as the full scope of applications possible through the instant invention, the DBP can be designed as set forth above to include the added feature of a pre- and/or postdomain amino acid sequence of arbitrary length. This would include, for example, the coupling of the basic DBP to an endonuclease or to a reporter or to a sequence by which the DPB could be coupled to a solid support.

Accordingly, the instant invention includes DBP's that bind to a predetermined target double-stranded DNA sequence of 3n (where n≧1) base pairs in length of the form:

NH 2 —X 0-m —ZiF 1 —[{linker}—ZiFi] . . . —[{linker}—ZiF n ]-X 0-p —COOH

wherein each ZiF 1 to ZiF n is a ZF domain of the form set forth above; {linker} is an amino acid sequence as set forth above; X 0-m stands for a sequence of from 0 to m amino acids and X 0-p stands for a sequence of from 0 to p amino acids. The values for m and p and the identities of the amino acids are determined by the particular protein(s) or amino acid sequence(s) to be coupled to the DBP for a given application.

In a further embodiment of the invention, the Zn +2 atom, which forms a complex with the two cysteine and two histidine amino acids in a specific ZF motif, can be substituted by a Co +2 or a Cd +2 atom, thus making a “cobalt finger” or a “cadmium finger.”

The rules presented in Table 2 (“rule set A”) are to be regarded as the “first choice” rules for optimal combinations in ZF-DNA recognition. However, it should be emphasized, as indicated in column B (“rule set B”) of Table 1 or Table 3, that there are many alternative AA combinations that would also be expected to be important in the design of DNA-binding proteins capable of forming useful ZF-DNA complexes.

TABLE 4

Scanning the complete S. Cerevisiae genome for conflicts - DBP's designed against the coding region of each gene

Ratio of

Binding

Energy to

Specific Amino Acids in DBP

DBP

Spurious

Chrom-

Zf1

Zf2

Zf3

Zf4

Zf5

Zf6

Zf7

Zf8

Zf9

Binding

Binding

osome

Gene

Optimal DNA Sequence in Gene*

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Energy

Energy

1

1

CCT ACT CTC AGA TTC CAC TTC ACT CCA

E

N3

Q2

Q

N3

Q2

E

I

R2

Q

N

Q

I

I

R2

E

N

E

I

I

R2

Q

N3

Q2

E

E

Q

7374132

132836

1

2

TCA GAG CTC ACT TAG CCC AAT ACT ACA

I

D

Q

R

N

R

E

I

R2

Q

N3

Q2

I

N

R

E

Q3

R2

Q

N

Q3

Q

N3

Q2

Q

D

Q

24192270

166073

1

3

GCC GCT TGG GAC GTC GGA GAA GGA GCC

R

Q3

R2

R

N3

Q2

I

H

R

R

N

Q3

R

I

R2

R

D

Q

R

N

Q

R

N

Q

R

Q3

R2

8480520

701860

1

4

GAA AAG CAT ACA GCT TDC GAT ACA TCA

R

N

Q

Q

Q

R

E

Q1

02

Q

D

Q

R

N3

Q2

I

Q3

R2

R

Q

Q2

Q

D

Q

I

D

Q

19226970

313442

1

5

AGT AGC ATA ATA GGA TCT AGT ACT GDC

Q

H1

Q2

Q

H1

R2

Q

I

Q

Q

I

Q

R

N

Q

I1

N3

Q2

Q

H1

Q2

Q

N3

Q2

R

Q3

R2

15168192

176738

1

6

GCC GTG GAA ACA ATT GCA GAG GAG ATG

R

Q3

R2

R

I

R

R

N

Q

Q

D

Q

Q

I

Q3

R

D

Q

R

N

R

R

N

R

Q

I

R

30941379

176738

1

7

CCA AGT CGA GAC GCT TAA AGT TAA GTG

E

D

Q

Q

H1

Q2

E

N

Q

R

N

Q3

R

N3

Q2

I

N

Q

Q

H1

Q2

I

N

Q

R

I

R

9355725

320720

1

8

GAC TAC ACC GGC ATG CCT GDC AGC AAA

R

N

Q3

I

N

E

Q

H1

R2

R

H1

R2

Q

I

R

E

N3

Q2

R

Q3

R2

Q

H1

R2

R

N

Q

6539130

487737

1

9

ACT TGG ACT GCC GAG CGG GTC GAT CAA

Q

N3

Q2

I

H

R

Q

N3

Q2

R

Q3

R2

R

N

R

E

H

R

R

I

R2

R

Q

Q2

E

N

Q3

442890

1094811

1

10

GAC CCA ACT GCG CAC GCT GDC AAG GAG

R

N

Q3

E

D

Q

Q

N3

Q2

R

E

R

E

N

E

R

N3

Q2

R

Q3

R2

Q

Q

R

R

N

R

11213640

1011037

1

11

CCT GCC AGC AGT TGT CCG GAC CTG CAT

R

N3

Q2

R

Q3

R2

Q

H1

R2

Q

H1

Q2

I

H1

Q2

R

E

R

R

N

Q3

E

I

R

E

Q1

Q2

6292670

563027

1

12

GAT AAC ACA GTG CAG AAG ACT CCT ACA

R

Q

Q2

Q

Q1

R2

Q

D

Q

R

I

R

E

Q

R

Q

Q

R

Q

N3

Q2

E

N3

Q2

Q

D

Q

18371043

492068

1

13

TAT GCA DCC GAT ACA GAG GGT GTC GAG

I

N

Q3

R

D

Q

E

Q3

R2

R

Q

Q2

Q

D

Q

R

N

R

R

H

Q2

R

I

R2

R

N

R

7619823

768933

1

14

CAA GAG CAC GAC GGC CGC AGT AAG CAC

E

N

Q3

R

N

R

E

N

E

R

N

Q3

R

H1

R2

E

H1

R2

Q

H1

Q2

Q

Q

R

E

N

E

4512410

1279511

1

15

GAG ATA CCC GTG ATA CGT CGC GGT AAA

R

N

R

Q

I

Q

E

Q3

R2

R

I

R

Q

I

Q

E

H

Q2

E

H1

R2

R

H

Q2

R

N

Q

2512107

903296

1

16

AAT GGG GCA CGA CCT DCA GAG GGT GAT

Q

N

Q3

R

H

R

R

D

Q

E

N

Q

E

N3

Q2

E

D

Q

R

N

R

R

H

Q2

R

Q

Q2

10115586

700491

1

17

GAG AGA CDC CAG GCG TGA GAC ACG TCT

R

N

R

Q

N

Q

E

Q3

R2

E

Q

R

R

E

R

I

N

Q

R

N

Q3

Q

E

R

I1

N3

Q2

4430376

1101825

1

18

ACC TCC GCT GTC ATG GGT ACG GGT GGC

Q

Q3

R2

I

Q3

R2

R

N3

Q2

R

I

R2

Q

I

R

R

H

Q2

Q

E

R

R

H

Q2

R

H1

R2

4927770

713565

1

19

GAA CCG AGT TAG GGG CGA TCT AAG CGA

R

N

Q

E

D

R

Q

H1

Q2

I

N

R

R

H

R

E

N

Q

I1

N3

Q2

Q

Q

R

E

N

Q

2905470

1180262

1

20

GAT GGA ACA CCC AAG GGT CCT CGT GAA

R

Q

Q2

R

N

Q

Q

D

Q

E

Q3

R2

Q

Q

R

R

H

Q2

E

H

Q2

E

H

Q2

R

N

Q

11022512

583391

1

21

ACC GAC CAT ACA GGA CGT CCT GDC ACC

Q

Q3

R2

R

N

Q3

E

Q1

Q2

Q

D

Q

R

N

Q

E

H

Q2

R

N3

Q2

R

Q3

R2

Q

Q3

R2

9693576

1085516

1

22

GAA AGA CGG AAG CTC GAT CCT AAC GCT

R

N

Q

Q

N

Q

E

H

R

Q

Q

R

E

I

R2

R

Q

Q2

R

N3

Q2

Q

Q1

R2

R

N3

Q2

12066840

645941

1

23

AGT CAA CTG GGA AGG GTC CGG CAT CAT

Q

H1

Q2

E

N

Q3

E

I

R

R

N

Q

Q

Q

R

R

I

R2

E

H

R

E

Q1

Q2

E

Q1

Q2

7060608

422504

1

24

AGG ATG GTA CGT GGC ACG GGA CCA TCT

Q

Q

R

Q

I

R

R

I

Q

E

H

Q2

R

Q3

R2

Q

E

R

R

N

Q

E

D

Q

I1

N3

Q2

4607532

626666

1

25

ATG GAC CAC CCG CAT GCC CGC TGT GAG

Q

I

R

R

N

Q3

E

N

E

E

D

R

E

Q1

Q2

R

Q3

R2

E

H1

R2

I

H1

Q2

R

N

R

2450880

1266455

1

26

AAG ACC CDC ACG CCC GTG TCC GCA CCT

Q

Q

R

Q

Q3

R2

E

Q3

R2

Q

E

R

E

N3

Q2

R

I

R

I

Q3

R2

R

D

Q

E

N3

Q2

5803812

981266

1

27

GAT CAG CCC GCC GGC CCT GGT GCG GAC

R

Q

Q2

E

Q

R

E

Q3

R2

R

Q3

R2

R

H1

R2

E

N3

Q2

R

H

Q2

R

E

R

R

N

Q3

2742660

3269843

1

28

AGT CCG CAC GAG GGC CGG CGG GCT GAT

Q

H1

Q2

E

D

R

E

N

E

E

Q

R

R

H1

R2

E

H

R

E

H

R

R

N3

Q2

R

Q

Q2

2263544

1870532

1

29

AAT GGC GCT AAC CGG GAC AGT AGC GAC

Q

N

Q3

R

H1

R2

R

N3

Q2

Q

Q1

R2

E

H

R

R

N

Q3

Q

H1

Q2

Q

H1

R2

R

N

Q3

6611550

1263414

1

30

GCC ACT GCC GDC TCT GTC AGC GCT GCC

R

Q3

R2

Q

N3

Q2

R

Q3

R2

R

Q3

R2

I1

N3

Q2

R

I

R2

Q

H1

R2

R

N3

Q2

R

Q3

R2

10878345

738828

1

31

ACT CCG AGG CGA GDG CAA AGC GGA ACA

Q

N3

Q2

E

D

R

Q

Q

R

E

N

Q

R

E

R

E

N

q3

Q

H1

R2

R

N

Q

Q

D

Q

4999968

1239753

1

32

ACC GTC GCT GCC TCC GCT GTC GCT GCT

Q

Q3

R2

R

I

R2

R

N3

Q2

R

Q3

R2

I

Q3

R2

R

N3

Q2

R

I

R2

R

N3

Q2

R

N3

Q2

9376290

720036

1

33

ACG TAG CCA GAC GAG CTC AGT CAA GAG

Q

E

R

I

N

R

R

D

Q

R

N

Q3

R

N

R

E

I

R2

Q

H1

Q2

E

N

Q3

R

N

R

6475788

77552

1

34

ACC ACC CTG GTT ACC GTC DCC GGT GTC

Q

Q3

R2

Q

Q3

R2

E

I

R

R

I

Q3

Q

Q3

R2

R

I

R2

E

Q3

R2

R

H

Q2

R

I

R2

3659040

830292

1

35

ACA ACC CAG GAA AAC GCC TCC GAA GCC

Q

D

Q

Q

Q3

R2

E

Q

R

R

N

Q

Q

Q1

R2

R

Q3

R2

I

Q3

R2

R

N

Q

R

Q3

R2

15634620

713817

1

36

CAA CAA GCG AGA TGG GCG GAT ATC CCA

E

N

Q3

E

N

Q3

R

E

R

Q

N

Q

I

H

R

R

E

R

R

Q

Q2

Q

I

R2

E

D

Q

6125355

566708

1

37

GCC GGA TGC GAG GAC GCA AGC AGG GGA

R

Q3

R2

R

N

Q

I1

H1

R2

R

N

R

R

N

Q3

R

D

Q

Q

H1

R2

Q

Q

R

R

N

Q

5445990

1053906

1

38

AAA GGT ACC GCT ACG CCA CCT ACG GGT

R

N

Q

R

H

Q2

Q

Q3

R2

R

N3

Q2

Q

E

R

E

D

Q

E

N3

Q2

Q

E

R

R

H

Q2

6989373

950445

1

39

ACT GAT CGT GAA CCC CGT CAA GGT AAG

Q

N3

Q2

R

Q

Q2

E

H

Q2

R

N

Q

E

Q3

R2

E

H

Q2

E

N

Q3

R

H

Q2

Q

Q

R

9882648

722977

1

40

CAA CGG GAC TCC GCA GAC GGG AGC AAT

E

N

Q3

E

H

R

R

N

Q3

I

Q3

R2

R

D

Q

R

N

Q3

R

H

R

Q

H1

R2

Q

N

Q3

3614610

1572359

1

41

CCC GAG GAG GTA CCC CTA GAT CAC TAT

E

Q3

R2

R

N

R

R

N

R

R

I

Q

E

Q3

R2

E

I

Q

R

Q

Q2

E

N

E

I

N

Q3

5069952

739622

1

42

GAC CCT TAT GCT CTA TCC GAG CAC GAT

R

N

Q3

E

N3

Q2

I

N

Q3

R

N3

Q2

E

I

Q

I

Q3

R2

R

N

R

E

N

E

R

Q

Q2

6148980

677592

1

43

CAA GGT GGA CAG CCG AAC ATA GCT GGT

E

N

Q3

R

H

Q2

R

N

Q

E

Q

R

E

D

R

Q

Q1

R2

Q

I

Q

R

N3

Q2

R

H

Q2

6691509

833912

1

44

CCG GAT TAC ACG TCT GCC TCG ACC GCA

E

D

R

R

Q

Q2

I

N

E

Q

E

R

I1

N3

Q2

R

Q3

R2

I

D

R

Q

Q3

R2

R

D

Q

27652514

1034213

1

45

GGT GCC GAT ACG GAT AAT GCG GTA ACT

R

H

Q2

R

Q3

R2

R

Q

Q2

Q

E

R

R

Q

Q2

Q

N

Q3

R

E

R

R

I

Q

Q

N3

Q2

11200230

830360

1

46

ATC AGC GAC TCT AGG CCG CAC GTT CAG

Q

I

R2

Q

H1

R2

R

N

Q3

I1

N3

Q2

Q

Q

R

E

D

R

E

N

E

R

I

Q3

E

Q

R

3766644

774309

1

47

ACG CCT GAA AGA GCG CAC ACT CCT GCC

Q

E

R

E

N3

Q2

R

N

Q

Q

N

Q

R

E

R

E

N

E

Q

N3

Q2

E

N3

Q2

R

Q3

R2

10318266

901129

1

48

TCT AGT GCC CGG AAC ACA CQG AGA GCA

I1

N3

Q2

Q

H1

Q2

R

Q3

R2

E

H

R

Q

Q1

R2

Q

D

Q

E

H

R

Q

N

Q

R

D

Q

3231252

1293053

1

49

AGC GCT GAT GAG AGA GAC GCG GAA GAT

Q

H1

R2

R

N3

Q2

R

Q

Q2

R

N

R

Q

N

Q

R

N

Q3

R

E

R

R

N

Q

R

Q

Q2

17979930

777874

1

50

ACC GCC GCA CCA ACG GCA CTC GCC ACG

Q

Q3

R2

R

Q3

R2

R

D

Q

E

D

Q

Q

E

R

R

D

Q

E

I

R2

R

E

R

Q

E

R

5487912

1016572

1

51

ACG GGA GAT AGC ACT CCC TCA GGC ACG

Q

E

R

R

N

Q

R

Q

Q2

Q

H1

R2

Q

N3

Q2

E

Q3

R2

I

D

Q

R

H1

R2

Q

E

R

5807160

9266587

1

52

GAC GAG GGC GGC CGC ATA GTG CAC GCA

R

N

Q3

R

N

R

R

H1

R2

R

H1

R2

E

H1

R2

Q

I

Q

R

I

R

E

N

E

R

D

Q

2579344

1371038

1

53

ACC GCT GGC GCA GAC GCC ACT ACC AAG

Q

Q3

R2

R

N3

Q2

R

H1

R2

R

D

Q

R

N

Q3

R

Q3

R2

Q

N3

Q2

Q

H1

R2

Q

Q

R

7686450

1600463

1

54

TAT GAG CCG TAC CAG ATA CGT GCT AAT

I

N

Q3

R

N

R

E

D

R

I

N

E

E

Q

R

Q

I

Q

E

H

Q2

R

N3

Q2

Q

N

Q3

6770394

401149

1

55

CAG ACA CCA CCG AGC CCC GAT CAA GAG

E

Q

R

Q

D

Q

E

D

Q

E

D

R

Q

H1

R2

E

Q3

R2

R

Q

Q2

E

N

Q3

R

N

R

9717264

708788

1

56

CAT CGC GTT GGC ACT CGG TCC CGA AAG

E

Q1

Q2

E

H1

R2

R

I

Q3

R

H1

R2

Q

N3

Q2

E

H

R

I

Q3

R2

E

N

Q

Q

Q

R

2937552

1059390

1

57

GCT ATT GGG CCT GCC CGG TGT ACG GCC

R

N3

Q2

Q

I

Q3

R

H

R

E

N3

Q2

R

Q3

R2

E

H

R

I

H1

Q2

Q

Q

R

R

Q3

R2

3094125

1175589

1

58

ATT CCT GAT ACG GCG GTT GAC AAG GAG

Q

I

Q3

E

N3

Q2

R

Q

Q2

Q

E

R

R

E

R

R

I

Q3

R

N

Q3

Q

Q

R

R

N

R

12276765

572705

1

59

GAC GCC AGG GAC GAG CAA GGG GAC GAA

R

N

Q3

R

Q3

R2

Q

Q

R

R

N

Q3

R

N

R

E

N

Q3

R

H

R

R

N

Q3

R

N

Q

6852600

1938830

1

60

GTC GCC AAC GCT CAC GGT GTG GAA ACC

R

I

R2

R

Q3

R2

Q

Q1

R2

R

N3

Q2

E

N

E

R

H

Q2

R

I

R

R

N

Q

Q

Q3

R2

7299000

880912

1

61

AGA AGG GGC AAG CGT GGT CGT GAC GAT

Q

N

Q

Q

Q

R

R

H1

R2

Q

Q

R

E

H

Q2

R

H

Q2

E

H

Q2

R

N

Q3

R

Q

Q2

5511175

1080370

1

62

CAG CAG ACC GAC TAA ACT ACT GCA CGA

E

Q

R

E

Q

R

Q

H1

R2

R

N

Q3

I

N

Q

Q

N3

Q2

Q

N3

Q2

R

D

Q

E

N

Q

10230030

654559

1

63

CAG CAG ACC GAC TAA ACT ACT GCA CGA

E

Q

R

E

Q

R

Q

H1

R2

R

N

Q3

I

N

Q

Q

N3

Q2

Q

N3

Q2

R

D

Q

E

N

Q

10230030

654559

1

64

GAT GTG GGG AAC CAT GCC CAG GAT GAT

R

Q

Q2

R

I

R

R

H

R

Q

Q1

R2

E

Q1

Q2

R

Q3

R2

E

Q

R

R

Q

Q2

R

Q

Q2

10264770

906033

1

65

ACT GTG GGC AAC AGT ACG GCA ATT ACC

Q

N3

Q2

R

I

R

R

H1

R2

Q

Q1

R2

Q

H1

Q2

Q

E

R

R

D

Q

Q

I

Q3

Q

Q3

R2

10593486

512119

1

66

ACT GAC GAG CAT GAA GCT GAT GTC AAT

Q

N3

Q2

R

N

Q3

R

N

R

E

Q1

Q2

R

N

Q

R

N3

Q2

R

Q

Q2

R

I

R2

Q

N

Q3

31895100

3888784

1

67

GAC CCA GAA GTG CAG GCT GAC ATG AAG

R

N

Q3

E

D

Q

R

N

Q

R

I

R

E

Q

R

R

N3

Q2

R

N

Q3

Q

I

R

Q

Q

R

14004360

495857

1

68

GAT CAT TAG CAA AGT GAG CAA CAC ACG

R

Q

Q2

E

Q1

Q2

I

N

R

E

N

N3

Q

H1

Q2

R

N

R

E

N

Q3

E

N

E

Q

E

R

21159954

2844809

1

69

GAT CGG AAG TAA GAC CCC CGA TAT GAC

R

Q

Q2

R

H

R

Q

Q

R

I

N

Q

R

N

Q3

E

Q3

R2

E

N

Q

I

N

Q3

R

N

R

8164692

708759

1

70

GGT GCT CGG CAT ACA GCC CTG ATT GTT

R

H

Q2

R

N3

Q2

E

H

R

E

Q1

Q2

Q

D

Q

R

Q3

R2

E

I

R

Q

I

Q3

R

I

Q3

4056912

706071

1

71

CAT GTC AGC ACT GCA CAG CAG CCG AAA

E

Q1

Q2

R

I

R2

Q

H1

R2

Q

N3

Q2

R

D

Q

E

Q

R

R

N

R

E

D

R

R

N

Q

5930865

940863

1

72

GCT ACC GCT ACT GTG CCT TCC GCT CCC

R

N3

Q2

Q

H1

R2

R

N3

Q2

Q

N3

Q2

R

I

R

E

N3

Q2

I

Q3

R2

R

N3

Q2

E

Q3

R2

10216521

637218

1

73

GAT CGT GAA GCT ACC TTT AGA GAC GCC

R

Q

Q2

E

H

Q2

R

N

Q

R

N3

Q2

Q

Q3

R2

I

I

Q3

Q

N

Q

R

N

Q3

R

Q3

R2

11804220

440208

1

74

AAC GTT GCT GAG AGT CCT GGA ACG GGC

Q

Q1

R2

R

I

Q3

R

H

Q2

R

N

R

Q

H1

Q2

E

N3

Q2

R

N

Q

Q

Q

R

R

H1

R2

11792148

492924

1

75

GCT GAA GCC GAC TAT CTT GCC GAT GAG

R

N3

Q2

R

N

Q

R

Q3

R2

R

N

Q3

I

N

N3

E

I

Q2

R

Q3

R2

R

Q

Q2

R

N

R

9898740

835143

1

76

GAA TAA CAT TAG ACC GGG GCG CCA AAC

R

N

Q

I

N

Q

E

Q1

Q2

I

N

R

Q

H1

R2

R

H

R

R

E

R

E

D

Q

Q

Q1

R2

9295611

466898

1

77

CAA TGC ACA GAC AAA TTC GAT ACT CAC

E

N

Q3

I1

H1

R2

Q

D

Q

R

N

Q3

R

N

Q

I

I

R2

R

Q

Q2

Q

N3

Q2

E

N

E

38166822

59410

1

78

No DBP possible

1

79

GCT AAT CAC GTC GAC GTC GGG CAT GGA

R

N3

02

Q

N

Q3

E

N

E

R

I

R2

R

N

Q3

R

I

R2

R

H

R

E

Q1

Q2

R

N

Q

9510655

945100

1

80

CCT GCC CAG GCC GCT GAG CTG GTG GGT

E

N3

Q2

R

Q3

R2

E

Q

R

R

Q3

R2

R

N3

Q2

R

N

R

E

I

R

R

I

R

R

H

Q2

5592240

997835

1

81

ACC CAG GCA GTG CAG GAG CGA GCC AGG

Q

Q3

R2

E

Q

R

R

D

Q

R

I

R

R

N

R

R

N

R

E

N

Q

R

Q3

R2

Q

Q

R

6631281

1211740

1

82

CCA GGG GCT CCC GCT CCC TGG GCA GAA

E

N

Q

R

E

R

R

N3

Q2

E

Q3

R2

R

N3

Q2

E

Q3

R2

I

H

R

R

D

Q

R

N

Q

4854492

1135027

1

83

GTG CCT CCG CCG CAG CAA CCA CTA CAT

R

I

R

E

N3

Q2

E

D

R

E

D

R

E

Q

R

E

N

Q3

E

D

Q

E

I

Q

E

Q1

Q2

10134072

274029

1

84

CCT GAT GTA CAG TGG GAT ACA GCG AAT

E

N3

Q2

R

Q

Q2

R

I

Q

E

Q

R

I

H

R

R

Q

Q2

Q

D

Q

R

E

R

Q

N

Q3

10593990

455091

1

85

CCA ACG AAC GGT GCA CAG AAT ACG CAG

E

D

Q

Q

E

R

Q

Ql

R2

R

H

Q2

R

D

Q

R

N

R

Q

N

Q3

Q

E

R

E

Q

R

16355520

526388

1

86

GGT GAT CGC ACG CAA GCC TGC GGG GAA

R

H

Q2

R

Q

Q2

E

H1

R2

Q

E

R

E

N

Q3

R

Q3

R2

I1

H1

R2

R

H

R

R

N

Q

2939586

1473085

1

87

GAG AAG CCA ACA AGC AAC GCT GAG GAA

R

N

R

Q

Q

R

E

D

Q

Q

D

Q

Q

H1

R2

Q

Q1

R2

R

N1

Q2

R

N

R

R

N

Q

20535210

575100

1

88

GAG GCG ACA TAA GTT GTT AGC ACA GCA

R

N

R

R

E

R

Q

D

Q

I

N

Q

R

I

Q3

R

I

Q3

Q

H1

R2

Q

D

Q

R

D

Q

14004180

263582

1

89

GAT CAT GGG CTA TGG GAT ACT CCC TAC

R

Q

Q2

E

Q1

Q2

R

H

R

E

I

Q

I

H

R

R

Q

Q2

Q

N3

Q2

E

Q3

R2

I

N

E

5240610

432675

1

90

AAG TTA GAT ACA CTT AAC GAA GCT AGT

Q

Q

R

I

I

Q

R

Q

Q2

Q

D

Q

E

I

Q2

Q

Q1

R2

R

N

Q

E

N3

Q2

Q

H1

Q2

17980110

177343

1

91

AAT GCT CCC AGG GGC TCG GCC AGG ACC

Q

N

Q3

R

N3

Q2

E

Q3

R2

Q

Q

R

R

H1

R2

I

D

R

R

Q3

R2

Q

Q

R

Q

Q3

R2

4905765

1462454

1

92

GAT TCG CCA CGG CAC ACT CCG CAC AGA

R

Q

Q2

I

D

R

E

D

Q

E

H

R

E

N

E

Q

N3

Q2

E

D

R

E

N

E

Q

N

Q

2361600

1351886

1

93

GCG GAG TGA GCC GCC CAG GCC AAC GAC

R

E

R

R

N

R

I

N

Q

R

Q3

R2

R

Q3

R2

R

N

R

R

Q3

R2

Q

Q1

R2

R

N

Q3

9558540

1111971

1

94

ACA TCG CCG CCT ACC AGT CCC GCG GTG

Q

D

Q

I

D

R

E

D

R

E

N3

Q2

Q

Q3

R2

Q

H1

Q2

E

Q3

R2

R

E

R

R

I

R

3132513

1154321

1

95

GGT ATC GCC AGT CTC CGG GTC CAT ACC

R

H

Q2

Q

I

R2

R

Q3

R2

Q

H1

Q2

E

I

R2

E

H

R

R

I

R2

E

Q

Q2

Q

Q3

Q2

4725558

561264

1

96

ATC ACT CCC GGT CCA CAT TCT AGG AAG

Q

I

R2

Q

N3

Q2

E

Q3

R2

R

H

Q2

E

D

Q

E

Q1

Q2

I1

N3

Q2

Q

Q

R

Q

Q

R

6608547

709280

1

97

AAT GTC AGT TGT GAC GCT ACA CTT TTC

Q

N

Q3

R

I

R2

Q

H1

Q2

I

H1

Q2

R

N

Q3

R

N3

Q2

Q

N

Q

E

I

Q2

I

I

R2

8150676

162281

1

98

AAT ACT GTA GCT GCT GAG ACG ATT ACC

Q

N

Q3

Q

N3

Q2

R

I

Q

R

N3

Q2

R

N3

Q2

R

N

R

Q

E

R

Q

I

Q3

Q

Q3

R2

18607320

466494

1

99

AGC TGT GGA AAC AAT CGC AGG GGA GAT

Q

H1

R2

I

H1

Q2

R

N

Q

Q

Q1

R2

Q

N

Q3

E

H1

R2

Q

Q

R

R

N

Q

R

Q

Q2

19293534

242396

1

100

GTA GAA ATC TGC TGC ACA TGC CAC ACG

R

I

Q

R

N

Q

Q

I

R2

I1

H1

R2

I1

H1

R2

Q

D

Q

I1

H1

R2

E

N

E

Q

E

R

9178908

103292

1

104

GCT ACG GAG AAA CCG TGC ACT AAC TCT

R

N3

Q2

Q

E

R

R

N

R

R

N

Q

E

D

R

I1

H1

R2

Q

N3

Q2

Q

Q1

R2

I1

N3

Q2

10532100

418624

1

105

ACC GTT TCC TCC AAG TCA TAC ACC ACT

Q

Q3

R2

I

Q3

R2

I

Q3

R2

I

Q3

R2

Q

Q

R

I

D

Q

I

N

E

Q

Q3

R2

Q

N3

Q2

15664500

137917

1

107

CTA TAT ATT TGT GGC AGA AAT CAT ACC

E

I

Q

I

N

Q3

Q

I

Q3

I

H1

Q2

R

H1

R2

Q

N

Q

Q

N

Q3

E

Q1

Q2

Q

Q3

R2

36455616

57145

1

108

TAT CAT GAC AAC ATG GTA CAA ATT GAG

I

N

Q3

E

Q1

Q2

R

N

Q3

Q

Q1

R2

Q

I

R

R

Q

E

N

Q3

Q

I

Q3

R

N

R

25006833

153077

1

109

AAG ACC GCA CTA GAT CTT ACC AAG AGC

Q

Q

R

Q

Q3

R2

R

D

Q

E

I

Q

R

Q

Q2

E

I

Q2

Q

Q3

R2

Q

Q

R

Q

H1

R2

13895100

382466

1

110

ATG ACG ACA TCC AAG CCA GCT TTT ACC

Q

I

R

Q

E

R

Q

D

Q

I

Q3

R2

Q

Q

R

E

D

Q

R

N3

Q2

I

I

Q3

Q

Q3

R2

16928244

147676

*The optimal DNA sequences in genes 1-61 are shown as SEQ ID NOS: 5-65, respectively, in the Sequence Listing. The sequences in genes 62 and 63 are identica1 and shown as SEQ ID NO: 66. The sequences in genes 64-77 are shown as SEQ ID NOS: 67-80, respectively. The sequences in genes 79-100 are shown as SEQ ID NOS: 81-102, respectively. The sequences in genes 104 and 105 are shown as SEQ ID NOS: 103 and 104, respectively. The sequences in qenes

# 107-110 are shown as SEQ ID NOS: 105-108 respectively.

TABLE 5

Scanning the complete C. elegans for conflicts - DBP's designed against the coding region of each gene

Ratio of

Binding

Energy to

Specific Amino Acids in DBP

DBP

Spurious

Chrom-

Zf1

Zf2

Zf3

Zf4

Zf5

Zf6

Zf7

Zf8

Zf9

Binding

Binding

osome

Gene

Optimal DNA Sequence in Gene*

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Z1

Z2

Z3

Energy

Energy

1

1

ACC AAG CCG CCC GAC TCC TAG GAG ATG

Q

E

R

Q

Q

R

E

D

R

E

Q3

R2

R

N

Q3

I

Q3

R2

I

N

R

R

N

R

Q

I

R

23846400

183458

1

3

GAG GCC GAG CAC GAG CAC AGG AGC GAA

R

N

Q3

R

Q3

R2

R

N

R

E

N

E

R

N

R

E

N

E

Q

Q

R

Q

H1

R2

R

N

Q

58257900

162173

1

4

GAC AAT TCT CCC GGC GCC AAT GAT CAC

R

N

Q3

Q

N

Q3

I1

N3

Q2

E

Q3

R2

R

H1

R2

R

Q3

R2

Q

N

Q3

R

Q

Q2

E

N

E

83021040

99575

1

5

AGC ACG ACT CGG CAC ACC CGT TCC GCC

Q

H1

R2

Q

E

R

Q

N3

Q2

E

H

R

E

N

E

Q

Q3

R2

E

H

Q2

I

Q3

R2

R

Q3

R2

25095960

177149

1

6

CCA GGA AGG CGC ACT GGC AGA CGT AAG

E

D

Q

R

N

Q

Q

Q

R

E

H1

R2

Q

N3

Q2

R

H1

R2

Q

N

Q

E

H

Q2

Q

Q

R

34627332

148563

1

7

CCT ATT ACT CGT GGT GCC GCG GGA GCC

R

N3

Q2

Q

I

Q3

Q

N3

Q2

E

H

Q2

R

H

Q2

R

Q3

R2

R

E

R

R

N

Q

R

Q3

R2

32769390

208126

1

8

AAT AGC GAA CAG ATA TCT GAC AAC TCC

Q

N

Q3

Q

H1

R2

R

N

Q

E

Q

R

Q

I

Q

I1

N3

Q2

R

N

Q3

Q

Q1

R2

I

Q3

R2

85891770

58952

1

9

GTC GCG CAT ACT AAG GCT CGC TTT AAT

R

I

R2

R

E

R

E

Q1

Q2

Q

N3

Q2

Q

Q

R

R

N3

Q2

E

H1

R2

I

I

Q3

Q

N

Q3

22607199

144807

1

10

GAT ATT CGC GAT GGC AGC GGT GAC GAT

R

Q

Q2

Q

I

Q3

E

H1

R2

R

Q

Q2

R

H1

R2

Q

Q3

R2

R

H

Q2

R

N

Q3

R

Q

Q2

35024550

200334

1

11

CAT AAC GTC GAG GCT GCC CGC AAG GAG

E

Q1

Q2

Q

Q1

R2

R

I

R2

R

N

R

R

N3

Q2

R

Q3

R2

E

H1

R2

Q

Q

R

R

N

R

26896050

338100

1

12

ACC AGC CAT CAC GCC ATG CGA AGC ACC

Q

Q3

R2

Q

H1

R2

E

Q1

Q2

E

N

E

R

Q3

R2

Q

I

R

E

N

Q

Q

H1

R2

Q

Q3

R2

35287740

156180

1

13

AGG CAC CCC GGG AAG CGC CGG ACC GAA

Q

Q

R

E

N

E

E

Q3

R2

R

H

R

Q

Q

R

E

H1

R2

E

H

R

Q

Q3

R2

R

N

Q

14482326

394684

1

14

GGA GCA CCA GAC GCC CCG ACT AAG CCG

R

N

Q

R

D

Q

E

D

Q

R

N

Q3

R

Q3

R2

E

D

R

Q

N3

Q2

Q

Q

R

E

D

R

37857024

21565

1

15

GAT GCT CGC CTA CTC GCG AGG CCA AGA

R

Q

Q2

R

N3

Q2

E

H1

R2

E

I

Q

E

I

R2

R

E

R

Q

Q

R

E

D

Q

Q

N

Q

20671398

146603

1

16

AGA GCC GAT GCC CGC ACC AAG GCT GCT

Q

N

Q

R

Q3

R2

R

Q

Q2

R

Q3

R2

E

H1

R2

Q

Q3

R2

Q

Q

R

R

N3

Q2

R

N3

Q2

44071200

294768

1

17

ACA GAC GAG GCC AAG ATC TAC GCC GAA

Q

D

Q

R

N

Q3

R

N

R

R

Q3

R2

Q

Q

R

Q

I

R2

I

N

E

R

Q3

R2

R

N

Q

4248410

155670

1

18

CCA ACC GGT AGG CCG ATA GGT ACT CGC

E

D

Q

Q

Q3

R2

R

H

Q2

Q

Q

R

E

D

R

Q

I

Q

R

H

Q2

Q

H1

Q2

E

H1

R2

21033604

160124

1

19

CCT ACA AGG CCC CGT AGG AGG GCC GAT

E

N3

Q2

Q

D

Q

Q

Q

R

E

Q3

R2

E

H

Q2

Q

E

R

Q

Q

R

R

Q3

R2

R

Q

Q2

15698286

488647

1

20

ACC AAC GGA CAG GAT GGC GCC GAA CAA

Q

Q3

R2

Q

Q1

R2

R

N

Q

E

Q

R

R

Q

Q2

R

H1

R2

R

Q3

R2

R

N

Q

E

N

Q3

60312960

198256

1

21

GCA AGC CGC TAT GTC GAC GCT CGC CAA

R

D

Q

Q

H1

R2

E

H1

R2

I

N

Q3

R

I

R2

R

N

Q3

R

N3

Q2

E

H1

R2

E

N

Q3

22049052

158783

1

22

AGT CCG CCT AAG CGC CCT GTT CCG CCG

Q

H1

Q2

E

D

R

E

N3

Q2

Q

Q

R

E

H1

R2

E

N3

Q2

R

I

Q3

E

D

R

E

D

R

13743972

254069

1

23

AAG CCG ATC GCT GCG ACC GAA CCG CCT

Q

Q

R

E

H

R

Q

I

R2

R

N3

Q2

R

E

R

Q

Q3

R2

R

N

Q

E

D

R

E

N3

Q2

25602930

255727

1

24

AAT GAT CTA GCT CCC AGT CCT ACT GCG

Q

N

Q3

R

Q

Q2

E

I

Q

R

N3

Q2

E

Q3

R2

Q

H1

Q2

E

N3

Q2

Q

N3

Q2

R

E

R

39720375

180624

1

25

CAG AGG ACT CGC CGT ATC GTC GCT GGT

E

Q

R

Q

Q

R

Q

N3

Q2

E

H1

R2

E

H

Q2

Q

I

R2

R

I

R2

R

N3

Q2

R

H

Q2

20131686

173906

1

26

GCT ATG AGG TCA CGG GCT CCC CCT GAT

R

N3

Q2

Q

I

R

Q

Q

R

I

D

Q

E

H

R

R

N3

Q2

E

Q3

R2

E

N3

Q2

R

Q

Q2

2813218

193724

1

27

GAC ACA GGT CCC CAT CAC GGG ACA AGT

R

N

Q3

Q

D

Q

R

H

Q2

E

Q3

R2

E

Q1

Q2

E

N

E

R

H

R

Q

D

Q

Q

H1

Q2

31613868

189117

1

28

CAC GTT GGG ACC GCC AGG AGC CCG AAT

E

N

E

R

I

Q3

R

H

R

Q

Q3

R2

R

Q3

R2

Q

Q

R

Q

H1

R2

E

D

R

Q

N

Q3

30041550

183454

1

29

CGA GAA CGT CCC ATC AAG CGT GAA CAC

E

N

Q

R

N

Q

E

H

Q2

E

Q3

R2

Q

I

R2

Q

Q

R

E

H

Q2

R

N

Q

E

N

E

39080106

109209

1

30

GAT CCT TCG AGT ACG CCT ACG CAA GGA

R

Q

Q2

E

N3

Q2

I

D

R

Q

H1

Q2

Q

E

R

E

N3

Q2

Q

E

R

E

N

Q3

R

N

Q

35934354

145548

1

31

AAC GCC GCC TAG ACC CCG GGG AAT ACC

Q

Q1

R2

R

Q3

R2

R

Q3

R2

I

N

R

Q

Q3

R2

E

D

R

R

H

R

Q

N

Q3

Q

Q3

R2

24227280

379135

1

33

GTG GTG CAG GAG GGG CAG GAG GCC ACA

R

I

R

R

I

R

E

Q

R

R

N

R

R

H

R

E

Q

R

R

N

R

R

Q3

R2

Q

D

Q

35599014

164587

1

34

CGT ACA AGG AAT ACC CTG AAG GAC AAC

E

H

Q2

Q

D

Q

Q

Q

R

Q

N

Q3

Q

Q3

R2

E

I

R

Q

Q

R

R

N

Q3

Q

Q1

R2

98170218

71458

1

35

ACC TCC ACT CAG CGA CCA CCG GCG CCA

Q

Q3

R2

I

Q3

R2

Q

N3

Q2

E

Q

R

E

N

Q

E

D

Q

E

D

R

R

E

R

E

D

Q

36901980

123875

1

36

AAA GCG GTA CAA GCG ACG ACC CGT GCT

R

N

Q

R

E

R

R

I

Q

E

N

Q3

R

E

R

Q

E

R

Q

Q3

R2

E

H

Q2

R

N3

Q2

24232698

227970

1

37

ACA ACG ACC GAG GAG CCT ACC GAA GCC

Q

D

Q

Q

E

R

Q

Q3

R2

R

N

R

R

N

R

E

N3

Q2

Q

Q3

R2

R

N

Q

R

Q3

R2

49723200

288576

1

38

GAG AAC CGT CCC CAC CCG AAG CTG GCT

R

N

R

Q

Q1

R2

E

H

Q2

E

Q3

R2

E

N

E

E

D

R

Q

Q

R

E

I

R

R

N3

Q2

25381692

196538

1

39

CGT CCG GTG CCC GAG ACT GGG ACC GGT

E

H

Q2

E

H

R

R

I

R

E

Q3

R2

R

N

R

Q

N3

Q2

R

H

R

Q

Q3

R2

R

H

Q2

22963398

201668

1

40

AGG GAC CGT ACG GAA CAG GAC CCC CCT

Q

Q

R

R

N

Q3

E

H

Q2

Q

E

R

R

N

Q

E

Q

R

R

N

Q3

E

Q3

R2

E

N3

Q2

29852550

285512

1

41

AGG CAA CCC TGG AGG CGT CCC AGC ACC

Q

Q

R

E

N

Q3

E

Q3

R2

I

H

R

Q

Q

R

E

H

Q2

E

Q3

R2

Q

H1

R2

Q

Q3

R2

16371369

231386

1

42

CTC ACT ACC CCG GCA CCA AGG ACC AGT

E

I

R2

Q

N3

Q2

Q

Q3

R2

E

D

R

R

D

Q

E

D

Q

Q

Q

R

Q

Q3

R2

Q

H1

Q2

23768154

214650

1

43

GAC GAG CAC CTA AAG ACC GCC ACT CCG

R

N

Q3

R

N

R

E

N

E

E

I

Q

Q

Q

R

Q

Q3

R2

R

Q3

R2

Q

N3

Q2

E

D

R

32148360

235106

1

44

CCC GTC GGG TAG ACG GCG GTT ACC GCC

E

Q3

R2

R

I

R2

R

H

R

I

N

R

Q

E

R

R

E

R

R

I

Q3

Q

Q3

R2

R

H1

R2

15678117

218000

1

45

AGG CCA GGG GCC CCC TAC GCC CCA ACA

Q

Q

R

E

D

Q

R

H

R

R

Q3

R2

E

Q3

R2

I

N

E

R

Q3

R2

E

D

Q

Q

D

Q

12322980

331208

1

46

CAA GCT CCC GTA ACA CAA CCC CGG AGA

E

N

Q3

R

N3

Q2

E

Q3

R2

R

I

Q

Q

D

Q

E

N

Q3

E

Q3

R2

E

H

R

Q

N

Q

29693385

180837

1

47

CCC GGG GGC CCC CCT CCG GCG GAC GAT

E

Q3

R2

R

H

R

R

H1

R2

E

Q3

R2

E

N3

Q2

E

D

R

R

E

R

R

N

Q3

R

Q

Q2

21161601

339032

1

48

ACT GCC CAA ATC AAG GCC CCG AGA CAT

Q

N3

Q2

R

Q3

R2

E

N

Q3

Q

I

R2

Q

Q

R

R

Q3

R2

E

D

R

Q

N

Q

E

Q1

Q2

57865212

138864

1

49

ACT ACT CCC ACG CGG CGG ACA CCC AAC

Q

N3

Q2

Q

N3

Q2

E

Q3

R2

Q

E

R

E

H

R

E

H

R

Q

D

Q

E

Q3

R2

Q

Q1

R2

30357018

228773

1

50

ATC GAC CCG CAT GCG CTG GCG CAG ACG

Q

I

R2

R

N

Q3

E

D

R

E

Q1

Q2

R

E

R

E

I

R

R

E

R

E

Q

R

Q

E

R

17484525

223352

1

51

AGT ACC GCG GAT CAG GCG GCG TCC GTA

Q

H1

Q2

Q

Q3

R2

R

E

R

R

Q

Q2

E

Q

R

R

E

R

R

E

R

I

Q3

R2

R

I

Q

19081170

276357

1

52

GCA GCT CAA GCA GGC GAC AAC GCC GAA

R

D

Q

R

N3

Q2

E

N

Q3

R

D

Q

R

H1

R2

R

N

Q3

Q

Q1

R2

R

Q3

R2

R

N

Q

70750890

169007

1

53

GTG ACC GAC ACG CCC AGT AAG TCG GGA

R

I

R

Q

Q3

R2

R

N

Q3

Q

E

R

E

Q3

R2

Q

H1

Q2

Q

Q

R

I

D

R

R

N

Q

24010695

209162

1

54

GAC CTG GCG GCG GCC GCC GGT AGC AAG

R

N

Q3

E

I

R

R

E

R

R

E

R

R

Q3

R2

R

Q3

R2

R

H

Q2

Q

H1

R2

Q

Q

R

28604262

232239

1

55

ACC GCC GCC GAG CTC TGC GGC GCT GAA

Q

Q3

R2

R

Q3

R2

R

Q3

R2

R

N

R

E

I

R2

I1

H1

R2

R

H1

R2

R

N3

Q2

R

N

Q

70547100

74401

1

56

AAA GAC CGC AAA GCA GGG ACG CAA GAT

R

N

Q

R

N

Q3

E

H1

R2

R

N

Q

R

D

Q

R

H

R

Q

E

R

E

N

Q3

R

Q

Q2

35291445

172547

1

57

CCT ACG GCG CTA GAC AGG ACT CCG CAG

E

N3

Q2

Q

E

R

R

E

R

E

I

Q

R

N

Q3

Q

Q

R

Q

N3

Q2

E

D

R

E

Q

R

199096560

280252

1

58

AGA GCG CAC CGG CAG ACG CGC GGG AAT

Q

N

Q

R

E

R

E

N

E

E

H

R

E

Q

R

Q

E

R

E

H1

R2

R

H

R

Q

N

Q3

23780730

194692

1

59

GGA CGT CGC GCA GAC ACC GCC CAA AGA

R

N

Q

E

H

Q2

E

H1

R2

R

D

Q

R

N

Q3

Q

Q3

R2

R

Q3

R2

E

N

Q3

Q

N

Q

34512156

201230

1

60

AAT CAG TCA GAC CCA GAG GGT GAA GCT

Q

N

Q3

E

Q

R

I

D

Q

R

N

Q3

E

D

Q

R

N

R

R

H

Q2

R

N

Q

R

N3

Q2

58798980

120510

1

61

CAA CAT CGT CCC GGC GAC ACC GAC GAC

E

N

Q3

E

Q1

Q2

E

H

Q2

E

Q3

R2

R

H1

R2

R

N

Q3

Q

Q3

R2

R

N

Q3

R

N

Q3

43500744

201578

1

62

GGA GCC CGT GCG GCG GAT CCG CGC TAA

R

N

Q

R

Q3

R2

E

H

Q2

R

E

R

R

E

R

R

Q

Q2

E

D

R

E

H1

R2

I

N

Q

18935478

228209

1

63

GCC ACT CAG GCA GCA ACT CAG GCA GCC

R

Q3

R2

Q

N3

Q2

E

Q

R

R

D

Q

R

D

Q

Q

N3

Q2

E

Q

R

R

D

Q

R

Q3

R2

49245408

236014

1

64

CCA AAT GGT CAA GCC GGG GAG GCA AAC

E

D

Q

Q

N

Q3

R

H

Q2

E

N

Q3

R

Q3

R2

R

H

R

R

N

R

R

D

Q

Q

Q1

R2

72475200

122212

1

65

CCA ATG GCC ATC GAC GCG GCG ACC ACA

E

D

Q

Q

I

R

R

Q3

R2

Q

I

R2

R

N

Q3

R

E

R

R

E

R

Q

Q3

R2

Q

D

Q

40564530

138662

1

66

GAC CGT CAG GAT CGC GAT TAC CGG CCA

R

N

Q3

E

H

Q2

E

Q

R

R

Q

Q2

E

H1

R2

R

Q

Q2

I

N

E

E

H

R

E

D

Q

18477492

161318

1

67

ACA GCG GCA GCT ACT ACC TCT CCC GAA

Q

D

Q

R

E

R

R

D

Q

R

N3

Q2

Q

N3

Q2

Q

Q3

R2

I1

N3

Q2

E

Q3

R2

R

N

Q

57290895

157788

1

68

GCC CAG CCA ACC ACG GGG AGG GCT AGG

R

Q3

R2

E

Q

R

E

D

Q

Q

Q3

R2

Q

E

R

R

H

R

Q

Q

R

R

N3

Q2

Q

Q

R

29386800

292966

1

69

AAC AAC AGG CCA GCT GGA GGG AAT ACT

Q

Q1

R2

Q

Q1

R2

Q

Q

R

E

D

Q

R

N3

Q2

R

N

Q

R

H

R

Q

N

Q3

Q

N3

Q2

66919320

158830

1

70

AAC GCG AGC GGA ACC TAA CCG ACG CAA

Q

Q1

R2

R

E

R

Q

H1

R2

R

N

Q

Q

Q3

R2

I

N

Q

E

D

R

Q

E

R

E

N

Q3

24375168

247241

1

71

GCA CGC AAC GCT GCA CGC AGC GCA GCA

R

D

Q

E

H1

R2

Q

Q1

R2

R

N3

Q2

R

D

Q

Q

I

R2

R

H

2

E

Q3

R2

E

N

Q3

28378485

203936

1

72

AAT CCG CCC ACG TAC ATC GGT CCC CAA

Q

N

Q3

E

D

R

E

Q3

R2

Q

E

R

I

N

E

R

H

R

E

Q

R

R

E

R

R

Q3

R2

20305869

158287

1

73

GAG GTT CGG GCT TCA GGG CAG GCG GCC

R

N

R

R

I

Q3

E

H

R

R

N3

Q2

I

D

Q

Q

Q

R

E

N3

Q2

R

H

R

R

I

Q

21672135

188818

1

74

AAG CAG GCG CAA GGT AGG CCT GGG CTA

Q

Q

R

E

Q

R

R

E

R

E

N

Q3

R

H

Q2

R

E

R

E

Q1

Q2

R

N

R

R

N

R

36050427

156722

1

75

CAG ACA GTA GCC TCT GCG CAT GAG GAG

E

Q

R

Q

D

Q

R

I

Q

R

Q3

R2

I1

N3

Q2

Q

Q

R

R

Q3

R2

Q

Q3

R2

R

N3

Q2

29855007

211953

1

76

GCC CCC GAC CAA CTC AGG GCC ACC GCT

R

Q3

R2

E

Q3

R2

R

N

Q3

E

N

Q3

E

I

R2

Q

Q

R

R

N3

Q2

Q

Q1

R2

Q

N

Q

31503762

273280

1

77

GCT TAG GTA GCC CTG AAG GCT AAC AGA

R

N3

Q2

I

N

R

R

I

Q

R

Q3

R2

E

I

R

E

D

Q

E

H1

R2

E

N

Q3

E

N

Q

32961060

158008

1

78

GGC GAG GAC ACG GCA CCA CGC CAA CGA

R

H1

R2

R

N

R

R

N

Q3

Q

E

R

R

D

Q

R

H

Q2

I

N

R

I

D

R

Q

N

Q

30399876

184607

1

79

ACA AGC CAC GCT CCC GGT TAG TCG AGA

Q

D

Q

Q

H1

R2

E

N

E

R

N3

Q2

E

Q3

R2

Q

E

R

I

I

R

Q

Q1

R2

E

Q1

Q2

22475286

148967

1

80

GAG CAA ACC GTG GCC ACG TTG AAC CAT

R

N

R

E

N

Q3

Q

Q3

R2

R

I

R

R

Q3

R2

E

H

Q2

R

E

R

R

N

R

R

N

Q

50369850

79764

1

81

CCA AAC CTT ACA AGC CGT GCT GAG GAA

E

D

Q

Q

Q1

R2

E

I

Q2

Q

D

Q

Q

H1

R2

Q

Q

R

R

N

Q

R

N

Q3

Q

Q

R

42618420

109734

1

82

ACT GCT GGT GCA CCG AAG GAA GAC AAG

Q

N3

Q2

R

N3

Q2

R

H

Q2

R

D

Q

E

D

R

R

Q

Q2

E

Q3

R2

R

Q

Q2

Q

Q3

R2

99399690

118811

1

83

CTC CCA AGT GCG TCT GAT CCC GAT ACC

E

I

R2

E

D

Q

Q

H1

Q2

R

E

R

I1

N3

Q2

R

I

R2

R

Q3

R2

E

Q1

Q2

R

H1

R2

30293190

147363

1

84

CAT GTA GGA AGT AAC GTC GCC CAT GGC

E

Q1

Q2

R

I

Q

R

N

Q

Q

H1

Q2

Q

Q1

R2

Q

Q3

R2

E

D

Q

E

I

R

E

N

E

29013138

168290

1

85

GAA AAG GGC GAC GCC ACC CCA CTG CAC

R

N

Q

Q

Q

R

R

H1

R2

R

N

Q3

R

Q3

R2

E

I

R2

Q

Q

R

Q

N3

Q2

Q

N

Q

49252356

127883

1

86

ACT CGG GGC GGT GTG CTC AGG ACT AGA

Q

N3

Q2

E

H

R

R

H1

R2

R

H

Q2

R

I

R

E

N

E

R

Q3

R2

E

Q3

R2

Q

N

Q3

22559176

151162

1

87

ACA CGC CAG ACG GCC CAC GCC CCC AAT

Q

D

Q

E

H1

R2

E

Q

R

Q

E

R

R

Q3

R2

I1

H1

R2

R

Q

Q2

E

Q1

Q2

R

N3

Q2

22770018

332728

1

88

AAT GGT GCT TAT GTC TGC GAT CAT GCT

Q

N

Q3

R

H

Q2

R

N3

Q2

I

N

Q3

R

I

R2

R

H

Q2

E

H

R

Q

I

Q3

Q

E

R

36599346

105408

1

89

ACA TAT ACG GAC GGG GGT CGG ATT ACG

Q

D

Q

I

N

Q3

Q

E

R

R

N

Q3

R

H

R

I

H

R

E

N3

Q2

Q

Q

R

R

N

Q3

21505752

166494

1

90

GAT CAT AAC CCG GGT TGG CCT AAG GAC

R

Q

Q2

E

Q1

Q2

Q

Q1

R2

E

D

R

R

H

Q2

Q

D

Q

E

Q

R

E

N3

Q2

Q

Q1

R2

21718140

261012

1

91

GAT CAG GCC GTT AAG ACA CAG CCT AAC

R

Q

Q2

E

1

R

R

Q3

R2

R

I

Q3

Q

Q

R

E

Q3

R2

R

N3

Q2

R

Q

Q2

R

N3

Q2

30361419

297740

1

92

AAT GCA ACG GAT GCT CCC GCT GAT GCT

Q

N

Q3

R

D

Q

Q

E

R

R

Q

Q2

R

N3

Q2

Q

I

R2

Q

Q

R

R

N

R

Q

I

R

68828940

208472

1

93

GAT CCT ATC GGT GAT ATC AGG GAG ATG

R

Q

Q2

E

N3

Q2

Q

I

R2

R

H

Q2

R

Q

Q2

I

N

Q

R

H

R

Q

N

Q3

Q

E

R

41422185

110016

1

94

CAC TCT GAG GTC GGA TAA GGG AAT ACG

E

N

E

I1

N3

Q2

R

N

R

R

I

R2

R

N

Q

R

E

R

I

Q3

R2

R

N

Q

R

E

R

32161923

113354

1

95

GCT CCC AGC GCA GCT GCG TCC GGA GCG

R

N3

Q2

E

Q3

R2

Q

H1

R2

R

D

Q

R

N3

Q2

I

N

E

R

D

Q

Q

I

R

Q

D

Q

23772042

285203

1

96

GAT GGT CCC GGG CCT TAC GCA ATG ACA

R

Q

Q2

R

H

Q2

E

Q3

R2

R

H

R

E

N3

Q2

E

D

R

E

H1

R2

R

N

Q3

R

Q

Q2

23602050

141855

1

97

GAG ATG CGT ATC TCT CCG CGC GAC GAT

R

N

R

Q

I

R

E

H

Q2

Q

I

R2

I1

N3

Q2

R

D

Q

R

H

Q2

R

N

Q

R

Q3

R2

24759504

117310

1

98

ACT GAG GAG CCT AAG CCA GGT GAA GCC

Q

N3

Q2

R

N

R

R

N

R

E

N3

Q2

Q

Q

R

R

I

Q

R

H1

R2

Q

N3

Q2

Q

Q3

R2

76718610

17311796

1

99

AAC TAT GAC CCG AGG GTA GGC ACT ACC

Q

Q1

R2

I

N

Q3

R

N

Q3

R

E

R

Q

Q

R

R

N

Q

R

H1

R2

Q

N3

Q2

Q

Q3

R2

32201523

202169

1

100

ACT AAG CGT ACA AAG CTC GGA GCA ACC

Q

NE

Q2

Q

Q

R

E

H

Q2

Q

D

Q

Q

Q

R

E

I

R2

R

N

Q

R

D

Q

Q

Q3

R2

50819418

124234

*The Optimal DNA sequence in gene 1 is shown as SEQ ID NO: 109 in the Sequence Listing. The sequences in genes 3-31 are shown as SEQ ID NOS: 110-138, respectively. The sequences in genes 33-100 are shown as SEQ ID NOS: 139-206, respectively.

REFERENCES

1. Miller, J., McLachlan, A. D. and Klug, A. (1985) EMBO J. 4, 1609-1614.

2. Berg, J. M. (1988) Proc. Natl. Acad. Sci. USA 85, 99-102.

3. Gibson, T. J., Postma, J. P. M., Brown, R. S. and Argos, P. (1988) Protein Eng. 2, 209-218.

4. Lee, M. S., Gippert, G. P., Soman, K. V., Case, D. A. and Wright, P. E. (1989) Science 245, 635-637.

5. Nardelli, J., Gibson, T. J., Vesque, C. and Charnay, P. (1991) Nature 349, 175-178.

6. Thiesen, H. J. and Bach, C. (1991) FEBS Lett. 283, 23-26.

7. Pavletich, N. P. and Pabo, C. O. (1991) Science 252, 809-817.

8. Berg, J. M. (1992) Proc. Natl. Acad. Sci. USA89, 11109-11110.

9. Kriwacki, R. W., Schultz, S. C., Steitz, T. A. and Caradonna, J. P. (1992) Proc. Natl. Acad. Sci. USA 89, 9759-9763.

10. Jacobs, G. H. (1992) EMBO J. 11, 4507-4517.

11. Gogos, J. A., Hsu, T., Bolton, J. and Kafatos, F. C. (1992) Science 257, 1951-1955.

12. Fairall, L., Harrison, S. D., Travers, A. A. and Rhodes, D. (1992) J. Mol. Biol. 226, 349-366.

13. Klevit, R. E. (1991) Science 253, 1367 and 1393.

14. Desjarlais, J. R. and Berg, J. M. (1992) Proc. Natl. Acad. Sci. USA 89, 7345-7349.

15. Rebar, E. J., and Pabo, C. O., U.S. Pat. No. 5,789,538, Aug. 4, 1998.

16. Beerli, R. R., Segal, D. J., Dreier, B., and Barbas, C. F. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 14628-14633.

17. Jordan, S. R. and Pabo, C. O. (1988) Science 242, 893-899.

18. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. and Harrison S. C. (1988) Science 242, 899-907.

19. Letovsky, J., Dyran, W. S. (1989) Nucleic Acids Res. 17, 2639-2653.

20. Kissinger, C. R., Liu, B., Martin-Blanco, E., Kornberg, T. B. and Pabo, C. O. (1990) Cell 63, 579-590.

21. Wolberger, C., Vershon, A. K., Liu, B., Johnson, A. D. and Pabo, C. O. (1991) Cell 67, 517-528.

22. Seeman, N.C., Rosenberg, J. M. and Rich, A. (1976) Proc. Natl. Acad. Sci USA 73, 804-808.

23. Mikelsaar, R. -H., Bruskov, V. I. and Poltev, V. I. (1985) New precision space-filling atomic-molecular models, Pushchino.

24. Mikelsaar, R. (1986) Trends in Biotechnology 4, 162-163.

231 1 34 PRT Artificial Sequence Description of Artificial Sequence Hypothetical Zinc-Finger Binding Site 1Xaa Xaa Cys Xaa Xaa Xaa Xaa Cys Xaa Xaa Xaa Phe Xaa Xaa Xaa Xaa1 5 10 15Xaa Leu Xaa Xaa His Xaa Xaa Xaa Xaa Xaa His Xaa Xaa Xaa Xaa Glu 20 25 30Xaa Pro 2 8 PRT Artificial Sequence Description of Artificial Sequence Zinc-Finger Domain Segment 2Xaa Xaa Xaa Xaa Leu Xaa Xaa His1 5 3 27 PRT Artificial Sequence Description of Artificial Sequence Zinc-Finger Domain Segment 3Xaa Xaa Cys Xaa Xaa Xaa Xaa Cys Xaa Xaa Xaa Phe Xaa Xaa Xaa Xaa1 5 10 15Xaa Leu Xaa Xaa His Xaa Xaa Xaa Xaa Xaa His 20 25 4 7 PRT Artificial Sequence Description of Artificial Sequence Peptide Linker 4Xaa Xaa Xaa Xaa Glu Xaa Pro1 5 5 27 DNA Saccharomyces cerevisiae 5cctactctca gattccactt cactcca 27 6 27 DNA Saccharomyces cerevisiae 6tcagagctca cttagcccaa tactaca 27 7 27 DNA Saccharomyces cerevisiae 7gccgcttggg acgtcgcaga aggagcc 27 8 27 DNA Saccharomyces cerevisiae 8gaaaagcata cagcttccga tacatca 27 9 27 DNA Saccharomyces cerevisiae 9agtagcataa taggatctag tactgcc 27 10 27 DNA Saccharomyces cerevisiae 10gccgtggaaa caattgcaga ggagatg 27 11 27 DNA Saccharomyces cerevisiae 11ccaagtcgag acgcttaaag ttaagtg 27 12 27 DNA Saccharomyces cerevisiae 12gactacagcg gcatgcctgc cagcaaa 27 13 27 DNA Saccharomyces cerevisiae 13acttggactg ccgagcgggt cgatcaa 27 14 27 DNA Saccharomyces cerevisiae 14gacccaactg cgcacgctgc caaggag 27 15 27 DNA Saccharomyces cerevisiae 15gctgccagca gttgtgcgga cctgcat 27 16 27 DNA Saccharomyces cerevisiae 16gataacacag tgcagaagac tcctaca 27 17 27 DNA Saccharomyces cerevisiae 17tatgcacccg atacagaggg tgtcgag 27 18 27 DNA Saccharomyces cerevisiae 18caagagcacg acggccgcag taagcac 27 19 27 DNA Saccharomyces cerevisiae 19gagatacccg tgatacgtcg cggtaaa 27 20 27 DNA Saccharomyces cerevisiae 20aatggggcac gacctccaga gggtgat 27 21 27 DNA Saccharomyces cerevisiae 21gagagacccc aggcgtgaga cacgtct 27 22 27 DNA Saccharomyces cerevisiae 22acctccgctg tcatgggtac gggtggc 27 23 27 DNA Saccharomyces cerevisiae 23gaaccgagtt aggggcgatc taagcga 27 24 27 DNA Saccharomyces cerevisiae 24gatggaacac ccaagggtcg tcgtgaa 27 25 27 DNA Saccharomyces cerevisiae 25accgaccata caggacgtgc tgccacc 27 26 27 DNA Saccharomyces cerevisiae 26gaaagacgga agctcgatgc taacgct 27 27 27 DNA Saccharomyces cerevisiae 27agtcaactgg gaagggtccg gcatcat 27 28 27 DNA Saccharomyces cerevisiae 28aggatggtac gtgccacggg accatct 27 29 27 DNA Saccharomyces cerevisiae 29atggaccacc cgcatgcccg ctgtgag 27 30 27 DNA Saccharomyces cerevisiae 30aagaccccca cgcctgtgtc cgcacct 27 31 27 DNA Saccharomyces cerevisiae 31gatcagcccg ccggccctgg tgcggac 27 32 27 DNA Saccharomyces cerevisiae 32agtccgcacc agggccggcg ggctgat 27 33 27 DNA Saccharomyces cerevisiae 33aatggcgcta accgggacag tagcgac 27 34 27 DNA Saccharomyces cerevisiae 34gccactgccg cctctgtcag cgctgcc 27 35 27 DNA Saccharomyces cerevisiae 35actccgaggc gagcgcaaag cggaaca 27 36 27 DNA Saccharomyces cerevisiae 36accgtcgctg cctccgctgt cgctgct 27 37 27 DNA Saccharomyces cerevisiae 37acgtaggcag acgagctcag tcaagag 27 38 27 DNA Saccharomyces cerevisiae 38accaccctgg ttaccgtccc cggtgtc 27 39 27 DNA Saccharomyces cerevisiae 39acaacccagg aaaacgcctc cgaagcc 27 40 27 DNA Saccharomyces cerevisiae 40caacaagcga gatgggcgga tatccca 27 41 27 DNA Saccharomyces cerevisiae 41gccggatgcg aggacgcaag cagggga 27 42 27 DNA Saccharomyces cerevisiae 42aaaggtaccg ctacgccacc tacgggt 27 43 27 DNA Saccharomyces cerevisiae 43actgatcgtg aaccccgtca aggtaag 27 44 27 DNA Saccharomyces cerevisiae 44caacgggact ccgcagacgg gagcaat 27 45 27 DNA Saccharomyces cerevisiae 45cccgaggagg tacccctaga tcactat 27 46 27 DNA Saccharomyces cerevisiae 46gacccttatg ctctatccga gcacgat 27 47 27 DNA Saccharomyces cerevisiae 47caaggtggac agccgaacat agctggt 27 48 27 DNA Saccharomyces cerevisiae 48ccggattaca cgtctgcctc gaccgca 27 49 27 DNA Saccharomyces cerevisiae 49ggtgccgata cggataatgc ggtaact 27 50 27 DNA Saccharomyces cerevisiae 50atcagcgact ctaggccgca cgttcag 27 51 27 DNA Saccharomyces cerevisiae 51acgcctgaag aggcgcacac tcctgcc 27 52 27 DNA Saccharomyces cerevisiae 52tctagtgccc ggaacacacg gagagca 27 53 27 DNA Saccharomyces cerevisiae 53agcgctgatg agagagacgc ggaagat 27 54 27 DNA Saccharomyces cerevisiae 54accgccgcac caacggcact cgcgacg 27 55 27 DNA Saccharomyces cerevisiae 55acgggagata gcactccctc aggcacg 27 56 27 DNA Saccharomyces cerevisiae 56gacgagggcg gccgcatagt gcacgca 27 57 27 DNA Saccharomyces cerevisiae 57accgctggcg cagacgccac tagcaag 27 58 27 DNA Saccharomyces cerevisiae 58tatgagccgt accagatacg tgctaat 27 59 27 DNA Saccharomyces cerevisiae 59cagacaccac cgagccccga tcaagag 27 60 27 DNA Saccharomyces cerevisiae 60catcgcgttg gcactcggtc ccgaaag 27 61 27 DNA Saccharomyces cerevisiae 61gctattgggc ctgcccggtg tagggcc 27 62 27 DNA Saccharomyces cerevisiae 62attcctgata cggcggttga caaggag 27 63 27 DNA Saccharomyces cerevisiae 63gacgccaggg acgagcaagg ggacgaa 27 64 27 DNA Saccharomyces cerevisiae 64gtcgccaacg ctcacggtgt ggaaacc 27 65 27 DNA Saccharomyces cerevisiae 65agaaggggca agcgtggtcg tgacgat 27 66 27 DNA Saccharomyces cerevisiae 66cagcagagcg actaaactac tgcacga 27 67 27 DNA Saccharomyces cerevisiae 67gatgtgggga accatgccca ggatgat 27 68 27 DNA Saccharomyces cerevisiae 68actgtgggca acagtacggc aattacc 27 69 27 DNA Saccharomyces cerevisiae 69actgacgagc atgaagctga tgtcaat 27 70 27 DNA Saccharomyces cerevisiae 70gacccagaag tgcaggctga catgaag 27 71 27 DNA Saccharomyces cerevisiae 71gatcattagc aaagtgagca acacacg 27 72 27 DNA Saccharomyces cerevisiae 72gatgggaagt aagacccccg atatgag 27 73 27 DNA Saccharomyces cerevisiae 73ggtgctcggc atacagccct gattgtt 27 74 27 DNA Saccharomyces cerevisiae 74catgtcagca ctgcacagga gccgaaa 27 75 27 DNA Saccharomyces cerevisiae 75gctagcgcta ctgtgccttc cgctccc 27 76 27 DNA Saccharomyces cerevisiae 76gatcgtgaag ctacctttag agacgcc 27 77 27 DNA Saccharomyces cerevisiae 77aacgttggtg agagtcctgg aaggggc 27 78 27 DNA Saccharomyces cerevisiae 78gctgaagccg actatcttgc cgatgag 27 79 27 DNA Saccharomyces cerevisiae 79gaataacatt agagcggggc gccaaac 27 80 27 DNA Saccharomyces cerevisiae 80caatgcacag acaaattcga tactcac 27 81 27 DNA Saccharomyces cerevisiae 81gctaatcacg tcgacgtcgg gcatgga 27 82 27 DNA Saccharomyces cerevisiae 82cctgcccagg ccgctgagct ggtgggt 27 83 27 DNA Saccharomyces cerevisiae 83acccaggcag tggaggagcg agccagg 27 84 27 DNA Saccharomyces cerevisiae 84cgagcggctc ccgctccctg ggcagaa 27 85 27 DNA Saccharomyces cerevisiae 85gtgcctccgc cgcagcaacc actacat 27 86 27 DNA Saccharomyces cerevisiae 86cctgatgtac agtgggatac agcgaat 27 87 27 DNA Saccharomyces cerevisiae 87ccaacgaacg gtgcagagaa tacgcag 27 88 27 DNA Saccharomyces cerevisiae 88ggtgatcgca cgcaagcctg cggggaa 27 89 27 DNA Saccharomyces cerevisiae 89gagaagccaa caagcaacgc tgaggaa 27 90 27 DNA Saccharomyces cerevisiae 90gaggcgacat aagttgttag cacagca 27 91 27 DNA Saccharomyces cerevisiae 91gatcatgggc tatgggatac tccctac 27 92 27 DNA Saccharomyces cerevisiae 92aagttagata cacttaacga acctagt 27 93 27 DNA Saccharomyces cerevisiae 93aatgctccca ggggctcggc caggacc 27 94 27 DNA Saccharomyces cerevisiae 94gattcgccac ggcacactcc gcacaga 27 95 27 DNA Saccharomyces cerevisiae 95gcggagtgag ccgccgaggc caacgac 27 96 27 DNA Saccharomyces cerevisiae 96acatcgccgc ctaccagtcc cgcggtg 27 97 27 DNA Saccharomyces cerevisiae 97ggtatcgcca gtctccgggt ccatacc 27 98 27 DNA Saccharomyces cerevisiae 98atcactcccg gtccacattc taggaag 27 99 27 DNA Saccharomyces cerevisiae 99aatgtcagtt gtgacgctag acttttc 27 100 27 DNA Saccharomyces cerevisiae 100aatactgtag ctgctgagac gattacc 27 101 27 DNA Saccharomyces cerevisiae 101agctgtggaa acaatcgcag gggagat 27 102 27 DNA Saccharomyces cerevisiae 102gtagaaatct gctgcacatg ccacacg 27 103 27 DNA Saccharomyces cerevisiae 103gctacggaga aaccgtgcac taactct 27 104 27 DNA Saccharomyces cerevisiae 104accgtttcct ccaagtcata caccact 27 105 27 DNA Saccharomyces cerevisiae 105ctatatattt gtggcagaaa tcatacc 27 106 27 DNA Saccharomyces cerevisiae 106tatcatgaca acatggtaca aattgag 27 107 27 DNA Saccharomyces cerevisiae 107aagaccgcac tagatcttac caagagc 27 108 27 DNA Saccharomyces cerevisiae 108atgacgacat ccaagccagc ttttacc 27 109 27 DNA Caenorhabditis elegans 109acgaagccgc ccgactccta ggagatg 27 110 27 DNA Caenorhabditis elegans 110gacgccgagc acgagcacag gagcgaa 27 111 27 DNA Caenorhabditis elegans 111gacaattctc ccggcgccaa tgatcac 27 112 27 DNA Caenorhabditis elegans 112agcacgactc ggcacacccg ttccgcc 27 113 27 DNA Caenorhabditis elegans 113ccaggaaggc gcactggcag acgtaag 27 114 27 DNA Caenorhabditis elegans 114gctattactc gtggtgccgc gggagcc 27 115 27 DNA Caenorhabditis elegans 115aatagcgaac agatatctga caactcc 27 116 27 DNA Caenorhabditis elegans 116gtcgcgcata ctaaggctcg ctttaat 27 117 27 DNA Caenorhabditis elegans 117gatattcgcg atggcaccgg tgacgat 27 118 27 DNA Caenorhabditis elegans 118cataacgtcg aggctgcccg caaggag 27 119 27 DNA Caenorhabditis elegans 119accagccatc acgccatgcg aagcacc 27 120 27 DNA Caenorhabditis elegans 120aggcaccccg ggaagcgccg gaccgaa 27 121 27 DNA Caenorhabditis elegans 121ggagcaccag acgccccgac taagccg 27 122 27 DNA Caenorhabditis elegans 122gatgctcgcc tactcgcgag gccaaga 27 123 27 DNA Caenorhabditis elegans 123agagccgatg cccgcaccaa ggctgct 27 124 27 DNA Caenorhabditis elegans 124acagacgagg ccaagatcta cgccgaa 27 125 27 DNA Caenorhabditis elegans 125ccaaccggta ggccgatagg tagtcgc 27 126 27 DNA Caenorhabditis elegans 126cctacaaggc cccgtacgag ggccgat 27 127 27 DNA Caenorhabditis elegans 127accaacggac aggatggcgc cgaacaa 27 128 27 DNA Caenorhabditis elegans 128gcaagccgct atgtcgacgc tcgccaa 27 129 27 DNA Caenorhabditis elegans 129agtccgccta agcgccctgt tccgccg 27 130 27 DNA Caenorhabditis elegans 130aagcggatcg ctgcgaccga accgcct 27 131 27 DNA Caenorhabditis elegans 131aatgatctag ctcccagtcc tactgcg 27 132 27 DNA Caenorhabditis elegans 132cagaggactc gccgtatcgt cgctggt 27 133 27 DNA Caenorhabditis elegans 133gctatgaggt cacgggctcc ccctgat 27 134 27 DNA Caenorhabditis elegans 134gacacaggtc cccatcacgg gacaagt 27 135 27 DNA Caenorhabditis elegans 135cacgttggga ccgccaggag cccgaat 27 136 27 DNA Caenorhabditis elegans 136cgagaacgtc ccatcaagcg tgaacac 27 137 27 DNA Caenorhabditis elegans 137gatccttcga gtacgcctac gcaagga 27 138 27 DNA Caenorhabditis elegans 138aacgccgcct agaccccggg gaatacc 27 139 27 DNA Caenorhabditis elegans 139gtggtgcagg aggggcagga ggccaca 27 140 27 DNA Caenorhabditis elegans 140cgtacaagga ataccctgaa ggacaac 27 141 27 DNA Caenorhabditis elegans 141acctccactc agcgaccacc ggcgcca 27 142 27 DNA Caenorhabditis elegans 142aaagcggtac aagcgacgac ccgtgct 27 143 27 DNA Caenorhabditis elegans 143acaacgaccg aggagcctac cgaagcc 27 144 27 DNA Caenorhabditis elegans 144gagaaccgtc cccacccgaa gctggct 27 145 27 DNA Caenorhabditis elegans 145cgtcgggtgc ccgagactgg gaccggt 27 146 27 DNA Caenorhabditis elegans 146agggaccgta cggaacagga cccccct 27 147 27 DNA Caenorhabditis elegans 147aggcaaccct ggaggcgtcc cagcacc 27 148 27 DNA Caenorhabditis elegans 148ctcactaccc cggcaccaag gaccagt 27 149 27 DNA Caenorhabditis elegans 149gacgagcacc taaagaccgc cactccg 27 150 27 DNA Caenorhabditis elegans 150cccgtcgggt agacggcggt taccggc 27 151 27 DNA Caenorhabditis elegans 151aggccagggg ccccctacgc cccaaca 27 152 27 DNA Caenorhabditis elegans 152caagctcccg taacacaacc ccggaga 27 153 27 DNA Caenorhabditis elegans 153cccgggggcc cccctccggc ggacgat 27 154 27 DNA Caenorhabditis elegans 154actgcccaaa tcaaggcccc gagacat 27 155 27 DNA Caenorhabditis elegans 155actactccca cgcggcggac acccaac 27 156 27 DNA Caenorhabditis elegans 156atcgacccgc atgcgctggc gcagacg 27 157 27 DNA Caenorhabditis elegans 157agtaccgcgg atcaggcggc gtccgta 27 158 27 DNA Caenorhabditis elegans 158gcagctcaag caggcgacaa cgccgaa 27 159 27 DNA Caenorhabditis elegans 159gtgaccgaca cgcccagtaa gtcggga 27 160 27 DNA Caenorhabditis elegans 160gacctggcgg cggccgccgg tagcaag 27 161 27 DNA Caenorhabditis elegans 161accgccgccg agctctgcgg cgctgaa 27 162 27 DNA Caenorhabditis elegans 162aaagaccgca aagcagggac gcaagat 27 163 27 DNA Caenorhabditis elegans 163cctacggcgc tagacaggac tccgcag 27 164 27 DNA Caenorhabditis elegans 164agagcgcacc ggcagacgcg cgggaat 27 165 27 DNA Caenorhabditis elegans 165ggacgtcgcg cagacaccgc ccaaaga 27 166 27 DNA Caenorhabditis elegans 166aatcagtcag acccagaggg tgaagct 27 167 27 DNA Caenorhabditis elegans 167caacatcgtc ccggcgacac cgacgac 27 168 27 DNA Caenorhabditis elegans 168ggagcccgtg cggcggatcc gcgctaa 27 169 27 DNA Caenorhabditis elegans 169gccactcagg cagcaactca ggcagcc 27 170 27 DNA Caenorhabditis elegans 170ccaaatggtc aagccgggga ggcaaac 27 171 27 DNA Caenorhabditis elegans 171ccaatggcca tcgacgcggc gaccaca 27 172 27 DNA Caenorhabditis elegans 172gaccgtcagg atcgcgatta ccggcca 27 173 27 DNA Caenorhabditis elegans 173acagcggcag ctactacctc tcccgaa 27 174 27 DNA Caenorhabditis elegans 174gcccagccaa ccacggggag ggctagg 27 175 27 DNA Caenorhabditis elegans 175aacaacaggc cagctggagg gaatact 27 176 27 DNA Caenorhabditis elegans 176aacgcgagcg gaacctaacc gacgcaa 27 177 27 DNA Caenorhabditis elegans 177gcacgcaacg ctgcacgcag cgcagca 27 178 27 DNA Caenorhabditis elegans 178aatccgccca cgtacatcgg tccccaa 27 179 27 DNA Caenorhabditis elegans 179gaggttcggg cttcagggca ggcggcc 27 180 27 DNA Caenorhabditis elegans 180aagcaggcgc aaggtaggcc tggggta 27 181 27 DNA Caenorhabditis elegans 181cagacagtag cctctgcgca tgaggag 27 182 27 DNA Caenorhabditis elegans 182gcccccgacc aactcagggc caccgct 27 183 27 DNA Caenorhabditis elegans 183gcttaggtag ccctgaaggc taacaga 27 184 27 DNA Caenorhabditis elegans 184ggcgaggaca cggcaccacg ccaacga 27 185 27 DNA Caenorhabditis elegans 185acaagccacg ctcccggtta gtcgaga 27 186 27 DNA Caenorhabditis elegans 186gagcaaaccg tggccacgtt gaaccat 27 187 27 DNA Caenorhabditis elegans 187ccaaacctta caagccgtgc ggaggaa 27 188 27 DNA Caenorhabditis elegans 188actgctggtg caccgaagga agacaag 27 189 27 DNA Caenorhabditis elegans 189ctcccaagtg cgtctgatcc cgatacc 27 190 27 DNA Caenorhabditis elegans 190catgtaggaa gtaacgtcgc ccatggc 27 191 27 DNA Caenorhabditis elegans 191gaaaagggcg acgccacccc actgcac 27 192 27 DNA Caenorhabditis elegans 192actcggggcg gtgtgctcag gactaga 27 193 27 DNA Caenorhabditis elegans 193acacgccaga cggcccacgc ccccaat 27 194 27 DNA Caenorhabditis elegans 194aatggtgctt atgtctgcga tcatgct 27 195 27 DNA Caenorhabditis elegans 195acatatacgg acgggggtcg gattacg 27 196 27 DNA Caenorhabditis elegans 196gatcataacc cgggttggcc taaggac 27 197 27 DNA Caenorhabditis elegans 197gatcaggccg ttaagacaca gcctaac 27 198 27 DNA Caenorhabditis elegans 198aatgcaacgg atgctcccgc tgatgct 27 199 27 DNA Caenorhabditis elegans 199gatcctatcg gtgatatcag ggagatg 27 200 27 DNA Caenorhabditis elegans 200cactctgagg tcggataagg gaatacg 27 201 27 DNA Caenorhabditis elegans 201gctcccagcg cagctgcgtc cggagcg 27 202 27 DNA Caenorhabditis elegans 202gatggtcccg ggccttacgc aatgaca 27 203 27 DNA Caenorhabditis elegans 203gagatgcgta tctctccgcg cgacgat 27 204 27 DNA Caenorhabditis elegans 204actgaggagc ctaaggcagg tgaagcc 27 205 27 DNA Caenorhabditis elegans 205aactatgacg cgagggtagg cactacc 27 206 27 DNA Caenorhabditis elegans 206actaagcgta caaagctcgg agcaacc 27 207 25 PRT Xenopus laevis 207Tyr Ile Cys Ser Phe Ala Asp Cys Gly Ala Ala Tyr Asn Lys Asn Trp1 5 10 15Lys Leu Gln Ala His Leu Cys Lys His 20 25 208 30 PRT Xenopus laevis 208Thr Gly Glu Lys Pro Phe Pro Cys Lys Glu Glu Gly Cys Glu Lys Gly1 5 10 15Phe Thr Ser Leu His His Leu Thr Arg His Ser Leu Thr His 20 25 30 209 31 PRT Xenopus laevis 209Thr Gly Glu Lys Asn Phe Thr Cys Asp Ser Asp Gly Cys Asp Leu Arg1 5 10 15Phe Thr Thr Lys Ala Asn Met Lys Lys His Phe Asn Arg Phe His 20 25 30 210 31 PRT Xenopus laevis 210Asn Ile Lys Ile Cys Val Tyr Val Cys His Phe Glu Asn Cys Gly Lys1 5 10 15Ala Phe Lys Lys His Asn Gln Leu Lys Val His Gln Phe Ser His 20 25 30 211 30 PRT Xenopus laevis 211Thr Gln Gln Leu Pro Tyr Glu Cys Pro His Glu Gly Cys Asp Lys Arg1 5 10 15Phe Ser Leu Pro Ser Arg Leu Lys Arg His Glu Lys Val His 20 25 30 212 29 PRT Xenopus laevis 212Ala Gly Tyr Pro Cys Lys Lys Asp Asp Ser Cys Ser Phe Val Gly Lys1 5 10 15Thr Trp Thr Leu Tyr Leu Lys His Val Ala Glu Cys His 20 25 213 26 PRT Xenopus laevis 213Gln Asp Leu Ala Val Cys Asp Val Cys Asn Arg Lys Phe Arg His Lys1 5 10 15Asp Tyr Leu Arg Asp His Gln Lys Thr His 20 25 214 32 PRT Xenopus laevis 214Glu Lys Glu Arg Thr Val Tyr Leu Cys Pro Arg Asp Gly Cys Asp Arg1 5 10 15Ser Tyr Thr Thr Ala Phe Asn Leu Arg Ser His Ile Gln Ser Phe His 20 25 30 215 30 PRT Xenopus laevis 215Glu Glu Gln Arg Pro Phe Val Cys Glu His Ala Gly Cys Gly Lys Cys1 5 10 15Phe Ala Met Lys Lys Ser Leu Glu Arg His Ser Val Val His 20 25 30 216 25 PRT Xenopus laevis 216Tyr Lys Cys Gly Leu Cys Glu Arg Ser Phe Val Glu Lys Ser Ala Leu1 5 10 15Ser Arg His Gln Arg Val His Lys Asn 20 25 217 29 PRT Saccharomyces cerevisiae 217Thr Asn Leu Lys Pro Tyr Pro Cys Gly Leu Cys Asn Arg Cys Phe Thr1 5 10 15Arg Arg Asp Leu Leu Ile Arg His Ala Gln Lys Ile His 20 25 218 23 PRT Mus musculus 218Tyr Gly Cys Asp Glu Cys Gly Lys Thr Phe Arg Gln Ser Ser Ser Leu1 5 10 15Leu Lys His Gln Arg Ile His 20 219 28 PRT Mus musculus 219Thr Gly Glu Lys Pro Tyr Thr Cys Asn Val Cys Asp Lys His Phe Ile1 5 10 15Glu Arg Ser Ser Leu Thr Val His Gln Arg Thr His 20 25 220 28 PRT Mus musculus 220Thr Gly Glu Lys Pro Tyr Lys Cys His Glu Cys Gly Lys Ala Phe Ser1 5 10 15Gln Ser Met Asn Leu Thr Val His Gln Arg Thr His 20 25 221 28 PRT Mus musculus 221Thr Gly Glu Lys Pro Tyr Gln Cys Lys Glu Cys Gly Lys Ala Phe Arg1 5 10 15Lys Asn Ser Ser Leu Ile Gln His Glu Arg Ile His 20 25 222 28 PRT Mus musculus 222Thr Gly Glu Lys Pro Tyr Lys Cys His Asp Cys Glu Lys Ala Phe Ser1 5 10 15Lys Asn Ser Ser Leu Thr Gln His Arg Arg Ile His 20 25 223 28 PRT Mus musculus 223Thr Gly Glu Lys Pro Tyr Glu Cys Met Ile Cys Gly Lys His Phe Thr1 5 10 15Gly Arg Ser Ser Leu Thr Val His Gln Val Ile His 20 25 224 28 PRT Mus musculus 224Thr Gly Glu Lys Pro Tyr Glu Cys Thr Glu Cys Gly Lys Ala Phe Ser1 5 10 15Gln Ser Ala Tyr Leu Ile Glu His Arg Arg Ile His 20 25 225 28 PRT Mus musculus 225Thr Gly Glu Lys Pro Tyr Glu Cys Asp Gln Cys Gly Lys Ala Phe Ile1 5 10 15Lys Asn Ser Ser Leu Ile Val His Gln Arg Ile His 20 25 226 28 PRT Mus musculus 226Thr Gly Glu Lys Pro Tyr Gln Cys Asn Glu Cys Gly Lys Pro Phe Ser1 5 10 15Arg Ser Thr Asn Leu Thr Arg His Gln Arg Thr His 20 25 227 23 PRT Drosophila melanogaster 227Phe Thr Cys Lys Ile Cys Ser Arg Ser Phe Gly Tyr Lys His Val Leu1 5 10 15Gln Asn His Glu Arg Thr His 20 228 28 PRT Drosophila melanogaster 228Thr Gly Glu Lys Pro Phe Glu Cys Pro Glu Cys Asp Lys Arg Phe Thr1 5 10 15Arg Asp His His Leu Lys Thr His Met Arg Leu His 20 25 229 28 PRT Drosophila melanogaster 229Thr Gly Glu Lys Pro Tyr His Cys Ser His Cys Asp Arg Gln Phe Val1 5 10 15Gln Val Ala Asn Leu Arg Arg His Leu Arg Val His 20 25 230 28 PRT Drosophila melanogaster 230Thr Gly Glu Lys Pro Tyr Thr Cys Glu Ile Cys Asp Gly Lys Phe Ser1 5 10 15Asp Ser Asn Gln Leu Lys Ser His Met Leu Val His 20 25 231 5 PRT Drosophila melanogaster 231Thr Gly Glu Lys Pro1 5

Claims

1. A method for designing a DNA-binding protein (DBP), with multiple zinc-finger (ZF) domains connected by linker sequences, that binds selectively to a target DNA sequence within a given gene, each of said ZF domains having the formulaA1XCX2-4CA2A3XFXZ3XXZ2LXZ1HX3-5H   (SEQ ID NO: 3) and each of said linkers having the formulaA4A5X0-2EA6 P   (SEQ ID NO 4), wherein(i) X is any amino acid; (ii) X2-4 is a peptide from 2 to 4 amino acids in length; (iii) X3-5 is a peptide from 3 to 5 amino acids in length; (iv) X0-2 is a peptide from 0 to 2 amino acids in length; (iv) A1 is selected from the group consisting of phenylalanine and tyrosine; (v) A2 is selected from the group consisting of glycine and aspartic acid; (vi) A3 is selected from the group consisting of lysine and arginine; (vii) A4 is selected from the group consisting of threonine and serine; (viii) A5 is selected from the group consisting of glycine and glutamic acid; (ix) A6 is selected from the group consisting of lysine and arginine; (x) C is cysteine; (xi) F is phenylalanine; (xii) L is leucine; (xiii) H is histidine; (xiv) E is glutamic acid; (xv) P is proline; and (xvi) Z1, Z2 and Z3 are the base-contacting amino acids, which method comprises an algorithm comprising the steps of: (a) setting a genome to be screened; (b) selecting the target DNA sequence in the genome for binding; (c) setting the number of ZF domains to nd; (d) dividing the target DNA sequence into nucleotide blocks wherein each block contains nz nucleotides using a first routine where nz is determined using the following relationship: nz=3nd; (e) assigning base-contacting amino acids at Z1, Z2 and Z3 to each ZF domain, according to the A Rules and/or B Rules set forth in Tables 1-3 of the specification, of a DBP which binds to the first nucleotide block from step (d) as numbered from the first 5′ nucleotide of the target gene sequence to generate a block-specific DBP and calculating the binding energy, Binding Energyblock, of each ZF domain of each such block-specific DBP as the product of the binding energies, Binding Energydomain, of all ZF domains of the DBP, each determined using the formula: Binding Energydomain=(5×the number of hydrogen bonds)+(2×the number of H2O contacts)+(the number of hydrophobic contacts); (f) subdividing the DBP from step (d) into blocks using a second routine to generate a subdivided DBP having three ZF domains; (g) screening the subdivided DBP from step (f) against the genome using a third routine to determine the number of binding sites in the genome for each subdivided DBP in the genome and assigning a binding energy for each such site using the following formula: Binding Energysite n=(5×the number of hydrogen bonds)+(2×the number of H2O contacts)+(the number of hydrophobic contacts); (h) calculating a ratio of binding energy, Rb, using a fourth routine for each nucleotide block-specific DBP from step (e) using the following formula: Rb=Binding Energyblock/the sum of all Binding Energysite n's for all subdivided DBP's from step (g); (i) repeating steps (f) through (h) for each subdivided DBP wherein nd≧4; (j) repeating steps (d) through (i) for each nucleotide block in the target DNA sequence containing nz nucleotides; (k) rank-ordering Rb numerical values obtained from step (h); and (l) selecting a DBP with an acceptable Rb value.

2. The method of claim 1 wherein the DBP selected is that whose Rb numerical value is the highest numerical value for all DBP's in step (h) that bind to the target DNA sequence.

3. The method of claim 1 wherein the DBP Rb numerical value determined in step (h) is at least 10,000.

4. The method of claim 1 wherein the number of ZF domains, nd, is nine.

5. The method of claim 1 wherein the rule s for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are selected from rule set A.

6. The method of claim 1 wherein the rules for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are selected from rule set B.

7. The method of claim 1 wherein rules for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are a combination selected from rule sets A and B.

8. A computer system for designing a DNA-binding protein (DBP), with multiple zinc-finger (ZF) domains connected by linker sequences, that binds selectively to a target DNA sequence within a given gene, each of said ZF domains having the formulaA1XCX2-4CA2A3XFXZ3XXZ2LXZ1HX3-5H   (SEQ ID NO 3) and each of said linkers having the formulaA4A5X0-2EA6 P   (SEQ ID NO 4), wherein(i) X is any amino acid; (ii) X2-4 is a peptide from 2 to 4 amino acids in length; (iii) X3-5 is a peptide from 3 to 5 amino acids in length; (iv) X0-2 is a peptide from 0 to 2 amino acids in length; (iv) A1 is selected from the group consisting of phenylalanine and tyrosine; (v) A2 is selected from the group consisting of glycine and aspartic acid; (vi) A3 is selected from the group consisting of lysine and arginine; (vii) A4 is selected from the group consisting of threonine and serine; (viii) A5 is selected from the group consisting of glycine and glutamic acid; (ix) A6 is selected from the group consisting of lysine and arginine; (x) C is cysteine; (xi) F is phenylalanine; (xii) L is leucine; (xiii) H is histidine; (xiv) E is glutamic acid; (xv) P is proline; and (xvi) Z1, Z2 and Z3 are the base-contacting amino acids, which computer system comprises a computer readable memory which executes a method for designing the DBP, wherein the method comprises the steps of: (a) setting a genome to be screened; (b) selecting the target DNA sequence in the genome for binding; (c) setting the number of ZF domains to nd; (d) dividing the target DNA sequence into nucleotide blocks wherein each block contains nz nucleotides using a first routine where nz is determined using the following relationship: nz=3nd; (e) assigning base-contacting amino acids at Z1, Z2 and Z3 to each ZF domain, according to the A Rules and/or B Rules set forth in Tables 1-3 of the specification, of a DBP which binds to the first nucleotide block from step (d) as numbered from the first 5′ nucleotide of the target gene sequence to generate a block-specific DBP and calculating the binding energy, Binding Energyblock, of each ZF domain of each such block-specific DBP as the product of the binding energies, Binding Energydomain, of all ZF domains of the DBP, using the formula: Binding Energydomain=(5×the number of hydrogen bonds)+(2×the number of H2O contacts)+(the number of hydrophobic contacts); (f) subdividing the DBP from step (d) into blocks using a second routine to generate a subdivided DBP having three ZF domains; (g) screening the subdivided DBP from step (f) against the genome using a third routine to determine the number of binding sites in the genome for each subdivided DBP in the genome and assigning a binding energy for each such site using the following formula: Binding Energysite n=(5×the number of hydrogen bonds)+(2×the number of H2O contacts)+(the number of hydrophobic contacts); (h) calculating a ratio of binding energy, Rb, using a fourth routine for each nucleotide block-specific DBP from step (e) using the following formula: Rb=Binding Energyblock/the sum of all Binding Energysite n's for all subdivided DBP's from step (g); (i) repeating steps (f) through (h) for each subdivided DBP wherein nd≧4; (j) repeating steps (d) through (i) for each nucleotide block in the target DNA sequence containing nz nucleotides; (k) rank-ordering Rb numerical values obtained from step (h); and (l) selecting a DBP with an acceptable Rb value.

9. The computer system according to claim 8 wherein the DBP selected is that whose Rb numerical value is the highest numerical value for all DBP's in step (h) that bind to the target DNA sequence.

10. The computer system according to claim 8 wherein the DBP Rb numerical value determined in step (h) is at least 10,000.

11. The computer system according to claim 8 wherein the number of ZF domains, nd, is nine.

12. The computer system according to claim 8 wherein the rules for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are selected from rule set A.

13. The computer system according to claim 8 wherein the rules for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are selected from rule set B.

14. The computer system according to claim 8 wherein the rules for assigning base-contacting amino acids at Z1, Z2 and Z3 for each nucleotide block in step (e) are a combination selected from rule sets A and B.