MODIFIED TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE (TDT) ENZYMES

FIELD OF THE INVENTION

The invention relates to the use of specific terminal deoxynucleotidyl transferase (TdT) enzymes or the homologous amino acid sequence of Polμ, Polβ, Polλ, and Polθ of any species or the homologous amino acid sequence of X family polymerases of any species in a method of nucleic acid synthesis, to methods of synthesizing nucleic acids, and to the use of kits comprising said enzymes in a method of nucleic acid synthesis. The invention also relates to the use of terminal deoxynucleotidyl transferases or homologous enzymes and 3′-blocked nucleoside triphosphates in a method of template independent nucleic acid synthesis.

BACKGROUND OF THE INVENTION

Nucleic acid synthesis is vital to modern biotechnology. The rapid pace of development in the biotechnology arena has been made possible by the scientific community's ability to artificially synthesise DNA, RNA and proteins.

Artificial DNA synthesis allows biotechnology and pharmaceutical companies to develop a range of peptide therapeutics, such as insulin for the treatment of diabetes. It allows researchers to characterise cellular proteins to develop new small molecule therapies for the treatment of diseases our aging population faces today, such as heart disease and cancer. It even paves the way forward to creating life, as the Venter Institute demonstrated in 2010 when they placed an artificially synthesised genome into a bacterial cell.

However, current DNA synthesis technology does not meet the demands of the biotechnology industry. Despite being a mature technology, it is practically impossible to synthesise a DNA strand greater than 200 nucleotides in length, and most DNA synthesis companies only offer up to 120 nucleotides. In comparison, an average protein-coding gene is of the order of 2000-3000 contiguous nucleotides, a chromosome is at least a million contiguous nucleotides in length and an average eukaryotic genome numbers in the billions of nucleotides. In order to prepare nucleic acid strands thousands of base pairs in length, all major gene synthesis companies today rely on variations of a ‘synthesise and stitch’ technique, where overlapping 40-60-mer fragments are synthesised and stitched together by enzymatic copying and extension. Current methods generally allow up to 3 kb in length for routine production.

The reason DNA cannot be synthesised beyond 120-200 nucleotides at a time is due to the current methodology for generating DNA, which uses synthetic chemistry (i.e., phosphoramidite technology) to couple a nucleotide one at a time to make DNA. Even if the efficiency of each nucleotide-coupling step is 99% efficient, it is mathematically impossible to synthesise DNA longer than 200 nucleotides in acceptable yields. The Venter Institute illustrated this laborious process by spending 4 years and 20 million USD to synthesise the relatively small genome of a bacterium.

Known methods of DNA sequencing use template-dependent DNA polymerases to add 3′-reversibly terminated nucleotides to a growing double-stranded substrate. In the ‘sequencing-by-synthesis’ process, each added nucleotide contains a dye, allowing the user to identify the exact sequence of the template strand. Albeit on double-stranded DNA, this technology is able to produce strands of between 500-1000 bps long. However, this technology is not suitable for de novo nucleic acid synthesis because of the requirement for an existing nucleic acid strand to act as a template.

Various attempts have been made to use a terminal deoxynucleotidyl transferase for de novo single-stranded DNA synthesis. Uncontrolled de novo single-stranded DNA synthesis, as opposed to controlled, takes advantage of TdT's deoxynucleoside 5′-triphosphate (dNTP) 3′-tailing properties on single-stranded DNA to create, for example, homopolymeric adaptor sequences for next-generation sequencing library preparation. In controlled extensions, reversible deoxynucleoside 5′-triphosphate termination technology needs to be employed to prevent uncontrolled addition of dNTPs to the 3′-end of a growing DNA strand. The development of a controlled single-stranded DNA synthesis process through TdT would be invaluable to in situ DNA synthesis for gene assembly or hybridization microarrays as it removes the need for an anhydrous environment and allows the use of various polymers incompatible with organic solvents.

However, TdT has not been shown to efficiently add nucleoside triphosphates containing 3′-O-reversibly terminating moieties for building up a nascent single-stranded DNA chain necessary for a de novo synthesis cycle. A 3′-O-reversible terminating moiety would prevent a terminal transferase like TdT from catalysing the nucleotide transferase reaction between the 3′-end of a growing DNA strand and the 5′-triphosphate of an incoming nucleoside triphosphate.

There is therefore a need to identify modified terminal deoxynucleotidyl transferases that readily incorporate 3′-O-reversibly terminated nucleotides. Said modified terminal deoxynucleotidyl transferases can be used to incorporate 3′-O-reversibly terminated nucleotides in a fashion useful for biotechnology and single-stranded DNA synthesis processes in order to provide an improved method of nucleic acid synthesis that is able to overcome the problems associated with currently available methods.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1. Incorporation of 3′-O—CH₂—N₃nucleoside 5′-triphosphates by terminal deoxynucleotidyl transferase (TdT) SEQ ID NOs 1-173. Incorporation rate is defined by quantity (pmol) of reversibly terminated nucleoside 5′-triphosphate incorporation to the 3′-end of a single-stranded DNA molecule per nanogram of TdT per minute. Wild-type bovine TdT activity is represented by the dotted line near y-axis=0. The dynamic range of the assay saturates at 2.0 pmol incorporate per nanogram of TdT per minute.

FIG. 2. Sequence alignment of selected orthologs of wild-type terminal deoxynucleotidyl transferases using the Clustal Omega multiple sequence alignment program provided by the European Molecular Biology Laboratory (EMBL) multiple sequence alignment site.

FIG. 3. Top panel: Base-modified substrates A*, C*, G*, and T* were supplied to engineered variants in a single nucleotide incorporation assay. A* describes 3′-aminooxy 6-azido 2′-deoxyadenosine 5′-triphosphate; C* describes 3′-aminooxy 4-azido 5-methyl 2′-deoxycytidine 5′-triphosphate; G* describes 3′-aminooxy 2-azido 2′-deoxyguanosine 5′-triphosphate; T* describes 3′-aminooxy 5-(-hydroxy-1-butynyl) 2′-deoxyuridine 5′-triphosphate. A pool of DNA initiators with degenerate ends was immobilised to a solid support and exposed to nucleotide addition mixture (NAM) solutions containing (1) TdT variant, (2) neutral pH buffer, (3) monovalent salt, (4) cobalt chloride, and (5) 3′-ONH₂-dXTP, where X is a modified nucleobase resulting in A*, C*, G*, or T*. The incubation temperature was 37° C. and the reaction time was 2.5 minutes. The solid support was then washed with a high salt solution at neutral pH followed by a low salt solution at neutral pH. The initiator pools were transformed into sequencing libraries and analysed by next-generation sequencing (NGS) on an Illumina NextSeq500 with PE30 reads. Bcl files were converted to fastq files with Illumina's bcl2fastq conversion software and analysed in R. The incorporation efficiency ([reads containing N+1 product]/{[reads containing N initiator]+[reads containing N+1 product]}) was calculated for the addition of each modified base against to all possible initiator contexts. The average incorporation efficiency across all contexts is presented in FIG. 3 (top panel). The single nucleotide incorporations by wild-type bovine and wild-type spotted gar TdT of the base-modified reversibly terminated nucleotides A*, C*, G*, and T* are indicated by the dotted line. The dotted line occurs at y=0 due to the inability of wild-type bovine or spotted gar TdTs to incorporate these base-modified reversibly terminated nucleotides in the assay. All of the presented mutations in the TdT variants resulted in improvements in TdT modified-base incorporation relative to wild-type bovine and wild-type spotted gar TdTs.

Bottom panel: Solid support synthesis of an 8-nt nucleic acid sequence using 3′-ONH₂nucleoside 5′-triphosphates with terminal deoxynucleotidyl transferase (TdT) SEQ ID NOs 1 & 344-727. The DNA sequence 5′-ATCGATCG-3′ was synthesized by repeated exposure of a solid support bound DNA initiator to nucleotide addition mixture (NAM) solutions containing (1) TdT, (2) neutral pH buffer, (3) monovalent salt, (4) cobalt chloride, and (5) 3′-ONH₂-dNTP, where N is selected from adenine, thymine, cytosine, or guanine. A cycle consists of the following: (A) NAM solution with a specified A, T, C, or G reversibly terminated nucleotide was incubated for 5 minutes on the solid support at 37 C; (B) the solid support was then washed with a high salt solution at neutral pH; (C) the solid support was then exposed to acidic aqueous sodium nitrite; and (D) the solid support was then washed with the same high salt solution at neutral pH from (B). (A)-(D) were then repeated 7 more times to synthesize the desired 8-nt sequence. Synthesized DNA were analysed by running reactions on a denaturing polyacrylamide gel and quantified by virtue of a fluorophore covalently attached to the DNA initiator. The fraction full length (8-nt species) was determined by taking fluorescence intensity of the 8-nt band and dividing by total lane intensity. Wild-type bovine and spotted gar TdT activities as it relates to fraction full-length are indicated by the dotted line. All mutations included in the TdT variants resulted in improvements in TdT relative to wild-type bovine and spotted gar TdTs.

FIG. 4. Spotted gar TdT homology structure based on the co-crystal structure of a preferred engineered Nuclera TdT variant bound to a DNA initiator and a reversibly terminated dNTP. An engineered TdT variant with a BRCT-domain truncation was expressed in Escherichia coli and purified through immobilized metal affinity chromatography followed by size exclusion chromatography. The aforementioned TdT (60 micromolar) was then co-crystallized by sitting drop vapor diffusion at 19° C. with a DNA oligonucleotide (5′-TTTTT[ddC]-3′; 120 micromolar), cobalt chloride (1 mM), in the absence (top) or presence (bottom) of dATP-ONH₂(1 mM) in the following reservoir solutions: Bis-Tris HCl (100 mM), NaCl (27 mM), 22% w/v PEG 3350 or Bis-Tris HCl (10 mM) and 27.5% w/v PEG MME 500, respectively. Plate-like crystals appeared and grew to maximum dimensions of 400×50×5 μm³over 1 week and diffracted to 2.6 and 2.5 angstroms, respectively, with a space group of P2₁2₁2₁and unit cell dimensions of a=56.5 Å, b=80.0 Å, c=88.2 Å. and a=55.6 Å, b=79.1 Å, c=88.6 Å, respectively. Data were indexed, integrated, and scaled using the automatic software pipeline at the Diamond Light Source. Molecular replacement with a homology model of Lepisosteus oculatus (spotted gar) followed by cycles of manual model building interspersed with rigid-body, simulated annealing, energy minimization and individual isotropic D-factor produced complete structural models (R_free=27.8% and 28.6%, respectively). Cobalt ions were identified by virtue of their anomalous scattering. The spotted gar TdT wild-type sequence (>95% sequence identity) with a BRCT-domain truncation was modelled onto the two structures.

FIG. 5. Surface representation of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with MENHNQI motif, which includes the ENHNQ motif, highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the MENHNQI and ENHNQ motifs controls access to the nucleotidyl transferase active site, and the mutations shown in this patent demonstrate that mutating this motif results in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 6. Surface representations (right is 180 degree rotation of left view) of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with SEGPCLAFMRA, which includes the FMRA motif, highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the SEGPLCLAFMRA and FMRA motifs (1) control access of the reversibly terminated nucleotide to the nucleotidyl transferase active site through steric effects and electrostatic interactions and (2) directly packs against the critical TGSR motif, which directly contacts the reversibly terminated nucleotide. Specifically in relation to the TGSR motif, the SEGPLCLAFMRA and FMRA motifs directly contact and modulate the positioning of R438, which directly contacts the reversibly terminated nucleotide. Mutations shown in this patent demonstrate that mutating these motifs result in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 7. Surface representation of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with HFTKMQK motif, which includes the MQK motif, highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the HFTKMQK and MQK motifs bind to the nucleic acid initiator and assist in positioning the 3′-end of the initiator for nucleophilic attack against the incoming nucleotide. Mutations shown in this patent demonstrate that mutating this motif results in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 8. Surface representation of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with SAAVCK motif highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the SAAVCK motif controls reversibly terminated nucleotide access to the nucleotidyl transferase active site. Mutations shown in this patent demonstrate that mutating this motif results in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 9. Surface (left) and cartoon/sphere (right) representation of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with the GKEC motif, which includes the KEC motif, highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the GKEC and KEC motifs control reversibly terminated nucleotide access to and direct binding to the nucleotidyl transferase active site. Mutations shown in this patent demonstrate that mutating this motif results in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 10. Surface representation of spotted gar TdT homology structure modelled onto the crystal structure of an engineered TdT variant as described in FIG. 4 with the DHFQK motif, which includes the DHFQ motif, highlighted in black. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the DHFQK and DHFQ motifs control nucleic acid initiator access to the nucleotidyl transferase active site by sterically impinging on the nucleic acid initiator. Mutations shown in this patent demonstrate that mutating this motif results in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 11. Cartoon representation of an engineered TdT variant crystal structure as described in FIG. 4 bound to a DNA initiator and dATP-ONH₂with the FARHERKMLLDNHA motif highlighted in black spheres. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the FARHERKMLLDNHA motif controls nucleotide and nucleic acid initiator binding in the nucleotidyl transferase active site by sterically impinging on the nucleotide and initiator. Additionally, motif FARHERKMLLDNHA is mutated to FARHERKMLLDRHA. The Asn to Arg mutation results in the Arg residue directly binding one out of two of the catalytic cobalt ions, which is required for activity. Mutations shown in this patent demonstrate that mutating residues within this motif adjust the positioning of critical amino acids in contact with either a Co²⁺, the reversibly terminated nucleotide, and/or the nucleic acid initiator to result in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 12. Cartoon representation of an engineered TdT variant crystal structure as described in FIG. 4 bound to a DNA initiator and dATP-ONH₂with the FARHERKMLLDNHALYDKTKK motif highlighted in black spheres. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the FARHERKMLLDNHALYDKTKK motif controls nucleotide and nucleic acid initiator binding in the nucleotidyl transferase active site by sterically impinging on the nucleotide and initiator. Additionally, motif FARHERKMLLDNHALYDKTKK is mutated to FARHERKMLLDRHALYDKTKK. The Asn to Arg mutation results in the Arg residue directly binding one out of two of the catalytic cobalt ions, which is required for activity. Mutations shown in this patent demonstrate that mutating residues within this motif adjust the positioning of critical amino acids in contact with either a Co²⁺, the reversibly terminated nucleotide, and/or the nucleic acid initiator to result in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 13. Cartoon representation of an engineered TdT variant crystal structure as described in FIG. 4 bound to a DNA initiator and dATP-ONH₂with the DYIDP motif, which contains the YIDP motif, highlighted in black spheres. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the DYIDP and YIDP motifs control nucleotide binding in the nucleotidyl transferase active site by modulating the positioning of A494 within the active site. This most C-terminal residue (Ala494) sterically impinges upon the incoming nucleotide. Mutating the YIDP motif, modulates the positioning of the most C-terminal Ala residue resulting in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 14. Cartoon representation of an engineered TdT variant crystal structure as described in FIG. 4 bound to a DNA initiator and dATP-ONH₂with the YYDIV motif highlighted in black spheres. TdT contains two entrances to the nucleotidyl transferase active site in which the DNA initiator and reversibly terminated dNTP can enter and bind. Determined by modelling and visual inspection of the active site, the YYDIV motif controls positioning of the nucleic acid initiator by sterically impinging upon the antepenultimate (III), penultimate (II), and ultimate (I) 3′-nucleotide in the nucleic acid initiator. In particular, this motif impinges upon pyrimidines (left, as crystallized, I & II shown in sphere representation), but especially purines (right, II modelled into the structure as a purine). Mutating the YYDIV motif, modulates the positioning and access of the nucleic acid initiator into the nucleotidyl transferase active site resulting in increased TdT incorporation activity of reversibly terminated nucleotides.

FIG. 15. Cartoon representation of an engineered TdT variant crystal structure as described in FIG. 4 bound to a DNA initiator and dATP-ONH₂with the APPVDNF, which contains the APPVDN motif, motif highlighted in black spheres. In the structure, the APPVDNF motif is shown with an Ala to Met mutation to MPPVDNF. Through modelling, it was determined that the APPVDNF and APPVDN motifs control positioning of the following motifs by directly packing against the YYDIV (upper right) and FARHERKMLLDNHALYDKTKK (lower left) motifs, both of which are shown in light grey spheres. Additionally determined through modelling, the APPVDNF and APPVDN motifs control positioning of the following motifs by determining the loop conformation of the TGSR motif (upper left) and the catalytic triad of aspartates (lower right) critical to the nucleotidyl transferase mechanism, both of which are shown in light grey spheres. Mutations in the APPVDNF and APPVDN motifs directly influence how the aforementioned critical protein motifs to modulate their contacts with the reversibly terminated nucleotide and nucleic acid initiator. Mutations in the APPVDNF and APPVDN motifs have been shown in this patent to result in increased TdT incorporation activity of reversibly terminated nucleotides.

SUMMARY OF THE INVENTION

Described herein are modified terminal deoxynucleotidyl transferase (TdT) enzymes or the homologous amino acid sequence of Polμ, Polβ, Polλ, and Polθ of any species or the homologous amino acid sequence of X family polymerases of any species. Terminal transferase enzymes are ubiquitous in nature and are present in many species. Many known TdT sequences have been reported in the NCBI database http://www.ncbi.nlm.nih.gov/.

The sequences of the various described terminal transferases show some regions of highly conserved sequence, and some regions which are highly diverse between different species. A sequence alignment for sequences from a selection of species is shown in FIG. 2.

The inventors have modified the terminal transferase from Lepisosteus oculatus TdT (spotted gar) (shown as SEQ ID 1). However the corresponding modifications can be introduced into the analagous terminal transferase sequences from any other species, including the sequences listed above in the various NCBI entries, including those shown in FIG. 2 or truncated versions thereof.

The amino acid sequence of the spotted gar (Lepisosteus oculatus) is shown below (SEQ ID 1)

MLHIPIFPPIKKRQKLPESRNSCKYEVKFSEVAIFLVERKMGSSRRKFLT

NLARSKGFRIEDVLSDAVTHVVAEDNSADELWQWLQNSSLGDLSKIEVLD

ISWFTECMGAGKPVQVEARHCLVKSCPVIDQYLEPSTVETVSQYACQRRT

TMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLLKSLPHAISSSK

DLEGLPCLGDQTKAVIEDILEYGQCSKVQDVLCDDRYQTIKLFTSVFGVG

LKTAEKWYRKGFHSLEEVQADNAIHFTKMQKAGFLYYDDISAAVCKAEAQ

AIGQIVEETVRLIAPDAIVTLIGGFRRGKECGHDVDFLITTPEMGKEVWL

LNRLINRLQNQGILLYYDIVESTFDKTRLPCRKFEAMDHFQKCFAIIKLK

KELAAGRVQKDWKAIRVDFVAPPVDNFAFALLGWTGSRQFERDLRRFARH

ERKMLLDNHALYDKTKKIFLPAKTEEDIFAHLGLDYIDPWQRNA

An engineered variant of this sequence was previously identified as SEQ ID NO 8 in publication WO2016/128731. Further engineered Improvements to this published sequence are described herein. The modified sequences disclosed herein are different to SEQ ID NO 8 disclosed in the prior art. WO2016/128731 SEQ ID NO 2 is a “mis-annotated” wild-type gar sequence.

SEQ ID NO 8 in publication WO2016/128731 is shown below with the engineered mutations identified:

MLHIPIFPPIKKRQKLPESRNSCKYEVKFSEVAIFLVERKMGSSRRKFLTNLARSKGFRIEDVLSDAV

embedded image

TVETVSQYACQRRTTMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLLKSLPHAISSSKDLEG

embedded image

AIHFTKMQKAGFLYYDDISAAVCKAEAQAIGQIVEETVRLIAPDAIVTLTGGFRRGKECGHDVDFLIT

TPEMGKEVWLLNRLINRLQNQGILLYYDIVESTFDKTRLPCRKFEAMDHFQKCFAIIKLKKELAAGRV

QKDWKAIRVDFVAPPVDNFAFALLGWIGSRQFERDLRRFARHERKMLLDNHALYDKTKKIFLPAKTEE

DIFAHLGLDYIDPWQRNA

The inventors have identified various amino acids modifications in the amino acid sequence having improved properties. Certain regions improve the solubility and handling of the enzyme. Certain other regions improve the ability to incorporate nucleotides with modifications; these modifications include modifications at the 3′-position of the sugar and modifications to the base.

Described herein are modified terminal deoxynucleotidyl transferase (TdT) enzymes comprising amino acid modifications when compared to a wild type sequence SEQ ID NO 1 or a truncated version thereof or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species or the homologous amino acid sequence of Polμ, Polβ, Polλ, and Polθ of any species or the homologous amino acid sequence of X family polymerases of any species, wherein the amino acid is modified at one or more of the amino acids:

V32, A33, I34, F35, A53, V68, V71, E97, I101, M108, G109, A110, Q115, V116, S125, T137, Q143, M152, E153, N154, H155, N156, Q157, I158, I165, N169, N173, S175, E176, G177, P178, C179, L180, A181, F182, M183, R184, A185, L188, H194, A195, I196, S197, S198, S199, K200, E203, G204, D210, Q211, T212, K213, A214, I216, E217, D218, L220, Y222, V228, D230, Q238, T239, L242, L251, K260, G261, F262, H263, S264, L265, E267, Q269, A270, D271, N272, A273, H275, F276, T277, K278, M279, Q280, K281, S291, A292, A293, V294, C295, K296, E298, A299, Q300, A301, Q304, I305, T309, V310, R311, L312, I313, A314, I318, V319, T320, G328, K329, E330, C331, L338, T341, P342, E343, M344, G345, K346, W349, L350, L351, N352, R353, L354, I355, N356, R357, L358, Q359, N360, Q361, G362, I363, L364, L365, Y366, Y367, D368, I369, V370, K376, T377, C381, K383, D388, H389, F390, Q391, K392, F394, I397, K398, K400, K401, E402, L403, A404, A405, G406, R407, D411, A421, P422, P423, V424, D425, N426, F427, A430, R438, F447, A448, R449, H450, E451, R452, K453, M454, L455, L456, D457, N458, H459, A460, L461, Y462, D463, K464, T465, K466, K467, T474, D477, D485, Y486, I487, D488, P489.

Modifications which improve the solubility include a modification within the amino acid region WLLNRLINRLQNQGILLYYDIV shown highlighted in the sequence below.

MLHIPIFPPIKKRQKLPESRNSCKYEVKFSEVAIFLVERKMGSSRRKFLTNLARSKGFRIEDVLSDAV

THVVAEDNSADELWQWLQNSSLGDLSKIEVLDISWFTECMGAGKPVQVEARHCLVKSCPVIDQYLEPS

TVETVSQYACQRRTTMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLLKSLPHAISSSKDLEG

LPCLGDQTKAVIEDILEYGQCSKVQDVLCDDRYQTIKLFTSVFGVGLKTAEKWYRKGFHSLEEVQADN

AIHFTKMQKAGFLYYDDISAAVCKAEAQAIGQIVEETVRLIAPDAIVTLTGGFRRGKECGHDVDFLIT

embedded image

QKDWKAIRVDFVAPPVDNFAFALLGWTGSRQFERDLRRFARHERKMLLDNHALYDKTKKIFLPAKTEE

DIFAHLGLDYIDPWQRNA

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. Regions were selected according to mutation data (FIGS. 1 and 3), sequence alignment (FIG. 2), and structural data obtained from spotted gar TdT co-crystallized with DNA and a 3′-modified dNTP (FIGS. 4-14). The second modification can be selected from one or more of the amino acid regions VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, YYDIV, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP shown highlighted in the sequence below.

Particular modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP shown highlighted in the sequence below.

Described herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence SEQ ID NO 1 or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDIV, VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

References to particular sequences include truncations thereof. Included herein are modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence SEQ ID NO 1 or a truncated version thereof, or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDIV, VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Truncated proteins may include at least the region shown below

TVSQYACQRRTTMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLL

KSLPHAISSSKDLEGLPCLGDQTKAVIEDILEYGQCSKVQDVLCDDRYQT

IKLFTSVFGVGLKTAEKWYRKGFHSLEEVQADNAIHFTKMQKAGFLYYDD

ISAAVCKAEAQAIGQIVEETVRLIAPDAIVTLTGGFRRGKECGHDVDFLI

TTPEMGKEVWLLNRLINRLQNQGILLYYDIVESTFDKTRLPCRKFEAMDH

FQKCFAIIKLKKELAAGRVQKDWKAIRVDFVAPPVDNFAFALLGWTGSRQ

FERDLRRFARHERKMLLDNHALYDKTKKIFLPAKTEEDIFAHLGLDYIDP

WQRNA

Described herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least the sequence:

TVSQYACQRRTTMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLL

KSLPHAISSSKDLEGLPCLGDQTKAVIEDILEYGQCSKVQDVLCDDRYQT

IKLFTSVEGVGLKTAEKWYRKGEHSLEEVQADNAIHFTKMQKAGFLYYDD

ISAAVCKAEAQAIGQIVEETVRLIAPDAIVTLTGGFRRGKECGHDVDFLI

TTPEMGKEVWLLNRLINRLQNQGILLYYDIVESTFDKTRLPCRKFEAMDH

FQKCFAIIKLKKELAAGRVQKDWKAIRVDEVAPPVDNFAFALLGWTGSRQ

FERDLRRFARHERKMLLDNHALYDKTKKIFLPAKTEEDIFAHLGLDYIDP

WQRNA

or the homologous regions in other species, wherein the sequence has one or more amino acid modifications in one or more of the amino acid regions WLLNRLINRLQNQGILLYYDI, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence.

Disclosed herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDI, VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Disclosed herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDI, VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Described herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence SEQ ID NO 1 or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDI, VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Homologous refers to protein sequences between two or more proteins that possess a common evolutionary origin, including proteins from superfamilies in the same species of organism as well as homologous proteins from different species. Such proteins (and their encoding nucleic acids) have sequence homology, as reflected by their sequence similarity, whether in terms of percent identity or by the presence of specific residues or motifs and conserved positions. A variety of protein (and their encoding nucleic acid) sequence alignment tools may be used to determine sequence homology. For example, the Clustal Omega multiple sequence alignment program provided by the European Molecular Biology Laboratory (EMBL) can be used to determine sequence homology or homologous regions.

Improved sequences as described herein can contain both modifications, namely

a. a first modification is within the amino acid region WLLNRLINRLQNQGILLYYDIV of the sequence of SEQ ID NO 1 or the homologous region in other species; and

b. a second modification is selected from one or more of the amino acid regions VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

The sequence can be truncated

Improved sequences as described herein can contain both modifications, namely

a. a first modification is within the amino acid region WLLNRLINRLQNQGILLYYDI of the sequence of SEQ ID NO 1 or the homologous region in other species; and

b. a second modification is selected from one or more of the amino acid regions VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

As a comparison with other species, the sequence of Bos taurus (cow) TdT is shown below:

MDPLCTASSGPRKKRPRQVGASMASPPHDIKFQNLVLFILEKKMGTTRRN

FLMELARRKGFRVENELSDSVTHIVAENNSGSEVLEWLQVQNIRASSQLE

LLDVSWLIESMGAGKPVEITGKHQLVVRTDYSATPNPGFQKTPPLAVKKI

SQYACQRKTTLNNYNHIFTDAFEILAENSEFKENEVSYVTFMRAASVLKS

LPFTIISMKDTEGIPCLGDKVKCIIEEIIEDGESSEVKAVLNDERYQSFK

LFTSVFGVGLKTSEKWFRMGFRSLSKIMSDKTLKFTKMQKAGFLYYEDLV

SCVTRAEAEAVGVLVKEAVWAFLPDAFVTMTGGFRRGKKIGHDVDFLITS

PGSAEDEEQLLPKVINLWEKKGLLLYYDLVESTFEKFKLPSRQVDTLDHF

QKCFLILKLHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWT

GSRQFERDIRRYATHERKMMLDNHALYDKTKRVFLKAESEEEIFAHLGLD

YIEPWERNA

The homologous regions in the sequences are highlighted below.

Modifications which improve the solubility include a modification within the amino acid region QLLPKVINLWEKKGLLLYYDLV shown highlighted in the sequence below.

LHHQRVDSSKSNQQEGKTWKAIRVDLVMCPYENRAFALLGWTGSRQFERDIRRYATHERKMMLDNHAL

YDKTKRVFLKAESEEEIFAHLGLDYIEPWERNA

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions LVLF, MGA, LNNYNHI, NEVSYVTFMRA, FTIISM, DKVKC, MGFRS, MSDKT, KFTKMQK, VSCVTR, EAEA, AVWAFL, GKKI, SPGSAE, YYDLV, DHFQK, MCPYENR, YATHERKMMLDNHALYDKTKR, and DYIEP shown highlighted in the sequence below.

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions LVLF, MGA, NNYNH, FMRA, FTI, VKC, FRS, MSDKT, MQK, EAEA, AVW, KKI, SPGSAE, DHFQ, MCPYEN, YATHERKMMLDNHA, and YIEP shown highlighted in the sequence below.

As a comparison with other species, the sequence of Mus musculus (mouse) TdT is shown below:

MDPLQAVHLGPRKKRPRQLGTPVASTPYDIRFRDLVLFILEKKMGTTRRA

FLMELARRKGFRVENELSDSVTHIVAENNSGSDVLEWLQLQNIKASSELE

LLDISWLIECMGAGKPVEMMGRHQLVVNRNSSPSPVPGSQNVPAPAVKKI

SQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKS

LPFPITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFK

LFTSVFGVGLKTAEKWFRMGFRTLSKIQSDKSLRFTQMQKAGFLYYEDLV

SCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMTGHDVDFLITS

PEATEDEEQQLLHKVTDFWKQQGLLLYCDILESTFEKFKQPSRKVDALDH

FQKCFLILKLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGW

TGSRQFERDLRRYATHERKMMLDNHALYDRTKGKTVTISPLDGKVSKLQK

ALRVFLEAESEEEIFAHLGLDYIEPWERNA

Modifications which improve the solubility include a modification within the amino acid region QLLHKVTDFWKQQGLLLYCDIL shown highlighted in the sequence below.

MDPLQAVHLGPRKKRPRQLGTPVASTPYDIRFRDLVLFILEKKMGTTRRAFLMELARRKGFRVENELS

DSVTHIVAENNSGSDVLEWLQLQNIKASSELELLDISWLIECMGAGKPVEMMGKHQLVVNRNSSPSPV

PGSQNVPAPAVKKISQYACQRRTTLNNYNQLFTDALDILAENDELRENEGSCLAFMRASSVLKSLPFP

ITSMKDTEGIPCLGDKVKSIIEGIIEDGESSEAKAVLNDERYKSFKLFTSVFGVGLKTAEKWFRMGFR

TLSKIQSDKSLRFTQMQKAGFLYYEDLVSCVNRPEAEAVSMLVKEAVVTFLPDALVTMTGGFRRGKMT

embedded image

KLDHGRVHSEKSGQQEGKGWKAIRVDLVMCPYDRRAFALLGWTGSRQFERDLRRYATHERKMMLDNHA

LYDRTKGKTVTISPLDGKVSKLQKALRVFLEAESEEEIFAHLGLDYIEPWERNA

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions LVLF, MGA, LNNYNQL, NEGSCLAFMRA, FPITSM, DKVKS, MGFRT, QSDKS, RFTQMQK, VSCVNR, EAEA, AVVTFL, GKMT, SPEATE, DHFQK, SGQ, MCPYDRR, YATHERKMMLDNHALYDRT, R, and DYIEP shown highlighted in the sequence below.

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions LVLF, MGA, LNNYNQ, NEGSCLAFMRA, FPI, VKS, FRT, SKIQSDKS, MQK, VSCVNR, EAEA, AVV, KMT, SPEATE, DHFQK, MCPYDR, YATHERKMMLDNHA, and YIEP shown highlighted in the sequence below.

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions LVLF, MGA, NNYNQ, FMRA, FPI, VKS, FRT, QSDKS, MQK, VSCVNR, EAEA, AVV, KMT, SPEATE, DHFQ, MCPYDR, YATHERKMMLDNHA, and YIEP shown highlighted in the sequence below.

Thus by a process of aligning sequences, it is immediately apparent which regions in the sequences of terminal transferases from other species correspond to the sequences described herein with respect to the spotted gar sequence shown in SEQ ID NO 1.

Sequence homology extends to all modified or wild-type members of family X polymerases, such as DNA Polμ (also known as DNA polymerase mu or POLM), DNA Polβ (also known as DNA polymerase beta or POLB), and DNA Polλ (also known known as DNA polymerase lambda or POLL). It is well known in the art that all family X member polymerases, of which TdT is a member, either have terminal transferase activity or can be engineered to gain terminal transferase activity akin to terminal deoxynucleotidyl transferase (Biochim Biophys Acta. 2010 May; 1804(5): 1136-1150). For example, when the following human TdT loop1 amino acid sequence

. . . ESTFEKLRLPSRKVDALDHF . . .

was engineered to replace the following human Polμ amino acid residues

. . . HSCCESPTRLAQQSHMDAF . . .,

the chimeric human Polμ containing human TdT loop1 gained robust terminal transferase activity (Nucleic Acids Res. 2006 September; 34(16): 4572-4582).

Furthermore, it was generally demonstrated in US patent application no. 2019/0078065 that family X polymerases when engineered to contain TdT loop1 chimeras could gain robust terminal transferase activity. Additionally, it was demonstrated that TdT could be converted into a template-dependent polymerase through specific mutations in the loop1 motif (Nucleic Acids Research, June 2009, 37(14):4642-4656). As it has been shown in the art, family X polymerases can be trivially modified to either display template-dependent or template-independent nucleotidyl transferase activities. Therefore, all motifs, regions, and mutations demonstrated in this patent can be trivially extended to modified X family polymerases to enable modified X family polymerases to incorporate 3′-modified nucleotides, reversibly terminated nucleotides, and modified nucleotides in general to effect methods of nucleic acid synthesis.

As a comparison with other family X polymerases, the human Polμ sequence is shown below:

MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGL

ARSKGFRVLDACSSEATHVVMEETSAEEAVSWQERRMAAAPPGCTPPALL

DISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPAWMPAYACQRPTPLT

HHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQ

GLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKT

ADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQ

VVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRV

MCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPPGA

AVGGSTRPCPSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRK

EKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA

Modifications which improve the solubility include a modification within the amino acid region GLLPRVMCRLQDQGLILYHQHQ shown highlighted in the sequence below.

MLPKRRRARVGSPSGDAASSTPPSTRFPGVAIYLVEPRMGRSRRAFLTGLARSKGFRVLDACSSEATH

VVMEETSAEEAVSWQERRMAAAPPGCTPPALLDISWLTESLGAGQPVPVECRHRLEVAGPRKGPLSPA

WMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPH

FGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKL

TQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKE

embedded image

CPSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEE

DIFRHLGLEYLPPEQRNA

Modifications which improve the incorporation of modified nucleotides can be at one or more of selected regions shown below. The second modification can be selected from one or more of the amino acid regions VAIY, LGA, LTHHNTG, SEGRLLTFCRAA, SPVTTL, EHSSR, EGLRT, REQP, KLTQQQKA, STPVLR, DVDA, AVGQA, GKLQ, HPKEGQ, YHQHQ, DAFER, VAPVSQ, FSRKEKGLWLNSHGLFDPEQK, AND EYLPP shown highlighted in the sequence below.

Thus by a process of aligning sequences, it is immediately apparent which regions in the sequences of all family X polymerases from any species correspond to the sequences described herein with respect to the spotted gar sequence shown in SEQ ID NO 1.

Furthermore, the A family polymerase, DNA Polθ (also known as DNA polymerase theta or POLQ) was demonstrated to display robust terminal transferase capability (eLife. 2016; 5: e13740). DNA Polθ was also demonstrated to be useful in methods of nucleic acid synthesis (GB patent application no. 2553274). In US patent application no. 2019/0078065, it was demonstrated that chimeras of DNA Polθ and family X polymerases could be engineered to gain robust terminal transferase activity and become competent for methods of nucleic acid synthesis. Therefore, all motifs, regions, and mutations demonstrated in this patent can be trivially extended to modified A family polymerases, especially DNA Polθ, to enable modified A family polymerases to incorporate 3′-modified nucleotides, reversibly terminated nucleotides, and modified nucleotides in general to effect methods of nucleic acid synthesis.

DETAILED DESCRIPTION OF THE INVENTION

Described herein are modified terminal deoxynucleotidyl transferase (TdT) enzymes. Terminal transferase enzymes are ubiquitous in nature and are present in many species. Many known TdT sequences have been reported in the NCBI database. The sequences described herein are modified from the sequence of the Spotted Gar, but the corresponding changes can be introduced into the homologous sequences from other species. Homologous amino acid sequences of Polμ, Polβ, Polλ, and Polθ or the homologous amino acid sequence of X family polymerases also possess terminal transferase activity. References to terminal transferase also include homologous amino acid sequences of Polμ, Polβ, Polλ, and Polθ or the homologous amino acid sequence of X family polymerases where such sequences possess terminal transferase activity.

Disclosed herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDIV, VAIF, MGA, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Described herein is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least the sequence ID 729:

TVSQYACQRRTTMENHNQIFTDAFAILAENAEFNESEGPCLAFMRAASLL

KSLPHAISSSKDLEGLPCLGDQTKAVIEDILEYGQCSKVQDVLCDDRYQT

IKLFTSVFGVGLKTAEKWYRKGFHSLEEVQADNAIHFTKMQKAGFLYYDD

ISAAVCKAEAQAIGQIVEETVRLIAPDAIVTLTGGFRRGKECGHDVDFLI

TTPEMGKEVWLLNRLINRLQNQGILLYYDIVESTFDKTRLPCRKFEAMDH

FQKCFAIIKLKKELAAGRVQKDWKAIRVDEVAPPVDNFAFALLGWTGSRQ

FERDLRRFARHERKMLLDNHALYDKTKKIFLPAKTEEDIFAHLGLDYIDP

WQRNA

or the equivalent homologous region in other species, wherein the sequence has one or more amino acid modifications in one or more of the amino acid regions WLLNRLINRLQNQGILLYYDIV, MENHNQI, SEGPCLAFMRA, HAISSS, DQTKA, KGFHS, QADNA, HFTKMQK, SAAVCK, EAQA, TVRLI, GKEC, TPEMGK, DHFQK, LAAG, APPVDNF, FARHERKMLLDNHALYDKTKK, and DYIDP of the sequence. The sequence above of 355 amino acids can be attached to other amino acids without affecting the function of the enzyme. For example there can be a further N-terminal sequence that is incorporated simply as a protease cleavage site, for example the sequence MENLYFQG.

Disclosed is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least one amino acid modification when compared to a wild type sequence SEQ ID NO 1 or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the modification is selected from one or more of the amino acid regions WLLNRLINRLQNQGILLYYDI, VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species.

Further disclosed is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising at least two amino acid modifications when compared to a wild type sequence SEQ ID NO 1 or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein;

a. a first modification is within the amino acid region WLLNRLINRLQNQGILLYYDIV of the sequence of SEQ ID NO 1 or the homologous region in other species; and

When compared to the sequence of Bos taurus (cow) TdT; SEQ ID NO 2,

a. a first modification is within the amino acid region QLLPKVINLWEKKGLLLYYDLV of the sequence of SEQ ID NO 2 or the homologous region in other species; and

b. a second modification is selected from one or more of the amino acid regions LVLF, MGA, NNYNH, FMRA, FTI, VKC, FRS, MSDKT, MQK, EAEA, AVW, KKI, SPGSAE, MCP, YATHERKMMLDNHA, and YIEP of the sequence of SEQ ID NO 2 or the homologous regions in other species.

When compared to the sequence of Mus musculus (mouse) TdT; SEQ ID NO 3,

a. a first modification is within the amino acid region QLLHKVTDFWKQQGLLLYCDIL of the sequence of SEQ ID NO 3 or the homologous region in other species; and

b. a second modification is selected from one or more of the amino acid regions LVLF, MGA, NNYNQ, FMRA, FPI, VKS, FRT, QSDKS, MQK, VSCVNR, EAEA, AVV, KMT, SPEATE, DHFQ, MCPYDR, YATHERKMMLDNHA, and YIEP of the sequence of SEQ ID NO 3 or the homologous regions in other species.

The modifications can be chosen from any amino acid that differs from the wild type sequence. The amino acid can be a naturally occurring amino acid. The modified amino acid can be selected from ala, arg, asn, asp, cys, gln, glu, gly, his, ile, leu lys, met, phe, pro, ser, thr, trp, val, and sec.

For the purposes of brevity, the modifications are further described in relation to SEQ ID NO 1, but the modifications are applicable to the sequences from other species, for example those sequences listed above having sequences in the NCBI database. The sequence modifications also apply to truncated versions of SEQ ID NO 1.

The sequences can be modified at positions in addition to those regions described. Embodiments on the invention may include for example sequences having modifications to amino acids outside the defined positions, providing those sequences retain terminal transferase activity. Embodiments of the invention may include for example sequences having truncations of amino acids outside the defined positions, providing those sequences retain terminal transferase activity. For example the sequences may be BRCT truncated as described in application WO2018215803 where amino acids are removed from the N-terminus whilst retaining or improving activity. Alterations, additions, insertions or deletions or truncations to amino acid positions outside the claimed regions are therefore within the scope of the invention, providing that the claimed regions as defined are modified as claimed. The sequences described herein refer to TdT enzymes, which are typically at least 300 amino acids in length. All sequences described herein can be seen as having at least 300 amino acids. The claims do not cover peptide fragments or sequences which do not function as terminal transferase enzymes.

The modification within the region WLLNRLINRLQNQGILLYYDIV or the corresponding region from other species help improve the solubility of the enzyme. The modification within the amino acid region WLLNRLINRLQNQGILLYYDIV can be at one or more of the underlined amino acids.

Particular changes can be selected from W-Q, N-P, R-K, L-V, R-L, L-W, Q-E, N-K, Q-K or I-L.

The sequence WLLNRLINRLQNQGILLYYDIV can be altered to QLLPKVINLWEKKGLLLYYDLV.

The second modification improves incorporation of nucleotides having a modification at the 3′ position in comparison to the wild type sequence. The second modification can be selected from one or more of the amino acid regions VAIF, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species. The second modification can be selected from two or more of the amino acid regions VAIF, EDN, MGA, ENHNQ, FMRA, HAI, TKA, FHS, QADNA, MQK, SAAVCK, EAQA, TVR, KEC, TPEMGK, DHFQ, LAAG, APPVDN, FARHERKMLLDNHA, and YIDP of the sequence of SEQ ID NO 1 or the homologous regions in other species shown highlighted in the sequence below.

The identified positions commence at positions V32, M108, F182, T212, D271, M279, E298, A421, L456, Y486. Modifications disclosed herein contain at least one modification at the defined positions.

In the sequence below the modified regions are numbered thus

WLLNRLINRLQNQGILLYYDIV, 349 to 370

VAIF, 32 to 35

MGA, 108 to 110

MENHNQI, 152 to 158

SEGPCLAFMRA, 175 to 185

HAISSS, 194 to 199

DQTKA, 210 to 214

KGFHS, 260 to 264

QADNA, 269 to 273

HFTKMQK, 275 to 281

SAAVCK, 291 to 296

EAQA, 298 to 301

TVRLI, 309 to 313

GKEC, 328 to 331

TPEMGK, 341 to 346

DHFQK, 388 to 392

LAAG, 403 to 406

APPVDNF, 421 to 427

FARHERKMLLDNHALYDKTKK, 447 to 467

DYIDP, 485 to 489

The modified amino acid can be in the region FMRA. The modified amino acid can be in the region QADNA. The modified amino acid can be in the region EAQA. The modified amino acid can be in the region APP. The modified amino acid can be in the region LDNHA. The modified amino acid can be in the region YIDP. The region FARHERKMLLDNHA is advantageous for removing substrate biases in modifications. The FARHERKMLLDNHA region appears highly conserved across species.

The modification selected from one or more of the amino acid regions FMRA, QADNA, EAQA, APP, FARHERKMLLDNHA, and YIDP can be at the underlined amino acid(s).

Rather than the invention being described by modifications in defined domains, the sequences can be defined by modifications at certain defined amino acids. Described herein are modified terminal deoxynucleotidyl transferase (TdT) enzymes comprising amino acid modifications when compared to a wild type sequence SEQ ID NO 1 or a truncated version thereof or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the amino acid is modified at one or more of the amino acids A53, V68, V71, E97, I101, G109, Q115, V116, S125, T137, Q143, M152, N154, H155, Q157, I158, I165, N169, S175, G177, C179, L180, A181, M183, A195, S197, S198, S199, K200, D210, Q211, T212, K213, A214, E217, T239, K260, F262, S264, Q269, D271, N272, A273, H275, T277, K281, S291, K296, Q300, T309, R311, L312, I313, G328, E330, C331, T341, P342, E343, M344, G345, K346, N352, R353, L354, I355, N356, L358, N360, Q361, G362, I363, Y366, Y367, D368, V370, H389, K392, L403, A405, G406, D411, A421, P422, V424, N426, F427, R438, F447, R452, K453, L455, Y462, K464, T465, K467, D485, I487 and/or D488.

Described herein are modified terminal deoxynucleotidyl transferase (TdT) enzymes comprising amino acid modifications when compared to a wild type sequence SEQ ID NO 1 or the homologous amino acid sequence of a terminal deoxynucleotidyl transferase (TdT) enzyme in other species, wherein the amino acid is modified at one or more of the amino acids

Specific amino acid changes can include any one of A53G, V68I, V71I, E97A, I101V, G109E, G109R, Q115E, V116I, V116S, S125R, T137A, Q143P, M152L, M152T, N154H, H155C, H155N, H155R, Q157K, Q157R, I158V, I158L, I158M, I165V, N169R, N173R, S175N, G177S, G177V, G177D, C179A, C179S, L180V, A181E, M183R, L188V, A195T, A195P, S197I, S197L, S198R, S198C, S199L, K200R, E203Q, G204D, D210E, Q211R, T212S, K213S, A214R, A214C, A214G, I216M, E217Q, D218E, L220I, L220F, L220Y, Y222C, V228A, D230E, Q238K, T239S, L242Q, L251P, K260M, F262L, L265F, S264T, E267D, Q269K, D271N, D271E, N272K, A273S, A273T, H275Q, T277S, K281R, S291N, S291T, K296R, Q300D, Q304R, Q304C, Q304H, I305V, T309A, R311W, R311H, L312G, L312K, L312A, I313M, A314T, I318L, V319L, T320A, G328A, E330N, E330S, C331I, L338I, T341S, P342A, E343G, E343Q, M344A, M344Q, M344K, G345R, K346R, N352Q, K353R, K353D, V354I, V354L, I355V, I355M, N356R, N356D, W358L, N360K, Q361K, G362E, I363L, Y366F, Y367C, D368H, D368E, V370I, K376I, T377S, T377L, T377A, C381S, K383R, H389N, H389A, K392Q, F394W, I397L, K398R, K400E, K400N, K401A, K401Q, E402Q, L403Q, L403R, A405D, G406R, R407C, D411N, A421L, A421M, A421V, P422A, P422C, V424Y, V424I, V424A, N426R, N426C, F427Y, A430T, R438K, F447W, R452K, L455I, K453R, Y462F, K464R, T465R, K467R, T474S, D477E, D485E, I487V, and/or D488P.

Amino acid changes include any two or more of A53G, V68I, V71I, E97A, I101V, G109E, G109R, Q115E, V116I, V116S, S125R, T137A, Q143P, M152L, M152T, N154H, H155C, H155N, H155R, Q157K, Q157R, I158V, I158L, I158M, I165V, N169R, N173R, S175N, G177S, G177V, G177D, C179A, C179S, L180V, A181E, M183R, L188V, A195T, A195P, S197I, S197L, S198R, S198C, S199L, K200R, E203Q, G204D, D210E, Q211R, T212S, K213S, A214R, A214C, A214G, I216M, E217Q, D218E, L220I, L220F, L220Y, Y222C, V228A, D230E, Q238K, T239S, L242Q, L251P, K260M, F262L, L265F, S264T, E267D, Q269K, D271N, D271E, N272K, A273S, A273T, H275Q, T277S, K281R, S291N, S291T, K296R, Q300D, Q304R, Q304C, Q304H, I305V, T309A, R311W, R311H, L312G, L312K, L312A, I313M, A314T, I318L, V319L, T320A, G328A, E330N, E330S, C331I, L338I, T341S, P342A, E343G, E343Q, M344A, M344Q M344K, G345R, K346R, N352Q, K353R, K353D, V354I, V354L, I355V, I355M, N356R, N356D, W358L, N360K, Q361K, G362E, I363L, Y366F, Y367C, D368H, D368E, V370I, K376I, T377S, T377L, T377A, C381S, K383R, H389N, H389A, K392Q, F394W, I397L, K398R, K400E, K400N, K401A, K401Q, E402Q, L403Q, L403R, A405D, G406R, R407C, D411N, A421L, A421M, A421V, P422A, P422C, V424Y, V424I, V424A, N426R, N426C, F427Y, A430T, R438K, F447W, R452K, L455I, K453R, Y462F, K464R, T465R, K467R, T474S, D477E, D485E, I487V, and/or D488P.

The modification of QADNA to KADKA, QADKA, KADNA, QADNS, KADNT, or QADNT is advantageous for the incorporation of 3′-O-modified nucleoside triphosphates to the 3′-end of nucleic acids and removing substrate biases during the incorporation of modified nucleoside triphosphates. The modification of APPVDN to MCPVDN, MPPVDN, ACPVDR, VPPVDN, LPPVDR, ACPYDN, LCPVDN, or MAPVDN is advantageous for the incorporation of 3′-O-modified nucleoside triphosphates to the 3′-end of nucleic acids and removing substrate biases during the incorporation of modified nucleoside triphosphates. The modification of FARHERKMLLDRHA to WARHERKMILDNHA, FARHERKMILDNHA, WARHERKMLLDNHA, FARHERKMLLDRHA, or FARHEKKMLLDNHA is also advantageous for the incorporation of 3′-O-modified nucleoside triphosphates to the 3′-end of nucleic acids and removing substrate biases during the incorporation of modified nucleoside triphosphates.

The modification can be selected from one or more of the following sequences FRRA, QADKA, EADA, MPP, FARHERKMLLDRHA, and YIPP. Included is a modified terminal deoxynucleotidyl transferase (TdT) enzyme wherein the second modification is selected from two or more of the following sequences FRRA, QADKA, EADA, MPP, FARHERKMLLDRHA, and YIPP. Included is a modified terminal deoxynucleotidyl transferase (TdT) enzyme wherein the second modification contains each of the following sequences FRRA, QADKA, EADA, MPP, FARHERKMLLDRHA, and YIPP.

Crystal structures shown herein show the following domains, which may be preferred as domains to modify:

FIG. 5. MENHNQI motif (152 to 158), which includes the ENHNQ motif

FIG. 6. SEGPCLAFMRA (175 to 185), which includes the FMRA motif, highlighted in black.

FIG. 7. HFTKMQK motif (275 to 281), which includes the MQK motif, highlighted in black.

FIG. 8. SAAVCK motif (291 to 296) highlighted in black.

FIG. 9. GKEC motif (328 to 331), which includes the KEC motif, highlighted in black.

FIG. 10. DHFQK motif (388 to 392), which includes the DHFQ motif, highlighted in black.

FIG. 11. FARHERKMLLDNHA motif (447 to 460) highlighted in black spheres. Additionally, motif FARHERKMLLDNHA is mutated to FARHERKMLLDRHA.

FIG. 12. FARHERKMLLDNHALYDKTKK motif (447 to 467) highlighted in black spheres. Additionally, motif FARHERKMLLDNHALYDKTKK is mutated to FARHERKMLLDRHALYDKTKK.

FIG. 13. DYIDP motif (485 to 489), which contains the YIDP motif, highlighted in black spheres.

FIG. 14. YYDIV motif (366 to 370) highlighted in black spheres.

FIG. 15. APPVDNF, which contains the APPVDN motif (421 to 427), motif highlighted in black spheres. In the structure, the APPVDNF motif is shown with an Ala to Met mutation to MPPVDNF.

In order to aid purification of the expressed sequence, the amino acid can be further modified. For example the amino acid sequence can contain one or more further histidine residues at the terminus. Included is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising any one of SEQ ID NOs 4 to 173 or a truncated version thereof. Sequences 4-173 are the full length sequences derived from the spotted gar. Included is a modified terminal deoxynucleotidyl transferase (TdT) enzyme comprising any one of SEQ ID NOs 174 to 343. Sequences 174 to 343 are N-truncated sequences as spotted gar/bovine chimeras. Sequences 344 to 727 are spotted Gar sequences in truncated form. Additionally, for these sequences, there is an N-terminal sequence that is incorporated simply as a protease cleavage site (MENLYFQG . . . ).

Also disclosed is a method of nucleic acid synthesis, which comprises the steps of:

(a) providing an initiator oligonucleotide;

(b) adding a 3′-blocked nucleoside triphosphate to said initiator oligonucleotide in the presence of a terminal deoxynucleotidyl transferase (TdT) as defined herein;

(d) cleaving the blocking group in the presence of a cleaving agent; and

(e) removal of the cleaving agent.

The method can add greater than 1 nucleotide by repeating steps (b) to (e).

References herein to ‘nucleoside triphosphates’ refer to a molecule containing a nucleoside (i.e. a base attached to a deoxyribose or ribose sugar molecule) bound to three phosphate groups. Examples of nucleoside triphosphates that contain deoxyribose are: deoxyadenosine triphosphate (dATP), deoxyguanosine triphosphate (dGTP), deoxycytidine triphosphate (dCTP) or deoxythymidine triphosphate (dTTP). Examples of nucleoside triphosphates that contain ribose are: adenosine triphosphate (ATP), guanosine triphosphate (GTP), cytidine triphosphate (CTP) or uridine triphosphate (UTP). Other types of nucleosides may be bound to three phosphates to form nucleoside triphosphates, such as naturally occurring modified nucleosides and artificial nucleosides.

Therefore, references herein to ‘3′-blocked nucleoside triphosphates’ refer to nucleoside triphosphates (e.g., dATP, dGTP, dCTP or dTTP) which have an additional group on the 3′ end which prevents further addition of nucleotides, i.e., by replacing the 3′-OH group with a protecting group.

It will be understood that references herein to ‘3′-block’, ‘3′-blocking group’ or ‘3′-protecting group’ refer to the group attached to the 3′ end of the nucleoside triphosphate which prevents further nucleotide addition. The present method uses reversible 3′-blocking groups which can be removed by cleavage to allow the addition of further nucleotides. By contrast, irreversible 3′-blocking groups refer to dNTPs where the 3′-OH group can neither be exposed nor uncovered by cleavage.

The 3′-blocked nucleoside 5′-triphosphate can be blocked by any chemical group that can be unmasked to reveal a 3′-OH. The 3′-blocked nucleoside triphosphate can be blocked by a 3′-O-azidomethyl, 3′-aminooxy, 3′-O—(N-oxime) (3′-O—N═CR₁R₂, where R₁and R₂are each a C1-C3 alkyl group, for example CH₃, such that the oxime can be O—N═C(CH₃)₂(N-acetoneoxime)), 3′-O-allyl group, 3′-O-cyanoethyl, 3′-O-acetyl, 3′-O-nitrate, 3′-phosphate, 3′-O-acetyl levulinic ester, 3′-O-tert butyl dimethyl silane, 3′-O-trimethyl(silyl)ethoxymethyl, 3′-O-ortho-nitrobenzyl, and 3′-O-para-nitrobenzyl.

The 3′-blocked nucleoside 5′-triphosphate can also be blocked by any chemical group that can be directly utilized in chemical ligations, such as copper-catalyzed or copper-free azide-alkyne click reactions and tetrazine-alkene click reactions. The 3′-blocked nucleoside triphosphate can include chemical moieties containing an azide, alkyne, alkene, and tetrazine.

References herein to ‘cleaving agent’ refer to a substance which is able to cleave the 3′-blocking group from the 3′-blocked nucleoside triphosphate. In one embodiment, the cleaving agent is a chemical cleaving agent. In an alternative embodiment, the cleaving agent is an enzymatic cleaving agent. The cleaving can be done in a single step, or can be a multi-step process, for example to transform an oxime (such as for example 3′-O—(N-oxime), 3′-O—N═C(CH₃)₂, into aminooxy (O—NH₂), followed by cleaving the aminooxy to OH.

It will be understood by the person skilled in the art that the selection of cleaving agent is dependent on the type of 3′-nucleotide blocking group used. For instance, tris(2-carboxyethyl)phosphine (TCEP) or tris(hydroxypropyl)phosphine (THPP) can be used to cleave a 3′-O-azidomethyl group, palladium complexes can be used to cleave a 3′-O-allyl group, or sodium nitrite can be used to cleave a 3′-aminooxy group. Therefore, in one embodiment, the cleaving agent is selected from: tris(2-carboxyethyl)phosphine (TCEP), a palladium complex or sodium nitrite.

In one embodiment, the cleaving agent is added in the presence of a cleavage solution comprising a denaturant, such as urea, guanidinium chloride, formamide or betaine. The addition of a denaturant has the advantage of being able to disrupt any undesirable secondary structures in the DNA. In a further embodiment, the cleavage solution comprises one or more buffers. It will be understood by the person skilled in the art that the choice of buffer is dependent on the exact cleavage chemistry and cleaving agent required.

References herein to an ‘initiator oligonucleotide’ or ‘initiator sequence’ refer to a short oligonucleotide with a free 3′-end which the 3′-blocked nucleoside triphosphate can be attached to. In one embodiment, the initiator sequence is a DNA initiator sequence. In an alternative embodiment, the initiator sequence is an RNA initiator sequence.

References herein to a ‘DNA initiator sequence’ refer to a small sequence of DNA which the 3′-blocked nucleoside triphosphate can be attached to, i.e., DNA will be synthesised from the end of the DNA initiator sequence.

In one embodiment, the initiator sequence is between 5 and 50 nucleotides long, such as between 5 and 30 nucleotides long (i.e. between 10 and 30), in particular between 5 and 20 nucleotides long (i.e., approximately 20 nucleotides long), more particularly 5 to 15 nucleotides long, for example 10 to 15 nucleotides long, especially 12 nucleotides long.

In one embodiment, the initiator sequence is single-stranded. In an alternative embodiment, the initiator sequence is double-stranded. It will be understood by persons skilled in the art that a 3′-overhang (i.e., a free 3′-end) allows for efficient addition.

In one embodiment, the initiator sequence is immobilised on a solid support. This allows TdT and the cleaving agent to be removed (in steps (c) and (e), respectively) without washing away the synthesised nucleic acid. The initiator sequence may be attached to a solid support stable under aqueous conditions so that the method can be easily performed via a flow setup.

In one embodiment, the initiator sequence is immobilised on a solid support via a reversible interacting moiety, such as a chemically-cleavable linker, an antibody/immunogenic epitope, a biotin/biotin binding protein (such as avidin or streptavidin), or glutathione-GST tag. Therefore, in a further embodiment, the method additionally comprises extracting the resultant nucleic acid by removing the reversible interacting moiety in the initiator sequence, such as by incubating with proteinase K.

In one embodiment, the initiator sequence contains a base or base sequence recognisable by an enzyme. A base recognised by an enzyme, such as a glycosylase, may be removed to generate an abasic site which may be cleaved by chemical or enzymatic means. A base sequence may be recognised and cleaved by a restriction enzyme.

In a further embodiment, the initiator sequence is immobilised on a solid support via a chemically-cleavable linker, such as a disulfide, allyl, or azide-masked hemiaminal ether linker. Therefore, in one embodiment, the method additionally comprises extracting the resultant nucleic acid by cleaving the chemical linker through the addition of tris(2-carboxyethyl)phosphine (TCEP) or dithiothreitol (DTT) for a disulfide linker; palladium complexes or an allyl linker; or TCEP for an azide-masked hemiaminal ether linker.

In one embodiment, the resultant nucleic acid is extracted and amplified by polymerase chain reaction using the nucleic acid bound to the solid support as a template. The initiator sequence could therefore contain an appropriate forward primer sequence and an appropriate reverse primer could be synthesised.

In one embodiment, the terminal deoxynucleotidyl transferase (TdT) of the invention is added in the presence of an extension solution comprising one or more buffers (e.g., Tris or cacodylate), one or more salts (e.g., Na⁺, K⁺, Mg²⁺, Mn²⁺, Cu²⁺, Zn²⁺, Co²⁺, etc. all with appropriate counterions, such as Cl) and inorganic pyrophosphatase (e.g., the Saccharomyces cerevisiae homolog). It will be understood that the choice of buffers and salts depends on the optimal enzyme activity and stability. The use of an inorganic pyrophosphatase helps to reduce the build-up of pyrophosphate due to nucleoside triphosphate hydrolysis by TdT. Therefore, the use of an inorganic pyrophosphatase has the advantage of reducing the rate of (1) backwards reaction and (2) TdT strand dismutation.

In one embodiment, step (b) is performed at a pH range between 5 and 10. Therefore, it will be understood that any buffer with a buffering range of pH 5-10 could be used, for example cacodylate, Tris, HEPES or Tricine, in particular cacodylate or Tris.

In one embodiment, step (d) is performed at a temperature less than 99° C., such as less than 95° C., 90° C., 85° C., 80° C., 75° C., 70° C., 65° C., 60° C., 55° C., 50° C., 45° C., 40° C., 35° C., or 30° C. It will be understood that the optimal temperature will depend on the cleavage agent utilised. The temperature used helps to assist cleavage and disrupt any secondary structures formed during nucleotide addition.

In one embodiment, steps (c) and (e) are performed by applying a wash solution. In one embodiment, the wash solution comprises the same buffers and salts as used in the extension solution described herein. This has the advantage of allowing the wash solution to be collected after step (c) and recycled as extension solution in step (b) when the method steps are repeated.

Also disclosed is a kit comprising a terminal deoxynucleotidyl transferase (TdT) as defined herein in combination with an initiator sequence and one or more 3′-blocked nucleoside triphosphates.

The invention includes the nucleic acid sequence used to express the modified terminal transferase. Included within the invention are the codon-optimized cDNA sequences which express the modified terminal transferase. Included are the codon-optimized cDNA sequences for each of the protein variants (SEQ ID NOs 4-727).

The nucleic acid sequence may be the sequence below (ID 728):

ATGCTGCATATTCCGATTTTCCCGCCGATTAAGAAGCGCCAGAAGCTGCC

GGAGAGCAGAAATTCCTGCAAATATGAAGTCAAGTTCTCTGAAGTTGCGA

TTTTCCTGGTTGAGCGCAAGATGGGTAGCAGCCGTCGCAAGTTTCTGACC

AACCTGGCGCGTAGCAAGGGCTTTCGTATCGAAGATGTTTTGAGCGATGC

GGTGACCCACGTTGTCGCCGAGGACAACAGCGCGGACGAGCTGTGGCAGT

GGCTCCAAAATTCCAGCCTGGGTGATCTGTCCAAAATTGAAGTCCTGGAC

ATTTCATGGTTCACCGAGTGTATGGGTGCCGGTAAACCTGTGCAAGTCGA

GGCCCGTCACTGCCTGGTCAAGAGCTGTCCGGTGATCGATCAGTACCTTG

AGCCATCCACGGTTGAAACGGTCAGCCAATATGCGTGCCAACGTCGTACG

ACCATGGAGAACCATAACCAGATTTTCACGGACGCATTTGCCATCCTGGC

GGAGAATGCTGAGTTTAACGAGAGCGAGGGTCCGTGCCTGGCGTTTATGC

GTGCAGCTAGCCTGCTGAAATCGTTGCCGCACGCAATTTCTAGCAGCAAA

GACCTGGAAGGTCTGCCGTGCCTGGGCGACCAGACGAAAGCCGTAATCGA

GGACATCTTAGAATACGGTCAGTGCAGCAAAGTTCAAGATGTGTTGTGTG

ATGACCGTTACCAGACCATCAAACTGTTCACGAGCGTTTTTGGCGTGGGC

CTGAAAACTGCAGAGAAGTGGTACCGCAAGGGTTTCCACTCTCTGGAAGA

AGTGCAAGCGGATAATGCGATCCATTTCACGAAAATGCAAAAAGCGGGCT

TCCTGTACTATGATGACATTAGCGCAGCAGTTTGTAAGGCTGAGGCCCAA

GCGATCGGTCAGATCGTCGAAGAGACTGTGCGTCTGATCGCACCGGATGC

GATTGTCACCCTGACGGGCGGTTTTCGCCGTGGTAAAGAGTGCGGTCACG

ACGTTGACTTTCTGATCACCACCCCGGAAATGGGCAAAGAAGTGTGGCTG

CTGAATCGTCTGATTAACCGTCTGCAGAATCAGGGTATTCTGTTGTATTA

TGACATTGTTGAGAGCACCTTCGACAAAACCCGTCTGCCGTGTCGCAAGT

TCGAGGCAATGGACCATTTTCAGAAGTGCTTTGCGATCATTAAGTTGAAG

AAAGAACTGGCGGCTGGCCGTGTGCAAAAAGACTGGAAAGCGATCCGTGT

TGATTTCGTGGCTCCGCCGGTCGACAATTTCGCCTTTGCATTGCTGGGTT

GGACCGGTAGCCGTCAGTTCGAGCGTGATCTGCGCCGCTTTGCGCGCCAC

GAACGTAAGATGCTGCTGGATAACCATGCACTGTACGATAAGACCAAAAA

GATTTTCCTGCCGGCCAAAACCGAAGAAGATATCTTTGCGCACCTGGGCT

TGGACTACATCGATCCATGGCAACGCAACGCGTAATGA

The invention includes a cell line producing the modified terminal transferase.

Examples

Expression of TdT Variants

Briefly, plasmids containing genes encoding terminal transferase enzymes were transformed into BL21 E. coli competent cells. Starter Luria broth (LB) cultures were grown overnight at 37° C. and inoculated into LB expression cultures. Expression cultures were grown to an optical density of 0.6 at 600 nm and induced by the addition of IPTG to 1 mM. Cultures were induced and grown overnight at 25° C. The following morning, cultures were lysed in a detergent lysis buffer and purified to homogeneity by immobilized metal affinity chromatography (IMAC).

Assaying the Incorporation of Reversible Terminators by TdT Variants

173 terminal transferase enzymes were expressed, purified, and compared against wild-type bovine TdT (SEQ ID NO 2). Purified engineered TdTs were then used in the following assays: a fluorescently labeled 15-nt ssDNA primer was incubated with 1×TdT buffer (Thermo Fisher Scientific), yeast inorganic pyrophosphatase (Sigma-Aldrich, 0.1 mU/μl), 3′-azidomethyl dTTP or 3′-aminooxy dATP, and engineered TdT (24 μg/μl) for 10 min at 37° C. Formamide (Fisher Scientific) was then used to quench the reaction, and samples were directly loaded onto and analysed by denaturing polyacrylamide gel electrophoresis. Gels were imaged and resulting gel bands were quantified with a Typhoon scanner (GE).

The results from the 173 TdT enzymes (SEQ ID NOs 1-173) are shown in FIG. 1.

Assaying the Incorporation of Base-Modified Reversible Terminators by TdT Variants

embedded image

192 terminal deoxynucleotidyl transferases (TdT) variants were expressed and purified as described above. The expressed variants had SEQ ID NOs:

345, 347, 352, 357, 359, 360, 361, 362, 364, 365, 366, 367, 368, 370, 371, 372, 375, 376, 377, 378, 380, 382, 383, 384, 385, 387, 388, 392, 393, 394, 395, 397, 398, 399, 401, 405, 406, 410, 411, 416, 418, 422, 426, 427, 430, 433, 436, 439, 440, 442, 444, 445, 446, 447, 450, 453, 454, 455, 457, 460, 461, 462, 463, 464, 467, 472, 473, 475, 476, 477, 478, 479, 480, 485, 486, 487, 489, 492, 494, 495, 497, 499, 500, 503, 505, 506, 507, 509, 510, 514, 516, 517, 519, 524, 525, 526, 527, 528, 529, 531, 532, 533, 535, 543, 544, 546, 550, 553, 555, 557, 559, 560, 561, 562, 564, 565, 567, 568, 570, 572, 573, 575, 580, 582, 584, 589, 593, 595, 598, 599, 600, 601, 604, 605, 606, 609, 611, 612, 614, 618, 619, 620, 623, 629, 637, 638, 639, 641, 643, 644, 646, 648, 649, 651, 652, 654, 657, 658, 660, 661, 662, 664, 665, 666, 667, 670, 673, 678, 679, 681, 684, 685, 687, 690, 692, 698, 699, 700, 703, 706, 707, 708, 711, 712, 715, 716, 717, 718, 720, 721, 722, 725.

The base-modified reversibly terminators A*, C*, G*, and T* were supplied as substrates to engineered variants in a single nucleotide incorporation assay. A pool of DNA initiators with degenerate ends ( . . . NNN, where N=A, C, G, T) was immobilised to a solid support and exposed to nucleotide addition mixture (NAM) solutions containing (1) a TdT variant, (2) neutral pH buffer, (3) monovalent salt, (4) cobalt chloride, and (5) 3′-ONH₂-dXTP, where X is the modified nucleobase resulting in A*, C*, G*, or T*. The incubation temperature was 37° C. and the reaction time was 2.5 minutes. The solid support was then washed with a high salt solution at neutral pH followed by a low salt solution at neutral pH. The initiator pools transformed into sequencing libraries and analysed by next-generation sequencing (NGS) on an Illumina NextSeq500 with paired-end 30 cycle reads (PE30 reads). Bcl files were converted to fastq files with Illumina's bcl2fastq conversion software and analysed in R. The incorporation efficiency ([reads containing N+1 product]/{[reads containing N initiator]+[reads containing N+1 product]}) was calculated for the addition of each modified base against to all possible initiator contexts. The average incorporation efficiency across all contexts is presented in FIG. 3 (top panel). Wild-type bovine and spotted gar TdT activities as it relates to the single nucleotide incorporation of the base-modified reversibly terminated nucleotides A*, C*, G*, and T* are indicated by the dotted line. The dotted line occurs at y=0 due to the inability of wild-type bovine or spotted gar TdTs to incorporate these base-modified reversibly terminated nucleotides in our assay. All of the presented mutations in the TdT variants resulted in improvements in TdT modified-base incorporation relative to wild-type bovine and wild-type spotted gar TdTs.

Assaying the Multicycling Capabilities of TdT Variants

Solid support synthesis of an 8-nt nucleic acid sequence using 3′-ONH₂nucleoside 5′-triphosphates with terminal deoxynucleotidyl transferase (TdT) SEQ ID NOs 1 & 344-727. The TdT variants were expressed and purified as described above. The DNA sequence 5′-ATCGATCG-3′ was synthesized by repeated exposure of a solid support bound DNA initiator to nucleotide addition mixture (NAM) solutions containing (1) TdT, (2) neutral pH buffer, (3) monovalent salt, (4) cobalt chloride, and (5) 3′-ONH₂-dNTP, where N is selected from adenine, thymine, cytosine, or guanine. A cycle consists of the following: (A) NAM solution with a specified A, T, C, or G reversibly terminated nucleotide were incubated for 5 minutes on the solid support at 37° C.; (B) the solid support was then washed with a high salt solution at neutral pH; (C) the solid support was then exposed to acidic aqueous sodium nitrite; and (D) the solid support was then washed with the same high salt solution at neutral pH from (B). (A)-(D) were then repeated 7 more times to synthesize the desired 8-nt sequence. Synthesized DNA were analysed by running reactions on a denaturing polyacrylamide gel and quantified by virtue of a fluorophore covalently attached to the DNA initiator. The fraction full length (8-nt species) was determined by taking fluorescence intensity of the 8-nt band and dividing by total lane intensity. Wild-type bovine and spotted gar TdT activities as it relates to fraction full-length are indicated by the dotted line at y=0 indicating that they are incapable of synthesizing any 8-nt product. All mutations included in the TdT variants resulted in improvements in TdT relative to wild-type bovine and spotted gar TdTs. Results are shown in FIG. 3 (bottom panel).

MODIFIED TERMINAL DEOXYNUCLEOTIDYL TRANSFERASE (TDT) ENZYMES

Information

Publication Number

Date Filed

Date Published

Inventors

CPC

International Classifications

Abstract

Description

Claims

Priority Claims (1)

PCT Information