WO2017050723A1 - Variants de la polymérase pol7 - Google Patents

Variants de la polymérase pol7 Download PDF

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Publication number
WO2017050723A1
WO2017050723A1 PCT/EP2016/072225 EP2016072225W WO2017050723A1 WO 2017050723 A1 WO2017050723 A1 WO 2017050723A1 EP 2016072225 W EP2016072225 W EP 2016072225W WO 2017050723 A1 WO2017050723 A1 WO 2017050723A1
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polymerase
amino acid
dna
dna polymerase
nanopore
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PCT/EP2016/072225
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English (en)
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David Fullagar
Aruna Ayer
Arkadiusz Bibillo
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Genia Technologies, Inc.
F. Hoffmann-La Roche Ag
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Publication of WO2017050723A1 publication Critical patent/WO2017050723A1/fr

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/10—Transferases (2.)
    • C12N9/12—Transferases (2.) transferring phosphorus containing groups, e.g. kinases (2.7)
    • C12N9/1241—Nucleotidyltransferases (2.7.7)
    • C12N9/1252—DNA-directed DNA polymerase (2.7.7.7), i.e. DNA replicase

Definitions

  • [001] Provided herein, among other things, are modified DNA polymerases containing amino acid alterations based on mutations identified in directed evolution experiments designed to select enzymes that are better suited for applications in recombinant DNA technologies.
  • DNA polymerases are a family of enzymes that use single-stranded DNA as a template to synthesize the complementary DNA strand.
  • DNA polymerases can add free nucleotides to the 3' end of a newly- forming strand resulting in elongation of the new strand in a 5' to 3' direction.
  • Most DNA polymerases are multifunctional proteins that possess both polymerizing and exonucleolytic activities. For example, many DNA polymerases have 3' ⁇ 5' exonuclease activity.
  • polymerases can recognize an incorrectly incorporated nucleotide and the 3' ⁇ 5' exonuclease activity of the enzyme allows the incorrect nucleotide to be excised (this activity is known as proofreading). Following nucleotide excision, the polymerase can re-insert the correct nucleotide and replication can continue. Many DNA polymerases also have 5' ⁇ 3' exonuclease activity.
  • the present invention provides modified DNA polymerases (e.g. , mutants) based on directed evolution experiments designed to select mutations that confer advantageous phenotypes under conditions used in industrial or research
  • variant polymerase comprising at least one alteration at a position corresponding to of S264E, L265Q, L265M, M377H, M377Y, E378Q, I379K, N382M, S383T, T384A, G385L, G385Q, G385M, G386Y, G386T, and R388W of SEQ ID NO:l (Pol7 (with His tag)).
  • a modified DNA polymerase having a DNA polymerase activity comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as set forth in SEQ ID NO: 1.
  • the modified DNA polymerase has at least 92%, 94%, 96%, or
  • a modified DNA polymerase having a DNA polymerase activity comprising an amino acid sequence having at least 90%) sequence identity to the amino acid sequence as set forth in SEQ ID NO: 1 having one or more amino acid substitutions relative to SEQ ID NO: l, such substitutions being selected from the group consisting of S264E, L265Q, L265M, M377H, M377Y, E378Q, I379K, N382M, S383T, T384A, G385L, G385Q, G385M, G386Y, G386T, and R388W of SEQ ID NO: 1 and combinations thereof.
  • a modified DNA polymerase has altered characteristic selected from enzyme activity, fidelity, processivity, elongation rate, stability, or solubility, when compared to SEQ ID NO: 1.
  • the altered characteristic is enzyme activity.
  • the altered characteristic is fidelity.
  • the altered characteristic is processivity.
  • the altered characteristic is elongation rate.
  • the altered characteristic is stability.
  • the altered characteristic is solubility.
  • a modified DNA polymerase having a DNA polymerase activity comprising an amino acid sequence having at least 90% sequence identity to the amino acid sequence as set forth in SEQ ID NO: l, which amino acid sequence includes one or more amino acid substitutions relative to SEQ ID NO: 1 , such substitutions being selected from the group consisting of S264E, L265Q, L265M, M377H, M377Y, E378Q, I379K, N382M, S383T, T384A, G385L, G385Q, G385M, G386Y, G386T, and R388W of SEQ ID NO: l and combinations thereof, wherein the one or more amino acid substitutions alter enzyme activity, fidelity, processivity, elongation rate, sequencing accuracy, long continuous read capability, stability, or solubility.
  • the altered characteristic is enzyme activity.
  • the altered characteristic is enzyme activity.
  • the altered characteristic is fidelity.
  • the altered characteristic is
  • the altered characteristic is elongation rate. In an embodiment, the altered characteristic is stability. In an embodiment, the altered characteristic is solubility. In one embodiment, the altered characteristic is an ability to bind and/or incorporate polyphosphates, e.g., e.g., quadraphosphate, pentaphosphate, hexaphosphate, heptaphosphate or octophosphate nucleotide.
  • polyphosphates e.g., e.g., quadraphosphate, pentaphosphate, hexaphosphate, heptaphosphate or octophosphate nucleotide.
  • the variant polymerase having altered enzyme activity as compared to SEQ ID NO: l is selected from S264E, L265Q, L265M, M377H, M377Y, E378Q, I379K, N382M, S383T, T384A, G385L, G385Q, G385M, G386Y, G386T, and R388W.
  • Figure 1 illustrates an exemplary template used in the displacement assay. Reference is made to Example 3.
  • Figure 2 shows a schematic of the k chem assay used herein to measure the rate of incorporation of polyphosphates. Reference is made to Example 6.
  • Figure 3 is a summary of the FRET based k 0ff assay used herein to measure kinetic properties of the variant polymerases. Reference is made to Example 4.
  • Figure 4 is a depiction of the k 0ff assay based on fluorescence polarization and an exemplary data trace. Reference is made to Example 5.
  • Figure 5 is a graph showing representative data from the displacement assay for wild-type and variant polymerases. Reference is made to Example 3.
  • Figure 6 is a graph of representative data from FRET based Kog- assay for a variant polymerase. Reference is made to Example 4.
  • Figure 7 is a graph of Dwell time vs current plot for a static capture experiment at lOOmV with Pol7 variant-DNA complex coupled to alpha-hemolysin nanopore in 20mM Hepes pH 7.5, 300mM NaCl, 3mM CaC12 and 5mM TCEP above and below the bilayer.
  • the average dwell time of each capture of dTNP- tagged nucleotide is 1.2 seconds.
  • Example 8 DETAILED DESCRIPTION
  • BIOLOGY, Harper Perennial, NY (1991) provide one of skill with a general dictionary of many of the terms used in this invention. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are described. Practitioners are particularly directed to Sambrook et al., 1989, and Ausubel FM et al., 1993, for definitions and terms of the art. It is to be understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary.
  • Numeric ranges are inclusive of the numbers defining the range. The term about is used herein to mean plus or minus ten percent (10%) of a value. For example, "about 100" refers to any number between 90 and 110.
  • nucleic acids are written left to right in 5' to 3' orientation; amino acid sequences are written left to right in amino to carboxy orientation, respectively.
  • amino acid in its broadest sense, refers to any compound and/or substance that can be incorporated into a polypeptide chain.
  • an amino acid has the general structure H 2 N— C(H)(R)— COOH.
  • an amino acid is a naturally- occurring amino acid.
  • an amino acid is a synthetic amino acid; in some embodiments, an amino acid is a D-amino acid; in some
  • an amino acid is an L-amino acid.
  • Standard amino acid refers to any of the twenty standard L-amino acids commonly found in naturally occurring peptides.
  • Nonstandard amino acid refers to any amino acid, other than the standard amino acids, regardless of whether it is prepared synthetically or obtained from a natural source.
  • synthetic amino acid encompasses chemically modified amino acids, including but not limited to salts, amino acid derivatives (such as amides), and/or substitutions.
  • Amino acids, including carboxy- and/or amino-terminal amino acids in peptides can be modified by methylation, amidation, acetylation, and/or substitution with other chemical without adversely affecting their activity. Amino acids may participate in a disulfide bond.
  • amino acid is used interchangeably with “amino acid residue,” and may refer to a free amino acid and/or to an amino acid residue of a peptide. It will be apparent from the context in which the term is used whether it refers to a free amino acid or a residue of a peptide. It should be noted that all amino acid residue sequences are represented herein by formulae whose left and right orientation is in the conventional direction of amino-terminus to carboxy-terminus.
  • Base Pair refers to a partnership of adenine (A) with thymine (T), or of cytosine (C) with guanine (G) in a double stranded DNA molecule.
  • Complementary refers to the broad concept of sequence complementarity between regions of two polynucleotide strands or between two nucleotides through base-pairing. It is known that an adenine nucleotide is capable of forming specific hydrogen bonds ("base pairing") with a nucleotide which is thymine or uracil. Similarly, it is known that a cytosine nucleotide is capable of base pairing with a guanine nucleotide.
  • DNA binding affinity typically refers to the activity of a DNA polymerase in binding DNA nucleic acid.
  • DNA binding activity can be measured in a two band-shift assay. See, e.g., Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual (3 rd ed., Cold Spring Harbor Laboratory Press, NY) at 9.63-9.75 (describing end- labeling of nucleic acids).
  • a reaction mixture is prepared containing at least about 0.5 ⁇ g of the polypeptide in about 10 ⁇ of binding buffer (50 mM sodium phosphate buffer (pH 8.0), 10% glycerol, 25 mM KC1, 25 mM MgCl 2 ). The reaction mixture is heated to 37° C. for 10 min.
  • the reaction mixture is loaded onto a native polyacrylamide gel in 0.5 x Tris-borate buffer.
  • the reaction mixture is subjected to electrophoresis at room temperature.
  • the gel is dried and subjected to autoradiography using standard methods. Any detectable decrease in the mobility of the labeled double-stranded nucleic acid indicates formation of a binding complex between the polypeptide and the double-stranded nucleic acid.
  • nucleic acid binding activity may be quantified using standard densitometric methods to measure the amount of radioactivity in the binding complex relative to the total amount of radioactivity in the initial reaction mixture.
  • Other methods of measuring DNA binding affinity are known in the art (see, e.g., Kong et al. (1993) J. Biol. Chem. 268(3): 1965-1975).
  • Elongation rate refers to the average rate at which a DNA polymerase extends a polymer chain.
  • a high elongation rate refers to an elongation rate higher than 2 nt/s (e.g., higher than 30,
  • Enzyme activity refers to the specificity and efficiency of a DNA polymerase. Enzyme activity of a DNA polymerase is also referred to as "polymerase activity,” which typically refers to the activity of a DNA polymerase in catalyzing the template-directed synthesis of a polynucleotide. Enzyme activity of a polymerase can be measured using various techniques and methods known in the art. For example, serial dilutions of polymerase can be prepared in dilution buffer (e.g., 20 mM Tris.Cl, pH 8.0, 50 mM
  • KC1, 0.5% NP 40, and 0.5% Tween-20 For each dilution, 5 ⁇ can be removed and added to 45 ⁇ of a reaction mixture containing 25 mM TAPS (pH 9.25), 50 mM KC1, 2 mM MgCl 2 , 0.2 mM dATP, 0.2 mM dGTP, 0.2 mM dTTP, 0.1 mM dCTP, 12.5 ⁇ g activated DNA, 100 ⁇ [a- 32 P]dCTP (0.05 ⁇ / ⁇ ) and sterile deionized water.
  • the reaction mixtures can be incubated at 37° C. (or 74° C.
  • thermostable DNA polymerases for 10 minutes and then stopped by immediately cooling the reaction to 4° C. and adding 10 ⁇ of ice-cold 60 mM EDTA. A 25 ⁇ aliquot can be removed from each reaction mixture. Unincorporated radioactively labeled dCTP can be removed from each aliquot by gel filtration (Centri-Sep, Princeton Separations, Adelphia, N.J.). The column eluate can be mixed with scintillation fluid (1 ml). Radioactivity in the column eluate is quantified with a scintillation counter to determine the amount of product synthesized by the polymerase.
  • One unit of polymerase activity can be defined as the amount of polymerase necessary to synthesize 10 nmole of product in 30 minutes (Lawyer et al. (1989) J. Biol. Chem. 264:6427-647). Other methods of measuring polymerase activity are known in the art (see, e.g. Sambrook et al. (2001) Molecular Cloning: A Laboratory Manual (3rd ed., Cold Spring Harbor Laboratory Press, NY)).
  • Purified means that a molecule is present in a sample at a concentration of at least 90% by weight, or at least 95% by weight, or at least 98% by weight of the sample in which it is contained.
  • Isolated An "isolated" molecule is a nucleic acid molecule that is separated from at least one other molecule with which it is ordinarily associated, for example, in its natural environment.
  • An isolated nucleic acid molecule includes a nucleic acid molecule contained in cells that ordinarily express the nucleic acid molecule, but the nucleic acid molecule is present extrachromasomally or at a chromosomal location that is different from its natural chromosomal location.
  • % homology is used interchangeably herein with the term “% identity” herein and refers to the level of nucleic acid or amino acid sequence identity between the nucleic acid sequence that encodes any one of the inventive polypeptides or the inventive polypeptide's amino acid sequence, when aligned using a sequence alignment program.
  • 80%> homology means the same thing as 80%> sequence identity determined by a defined algorithm, and accordingly a homologue of a given sequence has greater than 80%> sequence identity over a length of the given sequence.
  • Exemplary levels of sequence identity include, but are not limited to, 80, 85, 90, 95, 98%> or more sequence identity to a given sequence, e.g., the coding sequence for any one of the inventive polypeptides, as described herein.
  • Exemplary computer programs which can be used to determine identity between two sequences include, but are not limited to, the suite of BLAST programs, e.g., BLASTN, BLASTX, and TBLASTX, BLASTP and TBLASTN, publicly available on the Internet. See also, Altschul, et al., 1990 and Altschul, et al., 1997.
  • Sequence searches are typically carried out using the BLASTN program when evaluating a given nucleic acid sequence relative to nucleic acid sequences in the GenBank DNA Sequences and other public databases.
  • the BLASTX program is preferred for searching nucleic acid sequences that have been translated in all reading frames against amino acid sequences in the GenBank Protein Sequences and other public databases. Both BLASTN and BLASTX are run using default parameters of an open gap penalty of 11.0, and an extended gap penalty of 1.0, and utilize the BLOSUM-62 matrix. (See, e.g., Altschul, S. F., et al, Nucleic Acids Res. 25:3389-3402, 1997.)
  • a preferred alignment of selected sequences in order to determine "% identity" between two or more sequences is performed using for example, the CLUSTAL-W program in MacVector version 13.0.7, operated with default parameters, including an open gap penalty of 10.0, an extended gap penalty of 0.1, and a BLOSUM 30 similarity matrix.
  • Modified DNA polymerase refers to a DNA polymerase originated from another (i.e., parental) DNA polymerase and contains one or more amino acid alterations (e.g., amino acid substitution, deletion, or insertion) compared to the parental DNA polymerase.
  • a modified DNA polymerases of the invention is originated or modified from a naturally-occurring or wild-type DNA polymerase.
  • a modified DNA polymerase of the invention is originated or modified from a recombinant or engineered DNA polymerase including, but not limited to, chimeric DNA polymerase, fusion DNA polymerase or another modified DNA polymerase.
  • a modified DNA polymerase has at least one changed phenotypes compared to the parental polymerase.
  • Mutation refers to a change introduced into a parental sequence, including, but not limited to, substitutions, insertions, deletions (including truncations).
  • substitutions include, but are not limited to, the creation of a new character, property, function, phenotype or trait not found in the protein encoded by the parental sequence.
  • Mutant refers to a modified protein which displays altered characteristics when compared to the parental protein.
  • variant and “mutant” are used interchangeably herein.
  • Wild-type refers to a gene or gene product which has the characteristics of that gene or gene product when isolated from a naturally-occurring source.
  • fidelity refers to either the accuracy of DNA polymerization by template-dependent DNA polymerase or the measured difference in k 0ff of the correct nucleotide vs incorrect nucleotide binding to the template DNA.
  • the fidelity of a DNA polymerase is typically measured by the error rate (the frequency of incorporating an inaccurate nucleotide, i.e., a nucleotide that is not incorporated at a template-dependent manner).
  • the accuracy or fidelity of DNA polymerization is maintained by both the polymerase activity and the 3 '-5' exonuclease activity of a DNA polymerase.
  • the term "high fidelity” refers to an error rate less than 4.45x 1 ( ⁇ 6 (e.g., less than 4.0x l(T 6 , 3.5x l(T 6 , 3.0x l(T 6 ,
  • the fidelity or error rate of a DNA polymerase may be measured using assays known to the art.
  • the error rates of DNA polymerases can be tested as described herein or as described in Johnson, et al., Biochim Biophys Acta . 2010 May ;
  • Nanopore generally refers to a pore, channel or passage formed or otherwise provided in a membrane.
  • a membrane may be an organic membrane, such as a lipid bilayer, or a synthetic membrane, such as a membrane formed of a polymeric material.
  • the membrane may be a polymeric material.
  • the nanopore may be disposed adjacent or in proximity to a sensing circuit or an electrode coupled to a sensing circuit, such as, for example, a complementary metal-oxide semiconductor (CMOS) or field effect transistor (FET) circuit.
  • CMOS complementary metal-oxide semiconductor
  • FET field effect transistor
  • a nanopore has a characteristic width or diameter on the order of 0.1 nanometers (nm) to about lOOOnm.
  • Some nanopores are proteins.
  • Alpha-hemolysin, MspA are examples of a protein nanopore.
  • Nucleotide As used herein, a monomeric unit of DNA or RNA consisting of a sugar moiety (pentose), a phosphate, and a nitrogenous heterocyclic base.
  • the base is linked to the sugar moiety via the glycosidic carbon ( carbon of the pentose) and that combination of base and sugar is a nucleoside.
  • the nucleoside contains a phosphate group bonded to the 3 Or 5' position of the pentose it is referred to as a nucleotide.
  • a sequence of operatively linked nucleotides is typically referred to herein as a "base sequence” or "nucleotide sequence,” and is represented herein by a formula whose left to right orientation is in the
  • Oligonucleotide or Polynucleotide As used herein, the term
  • oligonucleotide is defined as a molecule including two or more deoxyribonucleotides and/or ribonucleotides, preferably more than three. Its exact size will depend on many factors, which in turn depend on the ultimate function or use of the oligonucleotide.
  • the oligonucleotide may be derived synthetically or by cloning.
  • polynucleotide refers to a polymer molecule composed of nucleotide monomers covalently bonded in a chain.
  • RNA ribonucleic acid
  • Polymerase As used herein, a “polymerase” refers to an enzyme that catalyzes the polymerization of nucleotide (i.e., the polymerase activity).
  • the enzyme will initiate synthesis at the 3 '-end of the primer annealed to a polynucleotide template sequence, and will proceed toward the 5' end of the template strand.
  • a "DNA polymerase” catalyzes the polymerization of
  • Primer refers to an oligonucleotide, whether occurring naturally or produced synthetically, which is capable of acting as a point of initiation of nucleic acid synthesis when placed under conditions in which synthesis of a primer extension product which is complementary to a nucleic acid strand is induced, e.g., in the presence of four different nucleotide
  • the primer is preferably single-stranded for maximum efficiency in amplification, but may alternatively be double-stranded. If double-stranded, the primer is first treated to separate its strands before being used to prepare extension products.
  • the primer is an oligodeoxyribonucleotide.
  • the primer must be sufficiently long to prime the synthesis of extension products in the presence of the thermostable enzyme. The exact lengths of the primers will depend on many factors, including temperature, source of primer and use of the method.
  • the oligonucleotide primer typically contains 15-25 nucleotides, although it may contain more or few nucleotides. Short primer molecules generally require colder temperatures to form sufficiently stable hybrid complexes with template.
  • Processivity refers to the ability of a polymerase to remain attached to the template and perform multiple modification reactions. “Modification reactions” include but are not limited to polymerization, and exonucleolytic cleavage. In some embodiments, “processivity” refers to the ability of a DNA polymerase to perform a sequence of polymerization steps without intervening dissociation of the enzyme from the growing DNA chains.
  • processing of a DNA polymerase is measured by the length of nucleotides (for example 20 nts, 300 nts, 0.5-1 kb, or more) that are polymerized or modified without intervening dissociation of the DNA polymerase from the growing DNA chain.
  • "Processivity” can depend on the nature of the polymerase, the sequence of a DNA template, and reaction conditions, for example, salt concentration, temperature or the presence of specific proteins.
  • high processivity refers to a processivity higher than 20 nts (e.g., higher than 40 nts, 60 nts, 80 nts, 100 nts, 120 nts, 140 nts, 160 nts, 180 nts, 200 nts, 220 nts, 240 nts, 260 nts, 280 nts, 300 nts, 320 nts, 340 nts, 360 nts, 380 nts, 400 nts, or higher) per association/disassociation with the template.
  • Processivity can be measured according the methods defined herein and in WO 01/92501 Al (MJ Bioworks, Inc., Improved Nucleic Acid Modifying Enzymes, published 06 Dec 2001).
  • Synthesis refers to any in vitro method for making new strand of polynucleotide or elongating existing
  • polynucleotide i.e., DNA or RNA
  • Synthesis includes amplification, which increases the number of copies of a polynucleotide template sequence with the use of a polymerase.
  • Polynucleotide synthesis results in the incorporation of nucleotides into a polynucleotide (i.e., a primer), thereby forming a new
  • Template DNA molecule refers to a strand of a nucleic acid from which a complementary nucleic acid strand is synthesized by a DNA polymerase, for example, in a primer extension reaction.
  • Template-dependent manner refers to a process that involves the template dependent extension of a primer molecule (e.g., DNA synthesis by DNA polymerase).
  • template-dependent manner typically refers to polynucleotide synthesis of RNA or DNA wherein the sequence of the newly synthesized strand of
  • polynucleotide is dictated by the well-known rules of complementary base pairing (see, for example, Watson, J. D. et al, In: Molecular Biology of the Gene, 4th Ed., W. A. Benjamin, Inc., Menlo Park, Calif. (1987)).
  • Tag refers to a detectable moiety that may be atoms or molecules, or a collection of atoms or molecules.
  • a tag may provide an optical, electrochemical, magnetic, or electrostatic (e.g., inductive, capacitive) signature, which signature may be detected with the aid of a nanopore.
  • a nucleotide may comprise a tag attached to the terminal phosphate.
  • Vector refers to a nucleic acid construct designed for transfer between different host cells.
  • An "expression vector” refers to a vector that has the ability to incorporate and express heterologous DNA fragments in a foreign cell. Many prokaryotic and eukaryotic expression vectors are commercially available. Selection of appropriate expression vectors is within the knowledge of those having skill in the art.
  • polymerase variants provided for herein are useful in the chip-based polynucleotide sequencing as described in WO2013/188841 (Genia Technologies, Inc., Chip Set-Up and High- Accuracy Nucleic Acid Sequencing, published 19 Dec 2013).
  • Desired characteristics of a polymerase that finds use in sequencing DNA are:
  • j Compatible with attachment to nanopore k.
  • a polyphosphates having 4, 5, 6, 7 or 8 phosphates e.g., quadraphosphate, pentaphosphate, hexaphosphate, heptaphosphate or octophosphate nucleotide
  • Thr384Ala+Gly385Leu or T384A+G385L representing mutations in positions 30 and 34 substituting alanine and glutamic acid for asparagine and serine, respectively.
  • Actinomyces phage Av-1 wild type sequences are provided herein (SEQ ID NO:3, nucleic acid coding region plus a His-tag; SEQ ID NO: l, protein coding region) and available elsewhere (National Center for Bioinformatics or GenBank Accession Numbers ABR67671.1).
  • Primers can be ordered from commercial companies, e.g., IDT DNA. Nanopore assembly and insertion
  • the methods described herein can use a nanopore having a polymerase attached to the nanopore.
  • many nanopores including, e.g., alpha-hemolysin (aHL), can be multimeric proteins having a plurality of subunits ⁇ e.g., 7 subunits for aHL).
  • the subunits can be identical copies of the same polypeptide.
  • multimeric proteins ⁇ e.g., nanopores
  • a-HL variants modified subunits
  • un-modified subunits un-modified subunits
  • methods for producing multimeric proteins ⁇ e.g., nanopores) having a defined ratio of modified subunits to un-modified subunits.
  • a method for assembling a protein having a plurality of subunits comprises providing a plurality of first subunits 2705 and providing a plurality of second subunits 2710, where the second subunits are modified when compared with the first subunits.
  • the first subunits are wild-type ⁇ e.g., purified from native sources or produced recombinantly).
  • the second subunits can be modified in any suitable way.
  • the second subunits have a protein ⁇ e.g., a polymerase) attached ⁇ e.g., as a fusion protein).
  • the modified subunits can comprise a chemically reactive moiety (e.g., an azide or an alkyne group suitable for forming a linkage).
  • the method further comprises performing a reaction ⁇ e.g., a Click chemistry cycloaddition) to attach an entity ⁇ e.g., a polymerase) to the chemically reactive moiety.
  • the method can further comprise contacting the first subunits with the second subunits 2715 in a first ratio to form a plurality of proteins 2720 having the first subunits and the second subunits.
  • one part modified aHL subunits having a reactive group suitable for attaching a polymerase can be mixed with six parts wild-type aHL subunits (i.e., with the first ratio being 1 :6).
  • the plurality of proteins can have a plurality of ratios of the first subunits to the second subunits.
  • the mixed subunits can form several nanopores having a distribution of stoichiometries of modified to un-modified subunits (e.g., 1 :6, 2:5, 3:4).
  • the proteins are formed by simply mixing the subunits.
  • a detergent e.g., deoxycholic acid
  • the nanopores can also be formed using a lipid (e.g., l,2-diphytanoyl-sn-glycero-3-phosphocholine (DPhPC) or l,2-di-0-phytanyl-sn-glycero-3-phosphocholine (DoPhPC)) and moderate temperature (e.g., less than about 100°C).
  • DPhPC l,2-diphytanoyl-sn-glycero-3-phosphocholine
  • DoPhPC l,2-di-0-phytanyl-sn-glycero-3-phosphocholine
  • mixing DPhPC with a buffer solution creates large multi-lamellar vesicles (LMV), and adding aHL subunits to this solution and incubating the mixture at 40°C for 30 minutes results in pore formation.
  • LMV
  • the resulting proteins can have a mixed stoichiometry (e.g., of the wild type and mutant proteins).
  • the stoichiometry of these proteins can follow a formula which is dependent upon the ratio of the concentrations of the two proteins used in the pore forming reaction. This formula is as follows:
  • the method can further comprise fractionating the plurality of proteins to enrich proteins that have a second ratio of the first subunits to the second subunits 2725.
  • nanopore proteins can be isolated that have one and only one modified subunit (e.g., a second ratio of 1 :6).
  • any second ratio is suitable.
  • a distribution of second ratios can also be fractionated such as enriching proteins that have either one or two modified subunits.
  • the total number of subunits forming the protein is not always 7 (e.g., a different nanopore can be used or an alpha-hemolysin nanopore can form having six subunits) as depicted in Figure 27 of WO2014/074727.
  • proteins having only one modified subunit are enriched.
  • the second ratio is 1 second subunit per (n-1) first subunits where n is the number of subunits comprising the protein.
  • the first ratio can be the same as the second ratio, however this is not required. In some cases, proteins having mutated monomers can form less efficiently than those not having mutated subunits. If this is the case, the first ratio can be greater than the second ratio (e.g., if a second ratio of 1 mutated to 6 non- mutated subunits are desired in a nanopore, forming a suitable number of 1 :6 proteins may require mixing the subunits at a ratio greater than 1 :6).
  • Proteins having different second ratios of subunits can behave differently (e.g., have different retention times) in a separation.
  • the proteins are fractionated using chromatography, such as ion exchange chromatography or affinity chromatography. Since the first and second subunits can be identical apart from the modification, the number of modifications on the protein can serve as a basis for separation.
  • either the first or second subunits have a purification tag (e.g., in addition to the modification) to allow or improve the efficiency of the fractionation.
  • a poly-histidine tag His-tag
  • streptavidin tag streptavidin tag
  • other peptide tag is used.
  • the first and second subunits each comprise different tags and the fractionation step fractionates on the basis of each tag.
  • a charge is created on the tag at low pH (Histidine residues become positively charged below the pKa of the side chain).
  • ion exchange chromatography can be used to separate the oligomers which have 0, 1 , 2, 3, 4, 5, 6, or 7 of the "charge-tagged" aHL subunits.
  • this charge tag can be a string of any amino acids which carry a uniform charge.
  • Figure 28 and Figure 29 show examples of fractionation of nanopores based on a His-tag.
  • Figure 28 shows a plot of ultraviolet absorbance at 280 nanometers, ultraviolet absorbance at 260 nanometers, and conductivity. The peaks correspond to nanopores with various ratios of modified and unmodified subunits.
  • Figure 29 of WO2014/074727 shows fractionation of aHL nanopores and mutants thereof using both His-tag and Strep -tags.
  • an entity e.g., a polymerase
  • the protein can be a nanopore and the entity can be a polymerase.
  • the method further comprises inserting the proteins having the second ratio subunits into a bilayer.
  • a nanopore can comprise a plurality of subunits.
  • a polymerase can be attached to one of the subunits and at least one and less than all of the subunits comprise a first purification tag.
  • the nanopore is alpha-hemolysin or a variant thereof.
  • all of the subunits comprise a first purification tag or a second purification tag.
  • the first purification tag can be a poly-histidine tag (e.g., on the subunit having the polymerase attached).
  • a polymerase e.g., DNA polymerase
  • the polymerase can be attached to the nanopore before or after the nanopore is incorporated into the membrane.
  • the nanopore and polymerase are a fusion protein (i.e. , single
  • the polymerase can be attached to the nanopore in any suitable way.
  • the polymerase is attached to the nanopore (e.g., hemolysin) protein monomer and then the full nanopore heptamer is assembled (e.g., in a ratio of one monomer with an attached polymerase to 6 nanopore (e.g., hemolysin) monomers without an attached polymerase).
  • the nanopore heptamer can then be inserted into the membrane.
  • Another method for attaching a polymerase to a nanopore involves attaching a linker molecule to a hemolysin monomer or mutating a hemolysin monomer to have an attachment site and then assembling the full nanopore heptamer (e.g., at a ratio of one monomer with linker and/or attachment site to 6 hemolysin monomers with no linker and/or attachment site).
  • a polymerase can then be attached to the attachment site or attachment linker (e.g., in bulk, before inserting into the membrane).
  • the polymerase can also be attached to the attachment site or attachment linker after the (e.g., heptamer) nanopore is formed in the membrane.
  • a plurality of nanopore -polymerase pairs are inserted into a plurality of membranes (e.g., disposed over the wells and/or electrodes) of the biochip.
  • the attachment of the polymerase to the nanopore complex occurs on the biochip above each electrode.
  • the polymerase can be attached to the nanopore with any suitable chemistry (e.g., covalent bond and/or linker).
  • the polymerase is attached to the nanopore with molecular staples.
  • molecular staples comprise three amino acid sequences (denoted linkers A, B and C).
  • Linker A can extend from a hemolysin monomer
  • Linker B can extend from the polymerase
  • Linker C then can bind Linkers A and B (e.g., by wrapping around both Linkers A and B) and thus the polymerase to the nanopore.
  • Linker C can also be constructed to be part of Linker A or Linker B, thus reducing the number of linker molecules .
  • the polymerase is linked to the nanopore using
  • SolulinkTM chemistry can be a reaction between HyNic (6-hydrazino- nicotinic acid, an aromatic hydrazine) and 4FB (4-formylbenzoate, an aromatic aldehyde).
  • the polymerase is linked to the nanopore using Click chemistry (available from LifeTechnologies for example).
  • Click chemistry available from LifeTechnologies for example.
  • zinc finger mutations are introduced into the hemolysin molecule and then a molecule is used (e.g., a DNA intermediate molecule) to link the polymerase to the zinc finger sites on the hemolysin.
  • Specific linkers contemplated as useful herein are (GGGGS)i_3, K-tag (RSKLG) on N-terminus, ATEV site (12-25), ATEV site + N- terminus of SpyCatcher (12-49). Apparatus Set-Up
  • the nanopore may be formed or otherwise embedded in a membrane disposed adjacent to a sensing electrode of a sensing circuit, such as an integrated circuit.
  • the integrated circuit may be an application specific integrated circuit (ASIC).
  • the integrated circuit is a field effect transistor or a complementary metal-oxide semiconductor (CMOS).
  • CMOS complementary metal-oxide semiconductor
  • the sensing circuit may be situated in a chip or other device having the nanopore, or off of the chip or device, such as in an off-chip configuration.
  • the semiconductor can be any semiconductor, including, without limitation, Group IV (e.g., silicon) and Group III-V
  • semiconductors e.g., gallium arsenide. See, for example, WO 2013/123450, for the apparatus and device set-up for sensing a nucleotide or tag.
  • Pore based sensors can be used for electro-interrogation of single molecules.
  • a pore based sensor can include a nanopore of the present disclosure formed in a membrane that is disposed adjacent or in proximity to a sensing electrode.
  • the sensor can include a counter electrode.
  • the membrane includes a trans side (i.e., side facing the sensing electrode) and a cis side (i.e., side facing the counter electrode).
  • This example illustrates the introduction of a mutation into a pol7 polymerase at a desired position.
  • DNA encoding the His-tagged wild-type pol7 was purchased from a commercial source (DNA 2.0, Menlo Park, California). The sequence was verified by sequencing.
  • mutant screen we expressed the polymerase as is (N-ter His-Pol7).
  • polymerase In order to test the pol hits on the chip, we engineered in a SpyCatcher domain in N-ter or C-ter of Pol7.
  • Rational positions to impact Pol7 -nucleotide binding were identified based on analysis of Phi29 crystal structure in its apo form, DNA bound form and DNA- nucleotide form. For the primary screen, each of the rational positions were mutated into Gly, Glu, Gin, Met, His, Tyr, Lys, Thr, Ala, Leu, Pro or Trp using the Q5 mutagenesis protocol.
  • the primers for each mutagenesis reaction was designed using the NEB base changer protocol and ordered in 96-well plate format from IDT.
  • the forward and reverse primers were 5 ' phosphorylated in high throughput (HTP) format using the T4 polynucleotidekinase (PNK) purchased from NEB.
  • a typical 25- ⁇ 1 reaction contained 15 ⁇ 1 of primer at 10 ⁇ , 5 ⁇ of 5X reaction buffer (from NEB), 1.25 ⁇ PNK enzyme, 3.75 ⁇ 1 water. The reaction was performed at 37°C for 30 min and the enzyme heat inactivated at 65°C for 20 min.
  • PCR mutagenesis was performed using Q5 DNA polymerase from NEB.
  • a typical 25 ⁇ 1 reaction contained 5 ⁇ 1 of Q5 buffer, 5 ⁇ 1 of GC enhancer, 0.5ul of lOmM dNTPs, 1.25 ⁇ of 10 ⁇ phosphorylated mutagenesis primers forward and reverse, 0.25 ⁇ Q5 polymerase and ⁇ of 5ng/ml wild type Pol7 template, i.e., His-Pol7, and 10.75 ⁇ H 2 0.
  • DNA encoding the variants in the pD441 vector was transformed into competent E. coli and glycerol stocks made. Starting from a tiny pick of the glycerol stock, 1 ml starter culture in LB with 0.2% Glucose and 100 ⁇ g/ml Kanamycin was grown for approximately 8 hrs. 25 ⁇ of log phase starter culture was transferred into 1 ml of expression media (Terrific Broth (TB) autoinduction media supplemented with 0.2%glucose, 50 mM Potassium
  • the lysate was supplemented with 200 ⁇ of 1M Potassium Phosphate, pH 7.5 (Final concentration to be about 0.5M Potassium phosphate in 400 ⁇ lysate) and was filtered through Pall filter plates (Part# 5053, 3 micron filters) via centrifugation at approximately 1500 rpm at 4C for 10 minutes.
  • the clarified lysates were then applied to equilibrated 96-well His-Pur Cobalt plates (Pierce Part# 90095) and bind for 15-30 min.
  • the Pol7 was eluted using 200 ⁇ elution buffer (50mM Tris Ph7.4, 200mM KC1, 5mM TCEP, 0.5% Tween20, 300mM Imidazole, 25%Glycerol) and collected after l-2min incubation. The eluate was reapplied to the same His-Pur plate2-3 times to obtain a concentrated Pol7 in eluate.
  • the purified polymerase was determined to be >95%> pure as evaluated by SDS-PAGE.
  • the protein concentration was determined to be ⁇ 3uM (0.35mg/ml) with a 260/280 ratio of 0.6 as evaluated by Nanodrop.
  • This example provides methods of determining the activity of the variant polymerases.
  • This assay characterizes the mutant polymerases' ability to incorporate polyphosphate nucleotides into a DNA strand as well as its ability to unwind and displace double-stranded DNA.
  • Reagent B (high salt):
  • Nucleotide condition 1 tests for activity at high concentration of the hexaphosphate.
  • Nucleotide condition 2 tests for activity at low concentration of the hexaphosphate.
  • Nucleotide condition 3 tests for misincorporation rate (i.e., fidelity). If a mutant polymerase shows significant activity with only 3 of the 4 necessary nucleotides, then we conclude that it does not discriminate between correct or incorrect nucleotides while extending a DNA strand.
  • Nucleotide condition 4 tests for exonuclease activity. If a polymerase shows significant activity with no nucleotides present, then we conclude the polymerase is exhibiting exonuclease activity.
  • FIG. 5 Representative data from the displacement assay for a variant polymerase are shown in FIG. 5. The activity of wild-type and four different variant polymerases was measured using the displacement assay in the presence of
  • results for a displacement assay for a variant Pol7 show that in the presence of polyphosphate dA, C, G3P nucleotides, the variant polymerases are able to incorporate and extend along a DNA template.
  • polymerase is bound to a fluorescein labeled DNA template-primer with a Cy3 (or Alexa555)-linked polyphosphate nucleotide in the presence of a non-catalytic divalent metal like Ca2+.
  • Cy3 or Alexa555
  • Reagent B contains the chase nucleotide.
  • the first nucleotide to be incorporated into the template/primer is Cytosine.
  • Reagent A 75mM NaCl, 25mM HEPES (pH 7.5), 2mM CaC12, 250nM Fluorescein-Temp late/Primer, 20uM dCnP-Cy3, and >250nM Polymerase
  • Reagent A 75mM NaCl, 25mM HEPES (pH 7.5), 2mM CaC12, 250nM Fluorescein-Temp late/Primer, 20uM dCnP-Cy3, and >250nM Polymerase
  • Reagent B 75mM NaCl, 25mM HEPES (pH 7.5), 2mM CaC12, and 200uM dCTP was prepared.
  • dCTP competes with dCnP-Cy3 for association, an increase in fluorescence is observed given the dCTP concentration is in excess.
  • the assay can be performed with either a stop flow device (Kintek Corp) or a fluorescent plate reader. The increase in fluorescence versus time was fit to a first order or second order exponential to provide the kinetic constant Koff for that particular polymerase.
  • the Koff for Pol7 variant G397Q was determined to be 0.1s "1 .
  • FIG. 3 for a schematic representation of the assay
  • FIG. 6 for the results of the Koff assay for variant Pol7 G397Q.
  • This example provides an alternative method using fluorescence polarization for determining the koff.
  • the Koff for variant polymerases can also be determined using a fluorescence polarization assay.
  • a schematic representation of the assay is given in Figure 4, and is performed as follows.
  • An assay buffer comprising 25mM Tris pH7.0, 75mM KC1, 0.01 % Triton-XlOO, IX BSA (lOOug/ml), 0.5mM EDTA, 2mM CaC12, 2mM DTT, is used to prepare an assay master mix containing 250nM hairpin fiuorescein-labeled DNA template and 250nM dC6P-C6-Cy3 tagged nucleotide. Fifty five microliters of the master mix are added to each of the wells of a black 96-well costar plate; and. 20 ul of polymerase mutants, purified from 1ml cultures, are added in a high throughput (HTP) format.
  • HTP high throughput
  • the plate is shaken on a plate shaker for 1 minute to allow for the formation of homogenous ternary complexes of polymerase-DNA template-nucleotide.
  • the plate is placed in a BMG polarstar plate reader (BMG LABTECH Inc., North Carolina) and target millipolarization is adjusted to 200mP and 10% to have a gain around 2000.
  • the excitation filter is set to 485nM and the emission filter is set to 590-20nM.
  • the injector is primed with 1ml of ImM dCTP chaser nucleotide solution. Data is collected with minimum 30 flashes per well per interval and 60sec total read time for the start. The flashes are increased to 50 or higher and longer read times are taken for the hit mutants that show slow dissociation. Data collection begins with the injection of 25 ⁇ 1 of ImM dCTP.
  • This example provides a FRET based assay for determing the k chem for variant polymerases.
  • reagent A polymerase is bound to fluorescein labeled DNA template-primer.
  • Reagent B contains Cy3 (or Alexa555)-linked polyphosphate nucleotide in the presence of a catalytic divalent metal like Mg2+.
  • the first nucleotide to be incorporated into the template/primer is Cytosine.
  • Reagent A 75rnM NaCl, 25mM HEPES (pH 7.5), 250nM Fluorescein-
  • Reagent B 75mM NaCl, 25mM HEPES (pH 7.5), lOmM MgC12, and 20uM dCnP-Cy3 was prepared.
  • polymerase-fluorescein-template- primer complex binds dCnP-Cy3 and quenches fluorescence.
  • Mg2+ enables the polymerase to incorporate the nucleotide, which releases the cleavage product, pyrophosphate with attached Cy3, nP-Cy3. Since the quencher is released, fluorescence increases.
  • the assay can be performed with either a stop flow device (Kintek Corp) or a fluorescent plate reader.
  • FIG. 2 See FIG. 2 for a schematic representation of the assay and a graph of an exemplary reaction.
  • This example provides methods of attaching a variant polymerase to a nanopore, e.g., a-hemolysin.
  • the polymerase may be coupled to the nanopore by any suitable means. See, for example, PCT/US2013/068967 (published as WO2014/074727; Genia Technologies, Inc.), PCT/US2005/009702 (published as WO2006/028508;
  • the polymerase e.g., a variant Pol7 DNA Polymerase
  • a protein nanopore e.g. alpha-hemolysin
  • the SpyTag and SpyCatcher system that spontaneously forms covalent isopeptide linkages under physiological conditions is used. See, for example, Li et al, J Mol Biol. 2014 Jan 23;426(2):309-17.
  • the pol7 variant SpyCatcher HisTag is expressed according to Example 2 and purified using a cobalt affinity column.
  • the SpyCatcher polymerase and the SpyTag oligomerized nanopore protein are incubated overnight at 4°C in 3mM SrCl 2 .
  • the 1 :6-polymerase-template complex is then purified using size-exclusion chromatography.
  • the linker is attached at either the N-terminal or C-terminal of the pol7 variant.
  • nanopore-bound variant polymerase The ability of a nanopore-bound variant polymerase to bind tagged nucleotides and effect measurable changes in nanopore currents can be assessed as follows.
  • An exemplary Pol7 polymerase is attached to a nanopore e.g. an alpha hemolysin nanopore, and is embedded in a lipid bilayer over a well on a semiconductor sensor chip, also called a biochip.
  • the lipid bilayer is formed and the nanopore with the attached variant polymerase (previously complexed with template DNA under low salt conditions) is inserted as described in
  • Static capture experiments are performed in the presence of Ca2+, which prevents catalysis and elongation of DNA, and allows for the detection of repeated capture of the same type of tagged nucleotide, e.g. dTnP-tag.
  • dTnP-tag a tagged thymidine nucleotide (tag can be for example, T30) by the variant Pol7-DNA complex is recorded at lOOmV in the presence of 20mM Hepes7.5, 300mM NaCl, 3mM CaC12 and 5mM TCEP above and below the bilayer.
  • ABR67671.1 which can be found on the world wide web at:

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Abstract

La présente invention concerne un variant de la polymérase Pol7 comprenant au moins une mutation choisie parmi les S264E, L265Q, L265M, M377H, M377Y, E378Q, I379K, N382M, S383T, T384A, G385L, G385Q, G385M, G386Y, G386T, et R388W de la SEQ ID NO : 1. Les variants de la polymérase Pol7 gardent l'activité de la polymérase et présentent au moins une caractéristique modifiée telle que décrite dans la description.
PCT/EP2016/072225 2015-09-22 2016-09-20 Variants de la polymérase pol7 WO2017050723A1 (fr)

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