US20170356037A9 - Mutant pores - Google Patents

Mutant pores Download PDF

Info

Publication number
US20170356037A9
US20170356037A9 US15/308,206 US201515308206A US2017356037A9 US 20170356037 A9 US20170356037 A9 US 20170356037A9 US 201515308206 A US201515308206 A US 201515308206A US 2017356037 A9 US2017356037 A9 US 2017356037A9
Authority
US
United States
Prior art keywords
polynucleotide
pore
amino acids
mutant
variant
Prior art date
Legal status (The legal status is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the status listed.)
Granted
Application number
US15/308,206
Other versions
US20170058337A1 (en
US10167503B2 (en
Inventor
James Anthony Clarke
Andrew John Heron
Lakmal Jayasinghe
Elizabeth Jayne Wallace
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Oxford Nanopore Technologies PLC
Original Assignee
Oxford Nanopore Technologies PLC
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Family has litigation
First worldwide family litigation filed litigation Critical https://patents.darts-ip.com/?family=53052882&utm_source=google_patent&utm_medium=platform_link&utm_campaign=public_patent_search&patent=US20170356037(A9) "Global patent litigation dataset” by Darts-ip is licensed under a Creative Commons Attribution 4.0 International License.
Priority claimed from GB201407809A external-priority patent/GB201407809D0/en
Priority claimed from GBGB1417712.5A external-priority patent/GB201417712D0/en
Priority claimed from GB201417708A external-priority patent/GB201417708D0/en
Application filed by Oxford Nanopore Technologies PLC filed Critical Oxford Nanopore Technologies PLC
Assigned to OXFORD NANOPORE TECHNOLOGIES LTD. reassignment OXFORD NANOPORE TECHNOLOGIES LTD. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: CLARKE, JAMES ANTHONY, HERON, ANDREW JOHN, JAYASINGHE, LAKMAL, WALLACE, ELIZABETH JAYNE
Publication of US20170058337A1 publication Critical patent/US20170058337A1/en
Publication of US20170356037A9 publication Critical patent/US20170356037A9/en
Application granted granted Critical
Publication of US10167503B2 publication Critical patent/US10167503B2/en
Active legal-status Critical Current
Anticipated expiration legal-status Critical

Links

Images

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6869—Methods for sequencing
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/195—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria
    • C07K14/35—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from bacteria from Mycobacteriaceae (F)

Definitions

  • the invention relates to mutant forms of Msp.
  • the invention also relates to polynucleotide characterisation using Msp.
  • Nanopores Transmembrane pores have great potential as direct, electrical biosensors for polymers and a variety of small molecules.
  • recent focus has been given to nanopores as a potential DNA sequencing technology.
  • Strand sequencing can involve the use of a polynucleotide binding protein to control the movement of the polynucleotide through the pore.
  • Msp The different forms of Msp are porins from Mycobacterium smegmatis .
  • MspA is a 157 kDa octameric porin from Mycobacterium smegmatis . Wild-type MspA does not interact with DNA in a manner that allows the DNA to be characterised or sequenced.
  • the structure of MspA and the modifications required for it to interact with and characterise DNA have been well documented (Butler, 2007, Nanopore Analysis of Nucleic Acids, Doctor of Economics Dissertation, University of Washington; Gundlach, Proc Natl Acad Sci USA. 2010 Sep. 14; 107(37):16060-5. Epub 2010 Aug. 26; and International Application No.
  • novel mutants of MspA which retain a negative charge at position 93 may be used to characterise polynucleotides, such as DNA, as long as they have a decreased net negative charge in the inner lining of the cap forming region and/or the barrel forming region.
  • the negative charge at position 93 does not affect the ability of the mutants to capture polynucleotides, interact with polynucleotides and discriminate between the nucleotides in polynucleotides.
  • the invention provides a mutant Msp monomer comprising a variant of the sequence shown in SEQ ID NO: 2, wherein the variant:
  • (c) comprises aspartic acid (D) or glutamic acid (E) at position 93;
  • (d) comprises one or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region of the monomer.
  • the invention also provides:
  • FIG. 1 shows DNA construct X which was used in Example 1.
  • Section a of DNA construct X corresponds to SEQ ID NO: 26.
  • Section b corresponds to four iSpC3 spacers.
  • C corresponds to the helicase enzyme T4 Dda—E94C/C109A/C136A/A360C (SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C) which can bind to the section labelled a.
  • Section d corresponds to SEQ ID NO: 27.
  • Section e corresponds to four 5′-nitroindoles.
  • Section f corresponds to SEQ ID NO: 28.
  • Section g corresponds to SEQ ID NO: 29 which is attached at its 3′ end to six iSp18 spacers which are attached at the opposite end to two thymines and 3′ cholesterol TEG (labelled h).
  • FIG. 2 shows DNA construct Y which was used in Example 1.
  • Section i of DNA construct X corresponds to 25 iSpC3 spacers, which are attached to the 5′ end of SEQ ID NO: 3 (labelled j).
  • Section j is the region of construct Y to which the helicase enzyme T4 Dda—E94C/C109A/C136A/A360C can bind (labelled c).
  • Section k corresponds to four iSp18 spacers.
  • Section d corresponds to SEQ ID NO: 27.
  • Section e corresponds to four 5′-nitroindoles.
  • Section 1 corresponds to SEQ ID NO: 4.
  • Section g corresponds to SEQ ID NO: 29 which is attached at its 3′ end to six iSp18 spacers which are attached at the opposite end to two thymines and 3′ cholesterol TEG (labelled h).
  • Sections B shows a zoomed in region of current trace A.
  • Sections B shows a zoomed in region of current trace A.
  • Sections B shows a zoomed in region of current trace A.
  • FIG. 20 shows a cartoon representation of the wild-type MspA nanopore.
  • Region 1 corresponds to the cap forming region and includes residues 1-72 and 122-184.
  • Region 2 corresponds to the barrel forming region and includes residues 73-82 and 112-121.
  • Region 3 corresponds to the constriction and loops region and includes residues 83-111.
  • SEQ ID NO: 1 shows the codon optimised polynucleotide sequence encoding the wild-type MspA monomer. This mutant lacks the signal sequence.
  • SEQ ID NO: 2 shows the amino acid sequence of the mature form of the wild-type MspA monomer. This mutant lacks the signal sequence.
  • SEQ ID NOs: 3 and 4 shows polynucleotide sequences used in Example 1.
  • SEQ ID Nos: 5 to 7 show the amino acid sequences of MspB, C and D.
  • SEQ ID NO: 8 shows the polynucleotide sequence encoding the Phi29 DNA polymerase.
  • SEQ ID NO: 9 shows the amino acid sequence of the Phi29 DNA polymerase.
  • SEQ ID NO: 10 shows the codon optimised polynucleotide sequence derived from the sbcB gene from E. coli . It encodes the exonuclease I enzyme (EcoExo I) from E. coli.
  • SEQ ID NO: 11 shows the amino acid sequence of exonuclease I enzyme (EcoExo I) from E. coli.
  • SEQ ID NO: 12 shows the codon optimised polynucleotide sequence derived from the xthA gene from E. coli . It encodes the exonuclease III enzyme from E. coli.
  • SEQ ID NO: 13 shows the amino acid sequence of the exonuclease III enzyme from E. coli . This enzyme performs distributive digestion of 5′ monophosphate nucleosides from one strand of double stranded DNA (dsDNA) in a 3′-5′ direction. Enzyme initiation on a strand requires a 5′ overhang of approximately 4 nucleotides.
  • SEQ ID NO: 14 shows the codon optimised polynucleotide sequence derived from the recJ gene from T. thermophilus . It encodes the RecJ enzyme from T. thermophilus (TthRecJ-cd).
  • SEQ ID NO: 15 shows the amino acid sequence of the RecJ enzyme from T thermophilus (TthRecJ-cd). This enzyme performs processive digestion of 5′ monophosphate nucleosides from ssDNA in a 5′-3′ direction. Enzyme initiation on a strand requires at least 4 nucleotides.
  • SEQ ID NO: 16 shows the codon optimised polynucleotide sequence derived from the bacteriophage lambda exo (redX) gene. It encodes the bacteriophage lambda exonuclease.
  • SEQ ID NO: 17 shows the amino acid sequence of the bacteriophage lambda exonuclease.
  • the sequence is one of three identical subunits that assemble into a trimer.
  • the enzyme performs highly processive digestion of nucleotides from one strand of dsDNA, in a 5′-3′ direction (http://www.neb.com/nebecomm/products/productM0262.asp). Enzyme initiation on a strand preferentially requires a 5′ overhang of approximately 4 nucleotides with a 5′ phosphate.
  • SEQ ID NO: 18 shows the amino acid sequence of Hel308 Mbu.
  • SEQ ID NO: 19 shows the amino acid sequence of Hel308 Csy.
  • SEQ ID NO: 20 shows the amino acid sequence of Hel308 Tga.
  • SEQ ID NO: 21 shows the amino acid sequence of Hel308 Mhu.
  • SEQ ID NO: 22 shows the amino acid sequence of TraI Eco.
  • SEQ ID NO: 23 shows the amino acid sequence of XPD Mbu.
  • SEQ ID NO: 24 shows the amino acid sequence of Dda 1993.
  • SEQ ID NO: 25 shows the amino acid sequence of Trwc Cba.
  • SEQ ID NO: 26-29 shows polynucleotide sequences used in Example 1.
  • a polynucleotide includes two or more polynucleotides
  • reference to “a helicase” includes two or more helicases
  • reference to “a monomer” refers to two or more monomers
  • reference to “a pore” includes two or more pores and the like.
  • the present invention provides mutant Msp monomers.
  • the mutant Msp monomers may be used to form the pores of the invention.
  • a mutant Msp monomer is a monomer whose sequence varies from that of a wild-type Msp monomer and which retains the ability to form a pore. Methods for confirming the ability of mutant monomers to form pores are well-known in the art and are discussed in more detail below.
  • the mutant monomers have improved polynucleotide reading properties i.e. display improved polynucleotide capture and nucleotide discrimination.
  • pores constructed from the mutant monomers capture nucleotides and polynucleotides more easily than the wild type.
  • pores constructed from the mutant monomers display an increased current range, which makes it easier to discriminate between different nucleotides, and a reduced variance of states, which increases the signal-to-noise ratio.
  • the number of nucleotides contributing to the current as the polynucleotide moves through pores constructed from the mutants is decreased. This makes it easier to identify a direct relationship between the observed current as the polynucleotide moves through the pore and the polynucleotide sequence.
  • a mutant monomer of the invention comprises a variant of the sequence shown in SEQ ID NO: 2.
  • SEQ ID NO: 2 is the wild-type MspA monomer.
  • a variant of SEQ ID NO: 2 is a polypeptide that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its ability to form a pore.
  • the ability of a variant to form a pore can be assayed using any method known in the art. For instance, the variant may be inserted into an amphiphilic layer along with other appropriate subunits and its ability to oligomerise to form a pore may be determined. Methods are known in the art for inserting subunits into membranes, such as amphiphilic layers.
  • subunits may be suspended in a purified form in a solution containing a triblock copolymer membrane such that it diffuses to the membrane and is inserted by binding to the membrane and assembling into a functional state.
  • subunits may be directly inserted into the membrane using the “pick and place” method described in M. A. Holden, H. Bayley. J. Am. Chem. Soc. 2005, 127, 6502-6503 and International Application No. PCT/GB2006/001057 (published as WO 2006/100484).
  • amino acids 90 and 91 are both aspartic acid (D). These amino acids in each monomer form part of an inner constriction of the pore ( FIG. 20 ).
  • the variant does not comprise aspartic acid (D) at position 90.
  • the variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at position 90.
  • the variant preferably does not have a negatively charged amino acid at position 90.
  • the variant does not comprise aspartic acid (D) at position 91.
  • the variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at position 91.
  • the variant preferably does not have a negatively charged amino acid at position 91.
  • the variant preferably comprises serine (S), glutamine (Q), leucine (L), methionine (M), isoleucine (I), alanine (A), valine (V), glycine (G), phenylalanine (F), tryptophan (W), tyrosine (Y), histidine (H), threonine (T), arginine (R), lysine (K), asparagine (N) or cysteine (C) at position 90 and/or position 91. Any combinations of these amino acids at positions 90 and 91 are envisaged by the invention.
  • the variant preferably comprises asparagine (N) at position 90 and/or position 91.
  • the variant more preferably comprises asparagine (N) at position 90 and position 91.
  • These amino acids are preferably inserted at position 90 and/or 91 by substitution.
  • amino acid 93 is aspartic acid (D). This amino acid in each monomer also forms part of an inner constriction of the pore ( FIG. 20 ).
  • the variant comprises aspartic acid (D) or glutamic acid (E) at position 93.
  • the variant therefore has a negative charge at position 93.
  • the glutamic acid (E) is preferably introduced by substitution.
  • amino acids 1 to 72 and 122 to 184 form the cap of the pore ( FIG. 20 ).
  • amino acids 73 to 82 and 112 to 121 form the barrel of the pore ( FIG. 20 ).
  • S73, G75, G77, N79, S81, G112, S114, S116, D118 and G120 face inwards into the channel of the pore.
  • S73, G75, G77, N79, S81 face inwards in the downwards strand and G112, S114, S116, D118 and G120 face inwards in the upwards strand.
  • the variant comprises one or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region of the monomer.
  • the variant preferably comprises two or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and the barrel forming region of the monomer.
  • the variant may comprise any number of modifications, such as 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more modifications.
  • the net negative charge may be decreased by any means known in the art.
  • the net negative charge is decreased in a manner that does not interfere with the ability of the mutant monomer to form a pore. This can be measured as discussed above.
  • the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region is decreased.
  • the inward facing amino acids in the cap forming region and/or the barrel forming region comprise fewer negatively charged amino acids than in SEQ ID NO: 2 and/or comprises more positively charged amino acids than in SEQ ID NO: 2.
  • the one or more modifications may lead to a net positive charge in the inward facing amino acids in the cap forming region and/or the barrel forming region
  • the net charge can be measured using methods known in the art.
  • the isolectric point may be used to define the net charge of the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • the one or more modifications are preferably one or more deletions of negatively charged amino acids. Removal of one or more negatively charged amino acids reduces the net negative charge of the inward facing amino acids in the cap forming region and/or barrel forming region.
  • a negatively charged amino acid is an amino acid with a net negative charge.
  • Negatively charged amino acids include, but are not limited to, aspartic acid (D) and glutamic acid (E). Methods for deleting amino acids from proteins, such as MspA monomers, are well known in the art.
  • the one or more modifications are preferably one or more substitutions of negatively charged amino acids with one or more positively charged, uncharged, non-polar and/or aromatic amino acids.
  • a positively charged amino acid is an amino acid with a net positive charge.
  • the positively charged amino acid(s) can be naturally-occurring or non-naturally-occurring.
  • the positively charged amino acid(s) may be synthetic or modified. For instance, modified amino acids with a net positive charge may be specifically designed for use in the invention.
  • a number of different types of modification to amino acids are well known in the art.
  • Preferred naturally-occurring positively charged amino acids include, but are not limited to, histidine (H), lysine (K) and arginine (R). Any number and combination of H, K and/or R may be substituted for the inward facing amino acids in the cap forming region and/or barrel forming region.
  • the uncharged amino acids, non-polar amino acids and/or aromatic amino acids can be naturally occurring or non-naturally-occurring. They may be synthetic or modified. Uncharged amino acids have no net charge. Suitable uncharged amino acids include, but are not limited to, cysteine (C), serine (S), threonine (T), methionine (M), asparagines (N) and glutamine (Q). Non-polar amino acids have non-polar side chains. Suitable non-polar amino acids include, but are not limited to, glycine (G), alanine (A), proline (P), isoleucine (I), leucine (L) and valine (V). Aromatic amino acids have an aromatic side chain.
  • Suitable aromatic amino acids include, but are not limited to, histidine (H), phenylalanine (F), tryptophan (W) and tyrosine (Y). Any number and combination of these amino acids may be substituted into the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • the one or more negatively charged amino acids are preferably substituted with alanine (A), valine (V), asparagine (N) or glycine (G).
  • Preferred substitutions include, but are not limited to, substitution of D with A, substitution of D with V, substitution of D with N and substitution of D with G.
  • the one or more modifications are preferably one or more introductions of positively charged amino acids.
  • the introduction of positive charge decreases the net negative charge.
  • the one or more positively charged amino acids may be introduced by addition or substitution. Any amino acid may be substituted with a positively charged amino acid.
  • One or more uncharged amino acids, non-polar amino acids and/or aromatic amino acids may be substituted with one or more positively charged amino acids. Any number of positively charged amino acids may be introduced.
  • Wild-type MspA comprises a polar glutamine (Q) at position 126.
  • the one or more modifications preferably reduce the net negative charge at position 126.
  • the one or more modifications preferably increase the net positive charge at positions 126. This can be achieved by replacing the polar amino acid at position 126 or an adjacent or a nearby inward facing amino acid with a positively charged amino acid.
  • the variant preferably comprises a positively charged amino acid at position 126.
  • the variant preferably comprises a positively charged amino acid at one or more of positions 123, 125, 127 and 128.
  • the variant may comprise any number and combination of positively charged amino acids at positions 123, 125, 127 and 128.
  • the positively charged amino acid(s) may be introduced by addition or substitution.
  • the one or more modifications are preferably one or more introductions of positively charged amino acids which neutralise one or more negatively charged amino acids.
  • the neutralisation of negative charge decreases the net negative charge.
  • the one or more positively charged amino acids may be introduced by addition or substitution. Any amino acid may be substituted with a positively charged amino acid.
  • One or more uncharged amino acids, non-polar amino acids and/or aromatic amino acids may be substituted with one or more positively charged amino acids. Any number of positively charged amino acids may be introduced. The number is typically the same as the number of negatively charged amino acids in the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • the one or more positively charged amino acids may be introduced at any position in the cap forming region and/or the barrel forming region as long as they neutralise the negative charge of the one or more negatively charged amino acids.
  • To effectively neutralise the negative charge there is typically 5 or fewer amino acids in the variant between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising.
  • Each positively charged amino acid is most preferably introduced adjacent in the variant to the negatively charged amino acid it is neutralising.
  • the one or more positively charged amino acids may be introduced at any position in the inward facing amino acids in the cap forming region and/or the barrel forming region as long as they neutralise the negative charge of the one or more negatively charged amino acids.
  • To effectively neutralise the negative charge there is typically 5 or fewer inward facing amino acids between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising.
  • Each positively charged amino acid is most preferably introduced at the inward facing position adjacent to the negatively charged amino acid it is neutralising.
  • Wild-type MspA comprises aspartic acid (D) at positions 118 and 134 and glutamic acid (E) at position 139.
  • Amino acid 118 in each monomer is present within the barrel of the pore ( FIG. 20 ).
  • the variant preferably comprises a positively charged amino acid at one or more of positions 114, 116, 120, 123, 70, 73, 75, 77 and 79. Positive charges at one or more of these positions neutralise the negative charge at position 118.
  • Positively charged amino acids may present at any number and combination of positions 114, 116, 120, 123, 70, 73, 75, 77 and 79.
  • the amino acids may be introduced by addition or substitution.
  • Amino acids 134 and 139 in each monomer are part of the cap ( FIG. 20 ).
  • the variant comprises a positively charged amino acid at one or more of positions 129, 132, 136, 137, 59, 61 and 63. Positive charges at one or more of these positions neutralise the negative charge at position 134. Positively charged amino acids may present at any number and combination of positions 129, 132, 136, 137, 59, 61 and 63.
  • the amino acids may be introduced by addition or substitution.
  • the variant preferably comprises a positively charged amino acid at one or more of positions 137, 138, 141, 143, 45, 47, 49 and 51. Positive charges at one or more of these positions neutralise the negative charge at position 139. Positively charged amino acids may present at any number and combination of positions 137, 138, 141, 143, 45, 47, 49 and 51. The amino acids may be introduced by addition or substitution.
  • the one or more modifications preferably reduce the net negative charge at one or more of positions 118, 126, 134 and 139.
  • the one or more modifications preferably reduce the net negative charge at 118; 126; 134; 139; 118 and 126; 118 and 134; 118 and 139; 126 and 134; 126 and 139; 134 and 139; 118, 126 and 134; 118, 126 and 139; 118, 134 and 139; 126, 134 and 139; or 118, 126, 134 and 139.
  • the variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at one or more of positions 118, 126, 134 and 139.
  • the variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at any of the combination of positions 118, 126, 134 and 139 disclosed above.
  • the variant more preferably comprises arginine (R), glycine (G) or asparagine (N) at one or more of positions 118, 126, 134 and 139, such as any of the combinations of positions 118, 126, 134 and 139 disclosed above.
  • the variant most preferably comprises D118R, Q126R, D134R and E139K.
  • methionine (M) may be substituted with arginine (R) by replacing the codon for methionine (ATG) with a codon for arginine (CGT) at the relevant position in a polynucleotide encoding the mutant monomer.
  • the polynucleotide can then be expressed as discussed below.
  • non-naturally-occurring amino acids may be introduced by including synthetic aminoacyl-tRNAs in the IVTT system used to express the mutant monomer.
  • they may be introduced by expressing the mutant monomer in E. coli that are auxotrophic for specific amino acids in the presence of synthetic (i.e. non-naturally-occurring) analogues of those specific amino acids. They may also be produced by naked ligation if the mutant monomer is produced using partial peptide synthesis.
  • the one or more modifications are preferably one or more chemical modifications of one or more negatively charged amino acids which neutralise their negative charge.
  • the one or more negatively charged amino acids may be reacted with a carbodiimide.
  • the variant preferably comprises one or more of:
  • the variant may comprise any number and combination of (a) to (c), including (a), (b), (c), (a) and (b), (b) and (c), (a) and (c) and (a), (b) and (c).
  • the variant preferably comprises G75S, G77S and L88N.
  • the variant most preferably comprises G75S, G77S, L88N, D90N, D91N, D118R, Q126R, D134R and E139K.
  • the variant preferably further comprises one or more of:
  • The may comprise any number and combination of (d) to (i).
  • the variant may include other mutations. Over the entire length of the amino acid sequence of SEQ ID NO: 2, a variant will preferably be at least 50% homologous to that sequence based on amino acid identity. More preferably, the variant may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95%, amino acid identity over a stretch of 100 or more, for example 125, 150, 175 or 200 or more, contiguous amino acids (“hard homology”).
  • Standard methods in the art may be used to determine homology.
  • the UWGCG Package provides the BESTFIT program which can be used to calculate homology, for example used on its default settings (Devereux et at (1984) Nucleic Acids Research 12, p387-395).
  • the PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (such as identifying equivalent residues or corresponding sequences (typically on their default settings)), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S. F et at (1990) J Mol Biol 215:403-10.
  • Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
  • SEQ ID NO: 2 is the mature form of the wild-type MspA monomer.
  • the variant may comprise any of the mutations in the MspB, C or D monomers compared with MspA.
  • the mature forms of MspB, C and D are shown in SEQ ID NOs: 5 to 7.
  • the variant may comprise the following substitution present in MspB: A138P.
  • the variant may comprise one or more of the following substitutions present in MspC: A96G, N102E and A138P.
  • the variant may comprise one or more of the following mutations present in MspD: Deletion of G1, L2V, E5Q, L8V, D13G, W21A, D22E, K47T, I49H, 168V, D91G, A96Q, N102D, S103T, V1041, S136K and G141A.
  • the variant may comprise combinations of one or more of the mutations and substitutions from Msp B, C and D.
  • Amino acid substitutions may be made to the amino acid sequence of SEQ ID NO: 2 in addition to those discussed above, for example up to 1, 2, 3, 4, 5, 10, 20 or 30 substitutions.
  • Conservative substitutions replace amino acids with other amino acids of similar chemical structure, similar chemical properties or similar side-chain volume.
  • the amino acids introduced may have similar polarity, hydrophilicity, hydrophobicity, basicity, acidity, neutrality or charge to the amino acids they replace.
  • the conservative substitution may introduce another amino acid that is aromatic or aliphatic in the place of a pre-existing aromatic or aliphatic amino acid.
  • Conservative amino acid changes are well-known in the art and may be selected in accordance with the properties of the 20 main amino acids as defined in Table 1 below. Where amino acids have similar polarity, this can also be determined by reference to the hydropathy scale for amino acid side chains in Table 1.
  • One or more amino acid residues of the amino acid sequence of SEQ ID NO: 2 may additionally be deleted from the polypeptides described above. Up to 1, 2, 3, 4, 5, 10, 20 or 30 residues may be deleted, or more.
  • Variants may include fragments of SEQ ID NO: 2. Such fragments retain pore forming activity. Fragments may be at least 50, 100, 150 or 200 amino acids in length. Such fragments may be used to produce the pores. A fragment preferably comprises the pore forming domain of SEQ ID NO: 2. Fragments must include one of residues 88, 90, 91, 105, 118 and 134 of SEQ ID NO: 2. Typically, fragments include all of residues 88, 90, 91, 105, 118 and 134 of SEQ ID NO: 2.
  • One or more amino acids may be alternatively or additionally added to the polypeptides described above.
  • An extension may be provided at the amino terminal or carboxy terminal of the amino acid sequence of SEQ ID NO: 2 or polypeptide variant or fragment thereof.
  • the extension may be quite short, for example from 1 to 10 amino acids in length. Alternatively, the extension may be longer, for example up to 50 or 100 amino acids.
  • a carrier protein may be fused to an amino acid sequence according to the invention. Other fusion proteins are discussed in more detail below.
  • a variant is a polypeptide that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its ability to form a pore.
  • a variant typically contains the regions of SEQ ID NO: 2 that are responsible for pore formation. The pore forming ability of Msp, which contains a ⁇ -barrel, is provided by ⁇ -sheets in each subunit.
  • a variant of SEQ ID NO: 2 typically comprises the regions in SEQ ID NO: 2 that form ⁇ -sheets.
  • One or more modifications can be made to the regions of SEQ ID NO: 2 that form ⁇ -sheets as long as the resulting variant retains its ability to form a pore.
  • a variant of SEQ ID NO: 2 preferably includes one or more modifications, such as substitutions, additions or deletions, within its ⁇ -helices and/or loop regions.
  • the monomers derived from Msp may be modified to assist their identification or purification, for example by the addition of a streptavidin tag or by the addition of a signal sequence to promote their secretion from a cell where the monomer does not naturally contain such a sequence.
  • Other suitable tags are discussed in more detail below.
  • the monomer may be labelled with a revealing label.
  • the revealing label may be any suitable label which allows the monomer to be detected. Suitable labels are described below.
  • the monomer derived from Msp may also be produced using D-amino acids.
  • the monomer derived from Msp may comprise a mixture of L-amino acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.
  • the monomer derived from Msp contains one or more specific modifications to facilitate nucleotide discrimination.
  • the monomer derived from Msp may also contain other non-specific modifications as long as they do not interfere with pore formation.
  • a number of non-specific side chain modifications are known in the art and may be made to the side chains of the monomer derived from Msp. Such modifications include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed by reduction with NaBH 4 , amidination with methylacetimidate or acylation with acetic anhydride.
  • the monomer derived from Msp can be produced using standard methods known in the art.
  • the monomer derived from Msp may be made synthetically or by recombinant means.
  • the monomer may be synthesized by in vitro translation and transcription (IVTT). Suitable methods for producing pores and monomers are discussed in International Application Nos. PCT/GB09/001690 (published as WO 2010/004273), PCT/GB09/001679 (published as WO 2010/004265) or PCT/GB10/000133 (published as WO 2010/086603).
  • the mutant monomer is chemically modified.
  • the mutant monomer can be chemically modified in any way and at any site.
  • the mutant monomer is preferably chemically modified by attachment of a molecule to one or more cysteines (cysteine linkage), attachment of a molecule to one or more lysines, attachment of a molecule to one or more non-natural amino acids, enzyme modification of an epitope or modification of a terminus. Suitable methods for carrying out such modifications are well-known in the art.
  • the mutant monomer may be chemically modified by the attachment of any molecule. For instance, the mutant monomer may be chemically modified by attachment of a dye or a fluorophore.
  • the mutant monomer is chemically modified with a molecular adaptor that facilitates the interaction between a pore comprising the monomer and a target nucleotide or target polynucleotide sequence.
  • the presence of the adaptor improves the host-guest chemistry of the pore and the nucleotide or polynucleotide sequence and thereby improves the sequencing ability of pores formed from the mutant monomer.
  • the principles of host-guest chemistry are well-known in the art.
  • the adaptor has an effect on the physical or chemical properties of the pore that improves its interaction with the nucleotide or polynucleotide sequence.
  • the adaptor may alter the charge of the barrel or channel of the pore or specifically interact with or bind to the nucleotide or polynucleotide sequence thereby facilitating its interaction with the pore.
  • the molecular adaptor is preferably a cyclic molecule, a cyclodextrin, a species that is capable of hybridization, a DNA binder or interchelator, a peptide or peptide analogue, a synthetic polymer, an aromatic planar molecule, a small positively-charged molecule or a small molecule capable of hydrogen-bonding.
  • the adaptor may be cyclic.
  • a cyclic adaptor preferably has the same symmetry as the pore.
  • the adaptor preferably has eight-fold symmetry since Msp typically has eight subunits around a central axis. This is discussed in more detail below.
  • the adaptor typically interacts with the nucleotide or polynucleotide sequence via host-guest chemistry.
  • the adaptor is typically capable of interacting with the nucleotide or polynucleotide sequence.
  • the adaptor comprises one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence.
  • the one or more chemical groups preferably interact with the nucleotide or polynucleotide sequence by non-covalent interactions, such as hydrophobic interactions, hydrogen bonding, Van der Waal's forces, ⁇ -cation interactions and/or electrostatic forces.
  • the one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence are preferably positively charged.
  • the one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence more preferably comprise amino groups.
  • the amino groups can be attached to primary, secondary or tertiary carbon atoms.
  • the adaptor even more preferably comprises a ring of amino groups, such as a ring of 6, 7 or 8 amino groups.
  • the adaptor most preferably comprises a ring of eight amino groups.
  • a ring of protonated amino groups may interact with negatively charged phosphate groups in the nucleotide or polynucleotide sequence.
  • the adaptor preferably comprises one or more chemical groups that are capable of interacting with one or more amino acids in the pore.
  • the adaptor more preferably comprises one or more chemical groups that are capable of interacting with one or more amino acids in the pore via non-covalent interactions, such as hydrophobic interactions, hydrogen bonding, Van der Waal's forces, ⁇ -cation interactions and/or electrostatic forces.
  • the chemical groups that are capable of interacting with one or more amino acids in the pore are typically hydroxyls or amines.
  • the hydroxyl groups can be attached to primary, secondary or tertiary carbon atoms.
  • the hydroxyl groups may form hydrogen bonds with uncharged amino acids in the pore.
  • Any adaptor that facilitates the interaction between the pore and the nucleotide or polynucleotide sequence can be used.
  • Suitable adaptors include, but are not limited to, cyclodextrins, cyclic peptides and cucurbiturils.
  • the adaptor is preferably a cyclodextrin or a derivative thereof.
  • the cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am. Chem. Soc. 116, 6081-6088.
  • the adaptor is more preferably heptakis-6-amino- ⁇ -cyclodextrin (am 7 - ⁇ CD), 6-monodeoxy-6-monoamino- ⁇ -cyclodextrin (am 1 - ⁇ CD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu 7 - ⁇ CD).
  • the guanidino group in gu 7 - ⁇ CD has a much higher pKa than the primary amines in am 7 - ⁇ CD and so it more positively charged.
  • This gu 7 - ⁇ CD adaptor may be used to increase the dwell time of the nucleotide in the pore, to increase the accuracy of the residual current measured, as well as to increase the base detection rate at high temperatures or low data acquisition rates.
  • the adaptor is preferably heptakis(6-deoxy-6-amino)-6-N-mono(2-pyridyl)dithiopropanoyl- ⁇ -cyclodextrin (am 6 amPDP 1 - ⁇ CD).
  • More suitable adaptors include ⁇ -cyclodextrins, which comprise 8 sugar units (and therefore have eight-fold symmetry).
  • the ⁇ -cyclodextrin may contain a linker molecule or may be modified to comprise all or more of the modified sugar units used in the ⁇ -cyclodextrin examples discussed above.
  • the molecular adaptor is preferably covalently attached to the mutant monomer.
  • the adaptor can be covalently attached to the pore using any method known in the art.
  • the adaptor is typically attached via chemical linkage. If the molecular adaptor is attached via cysteine linkage, the one or more cysteines have preferably been introduced to the mutant by substitution.
  • the mutant monomers of the invention can of course comprise a cysteine residue at one or more of positions 88, 90, 91, 103 and 105.
  • the mutant monomer may be chemically modified by attachment of a molecular adaptor to one or more, such as 2, 3, 4 or 5, of these cysteines. Alternatively, the mutant monomer may be chemically modified by attachment of a molecule to one or more cysteines introduced at other positions.
  • the molecular adaptor is preferably attached to one or more of positions 90, 91 and 103 of SEQ ID NO: 2.
  • cysteine residues may be enhanced by modification of the adjacent residues.
  • the basic groups of flanking arginine, histidine or lysine residues will change the pKa of the cysteines thiol group to that of the more reactive S ⁇ group.
  • the reactivity of cysteine residues may be protected by thiol protective groups such as dTNB. These may be reacted with one or more cysteine residues of the mutant monomer before a linker is attached.
  • the molecule may be attached directly to the mutant monomer.
  • the molecule is preferably attached to the mutant monomer using a linker, such as a chemical crosslinker or a peptide linker.
  • Suitable chemical crosslinkers are well-known in the art.
  • Preferred crosslinkers include 2,5-dioxopyrrolidin-1-yl 3-(pyridin-2-yldisulfanyl)propanoate, 2,5-dioxopyrrolidin-1-yl 4-(pyridin-2-yldisulfanyl)butanoate and 2,5-dioxopyrrolidin-1-yl 8-(pyridin-2-yldisulfanyl)octananoate.
  • the most preferred crosslinker is succinimidyl 3-(2-pyridyldithio)propionate (SPDP).
  • the molecule is covalently attached to the bifunctional crosslinker before the molecule/crosslinker complex is covalently attached to the mutant monomer but it is also possible to covalently attach the bifunctional crosslinker to the monomer before the bifunctional crosslinker/monomer complex is attached to the molecule.
  • the linker is preferably resistant to dithiothreitol (DTT).
  • Suitable linkers include, but are not limited to, iodoacetamide-based and Maleimide-based linkers.
  • the monomer may be attached to a polynucleotide binding protein.
  • the polynucleotide binding protein is preferably covalently attached to the mutant monomer.
  • the protein can be covalently attached to the monomer using any method known in the art.
  • the monomer and protein may be chemically fused or genetically fused.
  • the monomer and protein are genetically fused if the whole construct is expressed from a single polynucleotide sequence. Genetic fusion of a monomer to a polynucleotide binding protein is discussed in International Application No. PCT/GB09/001679 (published as WO 2010/004265).
  • the one or more cysteines have preferably been introduced to the mutant by substitution.
  • the mutant monomers of the invention can of course comprise cysteine residues at one or more of positions 10 to 15, 51 to 60, 136 to 139 and 168 to 172. These positions are present in loop regions which have low conservation amongst homologues indicating that mutations or insertions may be tolerated. They are therefore suitable for attaching a polynucleotide binding protein.
  • the reactivity of cysteine residues may be enhanced by modification as described above.
  • the polynucleotide binding protein may be attached directly to the mutant monomer or via one or more linkers.
  • the molecule may be attached to the mutant monomer using the hybridization linkers described in International Application No. PCT/GB10/000132 (published as WO 2010/086602).
  • peptide linkers may be used.
  • Peptide linkers are amino acid sequences. The length, flexibility and hydrophilicity of the peptide linker are typically designed such that it does not to disturb the functions of the monomer and molecule.
  • Preferred flexible peptide linkers are stretches of 2 to 20, such as 4, 6, 8, 10 or 16, serine and/or glycine amino acids.
  • More preferred flexible linkers include (SG) 1 , (SG) 2 , (SG) 3 , (SG) 4 , (SG) 5 and (SG) 8 wherein S is serine and G is glycine.
  • Preferred rigid linkers are stretches of 2 to 30, such as 4, 6, 8, 16 or 24, proline amino acids. More preferred rigid linkers include (P) 12 wherein P is proline.
  • the mutant monomer may be chemically modified with a molecular adaptor and a polynucleotide binding protein.
  • cysteine residues may be enhanced by modification of the adjacent residues. For instance, the basic groups of flanking arginine, histidine or lysine residues will change the pKa of the cysteines thiol group to that of the more reactive S ⁇ group.
  • the reactivity of cysteine residues may be protected by thiol protective groups such as dTNB. These may be reacted with one or more cysteine residues of the monomer before a linker is attached.
  • the molecule (with which the monomer is chemically modified) may be attached directly to the monomer or attached via a linker as disclosed in International Application Nos. PCT/GB09/001690 (published as WO 2010/004273), PCT/GB09/001679 (published as WO 2010/004265) or PCT/GB10/000133 (published as WO 2010/086603).
  • any of the proteins described herein may be modified to assist their identification or purification, for example by the addition of histidine residues (a his tag), aspartic acid residues (an asp tag), a streptavidin tag, a flag tag, a SUMO tag, a GST tag or a MBP tag, or by the addition of a signal sequence to promote their secretion from a cell where the polypeptide does not naturally contain such a sequence.
  • Histidine residues a his tag
  • aspartic acid residues an asp tag
  • streptavidin tag e.g., a flag tag, a SUMO tag, a GST tag or a MBP tag
  • a signal sequence to promote their secretion from a cell where the polypeptide does not naturally contain such a sequence.
  • An alternative to introducing a genetic tag is to chemically react a tag onto a native or engineered position on the protein. An example of this would be to react a gel-shift reagent to a cysteine engineered on
  • any of the proteins described herein, such as the mutant monomers and pores of the invention, may be labelled with a revealing label.
  • the revealing label may be any suitable label which allows the protein to be detected. Suitable labels include, but are not limited to, fluorescent molecules, radioisotopes e.g. 125 I, 35 S, enzymes, antibodies, antigens, polynucleotides and ligands such as biotin.
  • any of the proteins described herein, such as the monomers or pores of the invention, may be made synthetically or by recombinant means.
  • the protein may be synthesized by in vitro translation and transcription (IVTT).
  • IVTT in vitro translation and transcription
  • the amino acid sequence of the protein may be modified to include non-naturally occurring amino acids or to increase the stability of the protein.
  • amino acids may be introduced during production.
  • the protein may also be altered following either synthetic or recombinant production.
  • Proteins may also be produced using D-amino acids.
  • the protein may comprise a mixture of L-amino acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.
  • the protein may also contain other non-specific modifications as long as they do not interfere with the function of the protein.
  • a number of non-specific side chain modifications are known in the art and may be made to the side chains of the protein(s). Such modifications include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed by reduction with NaBH 4 , amidination with methylacetimidate or acylation with acetic anhydride.
  • any of the proteins described herein, including the monomers and pores of the invention, can be produced using standard methods known in the art.
  • Polynucleotide sequences encoding a protein may be derived and replicated using standard methods in the art.
  • Polynucleotide sequences encoding a protein may be expressed in a bacterial host cell using standard techniques in the art.
  • the protein may be produced in a cell by in situ expression of the polypeptide from a recombinant expression vector.
  • the expression vector optionally carries an inducible promoter to control the expression of the polypeptide.
  • Proteins may be produced in large scale following purification by any protein liquid chromatography system from protein producing organisms or after recombinant expression.
  • Typical protein liquid chromatography systems include FPLC, AKTA systems, the Bio-Cad system, the Bio-Rad BioLogic system and the Gilson HPLC system.
  • the invention also provides a construct comprising two or more covalently attached MspA monomers, wherein at least one of the monomers is a mutant monomer of the invention.
  • the construct of the invention retains its ability to form a pore. This may be determined as discussed above.
  • One or more constructs of the invention may be used to form pores for characterising, such as sequencing, polynucleotides.
  • the construct may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 monomers.
  • the construct preferably comprises two monomers.
  • the two or more monomers may be the same or different.
  • the construct may comprise one or more monomers which are not mutant monomers of the invention.
  • MspA mutant monomers which are non mutant monomers of the invention comprise comparative variants of SEQ ID NO: 2.
  • At least one monomer in the construct may comprise a comparative variant of the sequence shown in SEQ ID NO: 2 which comprises D90N, D91N, D93N, D118R, D134R and E139K.
  • At least one monomer in the construct may be any of the monomers disclosed in International Application No.
  • PCT/GB2012/050301 (published as WO/2012/107778), including those comprising a comparative variant of the sequence shown in SEQ ID NO: 2 which comprises G75S, G77S, L88N, D90N, D91N, D93N, D118R, Q126R, D134R and E139K.
  • a comparative variant of SEQ ID NO: 2 is at least 50% homologous to SEQ ID NO: 2 over its entire sequence based on amino acid identity.
  • the comparative variant may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the entire sequence.
  • At least one monomer in the construct is a mutant monomer of the invention. All of the monomers in the construct may be a mutant monomer of the invention. The mutant monomers may be the same or different. In a more preferred embodiment, the construct comprises two monomers of the invention.
  • the monomers in the construct are preferably genetically fused. Monomers are genetically fused if the whole construct is expressed from a single polynucleotide sequence.
  • the coding sequences of the monomers may be combined in any way to form a single polynucleotide sequence encoding the construct.
  • the monomers may be genetically fused in any configuration.
  • the monomers may be fused via their terminal amino acids.
  • the amino terminus of the one monomer may be fused to the carboxy terminus of another monomer.
  • the second and subsequent monomers in the construct (in the amino to carboxy direction) may comprise a methionine at their amino terminal ends (each of which is fused to the carboxy terminus of the previous monomer).
  • M is a monomer (without an amino terminal methionine)
  • mM is a monomer with an amino terminal methionine
  • the construct may comprise the sequence M-mM, M-mM-mM or M-mM-mM-mM.
  • the presences of these methionines typically results from the expression of the start codons (i.e. ATGs) at the 5′ end of the polynucleotides encoding the second or subsequent monomers within the polynucleotide encoding entire construct.
  • the first monomer in the construct may also comprise a methionine (e.g. mM-mM, mM-mM-mM or mM-mM-mM-mM).
  • the two or more monomers may be genetically fused directly together.
  • the monomers are preferably genetically fused using a linker.
  • the linker may be designed to constrain the mobility of the monomers.
  • Preferred linkers are amino acid sequences (i.e. peptide linkers). Any of the peptide linkers discussed above may be used.
  • the monomers are chemically fused.
  • Two monomers are chemically fused if the two parts are chemically attached, for instance via a chemical crosslinker. Any of the chemical crosslinkers discussed above may be used.
  • the linker may be attached to one or more cysteine residues introduced into a mutant monomer of the invention. Alternatively, the linker may be attached to a terminus of one of the monomers in the construct.
  • the present invention also provides polynucleotide sequences which encode a mutant monomer of the invention.
  • the mutant monomer may be any of those discussed above.
  • the polynucleotide sequence preferably comprises a sequence at least 50%, 60%, 70%, 80%, 90% or 95% homologous based on nucleotide identity to the sequence of SEQ ID NO: 1 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95% nucleotide identity over a stretch of 300 or more, for example 375, 450, 525 or 600 or more, contiguous nucleotides (“hard homology”). Homology may be calculated as described above.
  • the polynucleotide sequence may comprise a sequence that differs from SEQ ID NO: 1 on the basis of the degeneracy of the genetic code.
  • the present invention also provides polynucleotide sequences which encode any of the genetically fused constructs of the invention.
  • the polynucleotide preferably comprises two or more variants of the sequence shown in SEQ ID NO: 1.
  • the polynucleotide sequence preferably comprises two or more sequences having at least 50%, 60%, 70%, 80%, 90% or 95% homology to SEQ ID NO: 1 based on nucleotide identity over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95% nucleotide identity over a stretch of 600 or more, for example 750, 900, 1050 or 1200 or more, contiguous nucleotides (“hard homology”). Homology may be calculated as described above.
  • Polynucleotide sequences may be derived and replicated using standard methods in the art. Chromosomal DNA encoding wild-type Msp may be extracted from a pore producing organism, such as Mycobacterium smegmatis . The gene encoding the pore subunit may be amplified using PCR involving specific primers. The amplified sequence may then undergo site-directed mutagenesis. Suitable methods of site-directed mutagenesis are known in the art and include, for example, combine chain reaction. Polynucleotides encoding a construct of the invention can be made using well-known techniques, such as those described in Sambrook, J. and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • the resulting polynucleotide sequence may then be incorporated into a recombinant replicable vector such as a cloning vector.
  • the vector may be used to replicate the polynucleotide in a compatible host cell.
  • polynucleotide sequences may be made by introducing a polynucleotide into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector.
  • the vector may be recovered from the host cell. Suitable host cells for cloning of polynucleotides are known in the art and described in more detail below.
  • the polynucleotide sequence may be cloned into suitable expression vector.
  • the polynucleotide sequence is typically operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell.
  • Such expression vectors can be used to express a pore subunit.
  • operably linked refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner.
  • a control sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. Multiple copies of the same or different polynucleotide sequences may be introduced into the vector.
  • the expression vector may then be introduced into a suitable host cell.
  • a mutant monomer or construct of the invention can be produced by inserting a polynucleotide sequence into an expression vector, introducing the vector into a compatible bacterial host cell, and growing the host cell under conditions which bring about expression of the polynucleotide sequence.
  • the recombinantly-expressed monomer or construct may self-assemble into a pore in the host cell membrane.
  • the recombinant pore produced in this manner may be removed from the host cell and inserted into another membrane.
  • the different monomers or constructs may be expressed separately in different host cells as described above, removed from the host cells and assembled into a pore in a separate membrane, such as a rabbit cell membrane.
  • the vectors may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide sequence and optionally a regulator of the promoter.
  • the vectors may contain one or more selectable marker genes, for example a tetracycline resistance gene. Promoters and other expression regulation signals may be selected to be compatible with the host cell for which the expression vector is designed. A T7, trc, lac, ara or ⁇ L promoter is typically used.
  • the host cell typically expresses the monomer or construct at a high level. Host cells transformed with a polynucleotide sequence will be chosen to be compatible with the expression vector used to transform the cell.
  • the host cell is typically bacterial and preferably Escherichia coli . Any cell with a ⁇ DE3 lysogen, for example C41 (DE3), BL21 (DE3), JM109 (DE3), B834 (DE3), TUNER, Origami and Origami B, can express a vector comprising the T7 promoter.
  • any of the methods cited in Proc Natl Acad Sci USA. 2008 Dec. 30; 105(52):20647-52 may be used to express the Msp proteins.
  • the invention also comprises a method of producing a mutant monomer of the invention or a construct of the invention.
  • the method comprises expressing a polynucleotide of the invention in a suitable host cell.
  • the polynucleotide is preferably part of a vector and is preferably operably linked to a promoter.
  • the invention also provides various pores.
  • the pores of the invention are ideal for characterising, such as sequencing, polynucleotide sequences because they can discriminate between different nucleotides with a high degree of sensitivity.
  • the pores can surprisingly distinguish between the four nucleotides in DNA and RNA.
  • the pores of the invention can even distinguish between methylated and unmethylated nucleotides.
  • the base resolution of pores of the invention is surprisingly high.
  • the pores show almost complete separation of all four DNA nucleotides.
  • the pores further discriminate between deoxycytidine monophosphate (dCMP) and methyl-dCMP based on the dwell time in the pore and the current flowing through the pore.
  • dCMP deoxycytidine monophosphate
  • the pores of the invention can also discriminate between different nucleotides under a range of conditions.
  • the pores will discriminate between nucleotides under conditions that are favourable to the characterising, such as sequencing, of nucleic acids.
  • the extent to which the pores of the invention can discriminate between different nucleotides can be controlled by altering the applied potential, the salt concentration, the buffer, the temperature and the presence of additives, such as urea, betaine and DTT. This allows the function of the pores to be fine-tuned, particularly when sequencing. This is discussed in more detail below.
  • the pores of the invention may also be used to identify polynucleotide polymers from the interaction with one or more monomers rather than on a nucleotide by nucleotide basis.
  • a pore of the invention may be isolated, substantially isolated, purified or substantially purified.
  • a pore of the invention is isolated or purified if it is completely free of any other components, such as lipids or other pores.
  • a pore is substantially isolated if it is mixed with carriers or diluents which will not interfere with its intended use.
  • a pore is substantially isolated or substantially purified if it is present in a form that comprises less than 10%, less than 5%, less than 2% or less than 1% of other components, such as triblock copolymers, lipids or other pores.
  • a pore of the invention may be present in a membrane. Suitable membranes are discussed below.
  • a pore of the invention may be present as an individual or single pore.
  • a pore of the invention may be present in a homologous or heterologous population of two or more pores.
  • the invention also provides a homo-oligomeric pore derived from Msp comprising identical mutant monomers of the invention.
  • the homo-oligomeric pore may comprise any of the mutants of the invention.
  • the homo-oligomeric pore of the invention is ideal for characterising, such as sequencing, polynucleotides.
  • the homo-oligomeric pore of the invention may have any of the advantages discussed above.
  • the homo-oligomeric pore may contain any number of mutant monomers.
  • the pore typically comprises at least 7, at least 8, at least 9 or at least 10 identical mutant monomers, such as 7, 8, 9 or 10 mutant monomers.
  • the pore preferably comprises eight identical mutant monomers.
  • One or more, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10, of the mutant monomers is preferably chemically modified as discussed above.
  • the invention also provides a hetero-oligomeric pore derived from Msp comprising at least one mutant monomer of the invention.
  • the hetero-oligomeric pore of the invention is ideal for characterising, such as sequencing, polynucleotides.
  • Hetero-oligomeric pores can be made using methods known in the art (e.g. Protein Sci. 2002 July; 11(7):1813-24).
  • the hetero-oligomeric pore contains sufficient monomers to form the pore.
  • the monomers may be of any type.
  • the pore typically comprises at least 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9 or 10 monomers.
  • the pore preferably comprises eight monomers.
  • all of the monomers are mutant monomers of the invention and at least one of them differs from the others.
  • the pore comprises eight mutant monomers of the invention and at least one of them differs from the others. They may all differ from one another.
  • the mutant monomers is not a mutant monomer of the invention.
  • the remaining monomers are preferably mutant monomers of the invention.
  • the pore may comprise 9, 8, 7, 6, 5, 4, 3, 2 or 1 mutant monomers of the invention. Any number of the monomers in the pore may not be a mutant monomer of the invention.
  • the pore preferably comprises seven mutant monomers of the invention and a monomer which is not a monomer of the invention, such as a monomer comprising a comparative variant as discussed above.
  • the mutant monomers of the invention may be the same or different.
  • one or more, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10, of the mutant monomers is preferably chemically modified as discussed above.
  • the invention also provides a pore comprising at least one construct of the invention.
  • a construct of the invention comprises two or more covalently attached monomers derived from Msp wherein at least one of the monomers is a mutant monomer of the invention. In other words, a construct must contain more than one monomer.
  • the pore contains sufficient constructs and, if necessary, monomers to form the pore.
  • an octameric pore may comprise (a) four constructs each comprising two constructs, (b) two constructs each comprising four monomers or (b) one construct comprising two monomers and six monomers that do not form part of a construct.
  • Other combinations of constructs and monomers can be envisaged by the skilled person.
  • At least two of the monomers in the pore are in the form of a construct of the invention.
  • the construct, and hence the pore comprises at least one mutant monomer of the invention.
  • the pore typically comprises at least 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9 or 10 monomers, in total (at least two of which must be in a construct).
  • the pore preferably comprises eight monomers (at least two of which must be in a construct).
  • the construct containing pore may be a homo-oligomer (i.e. include identical constructs) or be a hetero-oligomer (i.e. where at least one construct differs from the others).
  • a pore typically contains (a) one construct comprising two monomers and (b) 5, 6, 7 or 8 monomers.
  • the construct may be any of those discussed above.
  • the monomers may be any of those discussed above, including mutant monomers of the invention and mutant monomers comprising a comparative variant of SEQ ID NO: 2 as discussed above.
  • Another typical pore comprises more than one construct of the invention, such as two, three or four constructs of the invention. If necessary, such pores further comprise sufficient additional monomers or constructs to form the pore.
  • the additional monomer(s) may be any of those discussed above, including mutant monomers of the invention and mutant monomers comprising a comparative variant of SEQ ID NO: 2 as discussed above.
  • the additional construct(s) may be any of those discussed above or may be a construct comprising two or more covalently attached MspA monomers each comprising a comparative variant of SEQ ID NO: 2 as discussed above.
  • a further pore of the invention comprises only constructs comprising 2 monomers, for example a pore may comprise 4, 5, 6, 7 or 8 constructs comprising 2 monomers.
  • At least one construct is a construct of the invention, i.e. at least one monomer in the at least one construct, and preferably each monomer in the at least one construct, is a mutant monomer of the invention. All of the constructs comprising 2 monomers may be constructs of the invention.
  • a specific pore according to the invention comprises four constructs of the invention each comprising two monomers, wherein at least one monomer in each construct, and preferably each monomer in each construct, is a mutant monomer of the invention.
  • the constructs may oligomerise into a pore with a structure such that only one monomer of each construct contributes to the channel of the pore.
  • the other monomers of the construct will be on the outside of the channel of the pore.
  • pores of the invention may comprise 5, 6, 7 or 8 constructs comprising 2 monomers where the channel comprises 8 monomers.
  • Mutations can be introduced into the construct as described above.
  • the mutations may be alternating, i.e. the mutations are different for each monomer within a two monomer construct and the constructs are assembled as a homo-oligomer resulting in alternating modifications.
  • monomers comprising MutA and MutB are fused and assembled to form an A-B:A-B:A-B:A-B pore.
  • the mutations may be neighbouring, i.e. identical mutations are introduced into two monomers in a construct and this is then oligomerised with different mutant monomers or constructs.
  • monomers comprising MutA are fused follow by oligomerisation with MutB-containing monomers to form A-A:B:B:B:B:B:B.
  • One or more of the monomers of the invention in a construct-containing pore may be chemically-modified as discussed above.
  • the invention provides a method of characterising a target polynucleotide.
  • the method involves measuring one or more characteristics of the target polynucleotide.
  • the target polynucleotide may also be called the template polynucleotide or the polynucleotide of interest.
  • a polynucleotide such as a nucleic acid
  • the polynucleotide or nucleic acid may comprise any combination of any nucleotides.
  • the nucleotides can be naturally occurring or artificial.
  • One or more nucleotides in the polynucleotide can be oxidized or methylated.
  • One or more nucleotides in the polynucleotide may be damaged.
  • the polynucleotide may comprise a pyrimidine dimer. Such dimers are typically associated with damage by ultraviolet light and are the primary cause of skin melanomas.
  • One or more nucleotides in the polynucleotide may be modified, for instance with a label or a tag. Suitable labels are described below.
  • the polynucleotide may comprise one or more spacers.
  • a nucleotide typically contains a nucleobase, a sugar and at least one phosphate group.
  • the nucleobase and sugar form a nucleoside.
  • the nucleobase is typically heterocyclic. Nucleobases include, but are not limited to, purines and pyrimidines and more specifically adenine (A), guanine (G), thymine (T), uracil (U) and cytosine (C).
  • A adenine
  • G guanine
  • T thymine
  • U uracil
  • C cytosine
  • the sugar is typically a pentose sugar.
  • Nucleotide sugars include, but are not limited to, ribose and deoxyribose.
  • the sugar is preferably a deoxyribose.
  • the polynucleotide preferably comprises the following nucleosides: deoxyadenosine (dA), deoxyuridine (dU) and/or thymidine (dT), deoxyguanosine (dG) and deoxycytidine (dC).
  • the nucleotide is typically a ribonucleotide or deoxyribonucleotide.
  • the nucleotide typically contains a monophosphate, diphosphate or triphosphate.
  • the nucleotide may comprise more than three phosphates, such as 4 or 5 phosphates. Phosphates may be attached on the 5′ or 3′ side of a nucleotide.
  • Nucleotides include, but are not limited to, adenosine monophosphate (AMP), guanosine monophosphate (GMP), thymidine monophosphate (TMP), uridine monophosphate (UMP), 5-methylcytidine monophosphate, 5-hydroxymethylcytidine monophosphate, cytidine monophosphate (CMP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxythymidine monophosphate (dTMP), deoxyuridine monophosphate (dUMP), deoxycytidine monophosphate (dCMP) and deoxymethylcytidine monophosphate.
  • the nucleotides are preferably selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP, dCMP and dUMP.
  • a nucleotide may be abasic (i.e. lack a nucleobase).
  • a nucleotide may also lack a nucleobase and a sugar (i.e. is a C3 spacer).
  • the nucleotides in the polynucleotide may be attached to each other in any manner.
  • the nucleotides are typically attached by their sugar and phosphate groups as in nucleic acids.
  • the nucleotides may be connected via their nucleobases as in pyrimidine dimers.
  • the polynucleotide may be single stranded or double stranded. At least a portion of the polynucleotide is preferably double stranded.
  • the polynucleotide can be a nucleic acid, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA).
  • the polynucleotide can comprise one strand of RNA hybridised to one strand of DNA.
  • the polynucleotide may be any synthetic nucleic acid known in the art, such as peptide nucleic acid (PNA), glycerol nucleic acid (GNA), threose nucleic acid (TNA), locked nucleic acid (LNA) or other synthetic polymers with nucleotide side chains.
  • PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds.
  • the GNA backbone is composed of repeating glycol units linked by phosphodiester bonds.
  • the TNA backbone is composed of repeating threose sugars linked together by phosphodiester bonds.
  • LNA is formed from ribonucleotides as discussed above having an extra bridge connecting the 2′ oxygen and 4′ carbon in the ribose moiety.
  • the polynucleotide is most preferably ribonucleic nucleic acid (RNA) or deoxyribonucleic acid (DNA).
  • the polynucleotide can be any length.
  • the polynucleotide can be at least 10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400 or at least 500 nucleotides or nucleotide pairs in length.
  • the polynucleotide can be 1000 or more nucleotides or nucleotide pairs, 5000 or more nucleotides or nucleotide pairs in length or 100000 or more nucleotides or nucleotide pairs in length.
  • any number of polynucleotides can be investigated.
  • the method of the invention may concern characterising 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 100 or more polynucleotides. If two or more polynucleotides are characterized, they may be different polynucleotides or two instances of the same polynucleotide.
  • the polynucleotide can be naturally occurring or artificial.
  • the method may be used to verify the sequence of a manufactured oligonucleotide.
  • the method is typically carried out in vitro.
  • Each analyte is typically present in any suitable sample.
  • the invention is typically carried out on two or more samples that are known to contain or suspected to contain the analytes.
  • the invention may be carried out on two or more samples to confirm the identity of two or more analytes whose presence in the samples is known or expected.
  • the first sample and/or second sample may be a biological sample.
  • the invention may be carried out in vitro using at least one sample obtained from or extracted from any organism or microorganism.
  • the first sample and/or second sample may be a non-biological sample.
  • the non-biological sample is preferably a fluid sample. Examples of non-biological samples include surgical fluids, water such as drinking water, sea water or river water, and reagents for laboratory tests.
  • the first sample and/or second sample is typically processed prior to being used in the invention, for example by centrifugation or by passage through a membrane that filters out unwanted molecules or cells, such as red blood cells.
  • the first sample and/or second sample may be measured immediately upon being taken.
  • the first sample and/or second sample may also be typically stored prior to assay, preferably below ⁇ 70° C.
  • the method may involve measuring two, three, four or five or more characteristics of the polynucleotide.
  • the one or more characteristics are preferably selected from (i) the length of the polynucleotide, (ii) the identity of the polynucleotide, (iii) the sequence of the polynucleotide, (iv) the secondary structure of the polynucleotide and (v) whether or not the polynucleotide is modified.
  • any combination of (i) to (v) may be measured in accordance with the invention, such as ⁇ i ⁇ , ⁇ ii ⁇ , ⁇ iii ⁇ , ⁇ iv ⁇ , ⁇ v ⁇ , ⁇ i,ii ⁇ , ⁇ i,ii ⁇ , ⁇ i,iv ⁇ , ⁇ i,v ⁇ , ⁇ ii,ii ⁇ , ⁇ iiiiv ⁇ , ⁇ iii,v ⁇ , ⁇ iii,v ⁇ , ⁇ iv,v ⁇ , ⁇ i,ii,iv ⁇ , ⁇ i,iii,v ⁇ , ⁇ i,iiii,v ⁇ , ⁇ i,iiii,v ⁇ , ⁇ i,iiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ iiiii,v ⁇ , ⁇ ii
  • the length of the polynucleotide may be measured for example by determining the number of interactions between the polynucleotide and the pore or the duration of interaction between the polynucleotide and the pore.
  • the identity of the polynucleotide may be measured in a number of ways.
  • the identity of the polynucleotide may be measured in conjunction with measurement of the sequence of the polynucleotide or without measurement of the sequence of the polynucleotide.
  • the former is straightforward; the polynucleotide is sequenced and thereby identified.
  • the latter may be done in several ways. For instance, the presence of a particular motif in the polynucleotide may be measured (without measuring the remaining sequence of the polynucleotide). Alternatively, the measurement of a particular electrical and/or optical signal in the method may identify the polynucleotide as coming from a particular source.
  • the sequence of the polynucleotide can be determined as described previously. Suitable sequencing methods, particularly those using electrical measurements, are described in Stoddart D et al., Proc Natl Acad Sci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc. 2010; 132(50):17961-72, and International Application WO 2000/28312.
  • the secondary structure may be measured in a variety of ways. For instance, if the method involves an electrical measurement, the secondary structure may be measured using a change in dwell time or a change in current flowing through the pore. This allows regions of single-stranded and double-stranded polynucleotide to be distinguished.
  • the presence or absence of any modification may be measured.
  • the method preferably comprises determining whether or not the polynucleotide is modified by methylation, by oxidation, by damage, with one or more proteins or with one or more labels, tags or spacers. Specific modifications will result in specific interactions with the pore which can be measured using the methods described below. For instance, methylcyotsine may be distinguished from cytosine on the basis of the current flowing through the pore during its interaction with each nucleotide.
  • the target polynucleotide is contacted with a pore of the invention.
  • the pore is typically present in a membrane. Suitable membranes are discussed below.
  • the method may be carried out using any apparatus that is suitable for investigating a membrane/pore system in which a pore is present in a membrane.
  • the method may be carried out using any apparatus that is suitable for transmembrane pore sensing.
  • the apparatus comprises a chamber comprising an aqueous solution and a barrier that separates the chamber into two sections.
  • the barrier typically has an aperture in which the membrane containing the pore is formed.
  • the barrier forms the membrane in which the pore is present.
  • the method may be carried out using the apparatus described in International Application No. PCT/GB08/000562 (WO 2008/102120).
  • a variety of different types of measurements may be made. This includes without limitation: electrical measurements and optical measurements. Possible electrical measurements include: current measurements, impedance measurements, tunnelling measurements (Ivanov A P et al., Nano Lett. 2011 Jan. 12; 11(1):279-85), and FET measurements (International Application WO 2005/124888). Optical measurements may be combined with electrical measurements (Soni G V et al., Rev Sci Instrum. 2010 January; 81(1):014301). The measurement may be a transmembrane current measurement such as measurement of ionic current flowing through the pore.
  • Electrical measurements may be made using standard single channel recording equipment as describe in Stoddart D et al., Proc Natl Acad Sci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc. 2010; 132(50):17961-72, and International Application WO 2000/28312.
  • electrical measurements may be made using a multi-channel system, for example as described in International Application WO 2009/077734 and International Application WO 2011/067559.
  • the method is preferably carried out with a potential applied across the membrane.
  • the applied potential may be a voltage potential.
  • the applied potential may be a chemical potential.
  • An example of this is using a salt gradient across a membrane, such as an amphiphilic layer. A salt gradient is disclosed in Holden et al., J Am Chem Soc. 2007 Jul. 11; 129(27):8650-5.
  • the current passing through the pore as a polynucleotide moves with respect to the pore is used to estimate or determine the sequence of the polynucleotide. This is strand sequencing.
  • the method may involve measuring the current passing through the pore as the polynucleotide moves with respect to the pore. Therefore the apparatus used in the method may also comprise an electrical circuit capable of applying a potential and measuring an electrical signal across the membrane and pore.
  • the methods may be carried out using a patch clamp or a voltage clamp. The methods preferably involve the use of a voltage clamp.
  • the method of the invention may involve the measuring of a current passing through the pore as the polynucleotide moves with respect to the pore. Suitable conditions for measuring ionic currents through transmembrane protein pores are known in the art and disclosed in the Example.
  • the method is typically carried out with a voltage applied across the membrane and pore.
  • the voltage used is typically from +5 V to ⁇ 5 V, such as from +4 V to ⁇ 4 V, +3 V to ⁇ 3 V or +2 V to ⁇ 2 V.
  • the voltage used is typically from ⁇ 600 mV to +600 mV or ⁇ 400 mV to +400 mV.
  • the voltage used is preferably in a range having a lower limit selected from ⁇ 400 mV, ⁇ 300 mV, ⁇ 200 mV, ⁇ 150 mV, ⁇ 100 mV, ⁇ 50 mV, ⁇ 20 mV and 0 mV and an upper limit independently selected from +10 mV, +20 mV, +50 mV, +100 mV, +150 mV, +200 mV, +300 mV and +400 mV.
  • the voltage used is more preferably in the range 100 mV to 240 mV and most preferably in the range of 120 mV to 220 mV. It is possible to increase discrimination between different nucleotides by a pore by using an increased applied potential.
  • the method is typically carried out in the presence of any charge carriers, such as metal salts, for example alkali metal salt, halide salts, for example chloride salts, such as alkali metal chloride salt.
  • Charge carriers may include ionic liquids or organic salts, for example tetramethyl ammonium chloride, trimethylphenyl ammonium chloride, phenyltrimethyl ammonium chloride, or 1-ethyl-3-methyl imidazolium chloride.
  • the salt is present in the aqueous solution in the chamber.
  • Potassium chloride (KCl), sodium chloride (NaCl), caesium chloride (CsCl) or a mixture of potassium ferrocyanide and potassium ferricyanide is typically used.
  • KCl, NaCl and a mixture of potassium ferrocyanide and potassium ferricyanide are preferred.
  • the charge carriers may be asymmetric across the membrane. For instance, the type and/or concentration of the charge carriers may be different on each side of the membrane.
  • the salt concentration may be at saturation.
  • the salt concentration may be 3 M or lower and is typically from 0.1 to 2.5 M, from 0.3 to 1.9 M, from 0.5 to 1.8 M, from 0.7 to 1.7 M, from 0.9 to 1.6 M or from 1 M to 1.4 M.
  • the salt concentration is preferably from 150 mM to 1 M.
  • the method is preferably carried out using a salt concentration of at least 0.3 M, such as at least 0.4 M, at least 0.5 M, at least 0.6 M, at least 0.8 M, at least 1.0 M, at least 1.5 M, at least 2.0 M, at least 2.5 M or at least 3.0 M.
  • High salt concentrations provide a high signal to noise ratio and allow for currents indicative of the presence of a nucleotide to be identified against the background of normal current fluctuations.
  • the method is typically carried out in the presence of a buffer.
  • the buffer is present in the aqueous solution in the chamber. Any buffer may be used in the method of the invention.
  • the buffer is phosphate buffer.
  • Other suitable buffers are HEPES and Tris-HCl buffer.
  • the methods are typically carried out at a pH of from 4.0 to 12.0, from 4.5 to 10.0, from 5.0 to 9.0, from 5.5 to 8.8, from 6.0 to 8.7 or from 7.0 to 8.8 or 7.5 to 8.5.
  • the pH used is preferably about 7.5.
  • the method may be carried out at from 0° C. to 100° C., from 15° C. to 95° C., from 16° C. to 90° C., from 17° C. to 85° C., from 18° C. to 80° C., 19° C. to 70° C., or from 20° C. to 60° C.
  • the methods are typically carried out at room temperature.
  • the methods are optionally carried out at a temperature that supports enzyme function, such as about 37° C.
  • Step (a) preferably comprises contacting the polynucleotide with a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore.
  • the method comprises (a) contacting the polynucleotide with the pore of the invention and a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore and (b) taking one or more measurements as the polynucleotide moves with respect to the pore, wherein the measurements are indicative of one or more characteristics of the polynucleotide, and thereby characterising the polynucleotide.
  • the method comprises (a) contacting the polynucleotide with the pore of the invention and a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore and (b) measuring the current through the pore as the polynucleotide moves with respect to the pore, wherein the current is indicative of one or more characteristics of the polynucleotide, and thereby characterising the polynucleotide.
  • the polynucleotide binding protein may be any protein that is capable of binding to the polynucleotide and controlling its movement through the pore. It is straightforward in the art to determine whether or not a protein binds to a polynucleotide.
  • the protein typically interacts with and modifies at least one property of the polynucleotide.
  • the protein may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides.
  • the protein may modify the polynucleotide by orienting it or moving it to a specific position, i.e. controlling its movement.
  • the polynucleotide binding protein is preferably derived from a polynucleotide handling enzyme.
  • a polynucleotide handling enzyme is a polypeptide that is capable of interacting with and modifying at least one property of a polynucleotide.
  • the enzyme may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides.
  • the enzyme may modify the polynucleotide by orienting it or moving it to a specific position.
  • the polynucleotide handling enzyme does not need to display enzymatic activity as long as it is capable of binding the polynucleotide and controlling its movement through the pore. For instance, the enzyme may be modified to remove its enzymatic activity or may be used under conditions which prevent it from acting as an enzyme. Such conditions are discussed in more detail below.
  • the polynucleotide handling enzyme is preferably derived from a nucleolytic enzyme.
  • the polynucleotide handling enzyme used in the construct of the enzyme is more preferably derived from a member of any of the Enzyme Classification (EC) groups 3.1.11, 3.1.13, 3.1.14, 3.1.15, 3.1.16, 3.1.21, 3.1.22, 3.1.25, 3.1.26, 3.1.27, 3.1.30 and 3.1.31.
  • the enzyme may be any of those disclosed in International Application No. PCT/GB10/000133 (published as WO 2010/086603).
  • Preferred enzymes are polymerases, exonucleases, helicases and topoisomerases, such as gyrases.
  • Suitable enzymes include, but are not limited to, exonuclease I from E. coli (SEQ ID NO: 11), exonuclease III enzyme from E. coli (SEQ ID NO: 13), RecJ from T. thermophilus (SEQ ID NO: 15) and bacteriophage lambda exonuclease (SEQ ID NO: 17) and variants thereof.
  • Three subunits comprising the sequence shown in SEQ ID NO: 15 or a variant thereof interact to form a trimer exonuclease.
  • the enzyme is preferably Phi29 DNA polymerase (SEQ ID NO: 9) or a variant thereof.
  • the topoisomerase is preferably a member of any of the Moiety Classification (EC) groups 5.99.1.2 and 5.99.1.3.
  • the enzyme is most preferably derived from a helicase, such as Hel308 Mbu (SEQ ID NO: 18), Hel308 Csy (SEQ ID NO: 19), Hel308 Mhu (SEQ ID NO: 21), TraI Eco (SEQ ID NO: 22), XPD Mbu (SEQ ID NO: 23) or a variant thereof.
  • a helicase such as Hel308 Mbu (SEQ ID NO: 18), Hel308 Csy (SEQ ID NO: 19), Hel308 Mhu (SEQ ID NO: 21), TraI Eco (SEQ ID NO: 22), XPD Mbu (SEQ ID NO: 23) or a variant thereof.
  • Any helicase may be used in the invention.
  • the helicase may be or be derived from a Hel308 helicase, a RecD helicase, such as TraI helicase or a TrwC helicase, a XPD helicase or a Dda helicase.
  • the helicase may be any of the helicases, modified helicases or helicase constructs disclosed in International Application Nos. PCT/GB2012/052579 (published as WO 2013/057495); PCT/GB2012/053274 (published as WO 2013/098562); PCT/GB2012/053273 (published as WO2013098561); PCT/GB2013/051925 (published as WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259) and PCT/GB2013/051928 (published as WO 2014/013262); and in PCT/GB2014/052736 (published as WO/2015/055981).
  • the helicase preferably comprises the sequence shown in SEQ ID NO: 25 (Trwc Cba) or as variant thereof, the sequence shown in SEQ ID NO: 18 (Hel308 Mbu) or a variant thereof or the sequence shown in SEQ ID NO: 24 (Dda) or a variant thereof.
  • Variants may differ from the native sequences in any of the ways discussed below for transmembrane pores.
  • a preferred variant of SEQ ID NO: 8 comprises E94C/A360C and then ( ⁇ M1)G1G2 (i.e. deletion of M1 and then addition G1 and G2).
  • helicases Any number of helicases may be used in accordance with the invention. For instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may be used. In some embodiments, different numbers of helicases may be used.
  • the method of the invention preferably comprises contacting the polynucleotide with two or more helicases.
  • the two or more helicases are typically the same helicase.
  • the two or more helicases may be different helicases.
  • the two or more helicases may be any combination of the helicases mentioned above.
  • the two or more helicases may be two or more Dda helicases.
  • the two or more helicases may be one or more Dda helicases and one or more TrwC helicases.
  • the two or more helicases may be different variants of the same helicase.
  • the two or more helicases are preferably attached to one another.
  • the two or more helicases are more preferably covalently attached to one another.
  • the helicases may be attached in any order and using any method.
  • Preferred helicase constructs for use in the invention are described in International Application Nos. PCT/GB2013/051925 (published as WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259) and PCT/GB2013/051928 (published as WO 2014/013262); and in PCT/GB2014/052736 (published as WO/2015/055981).
  • a variant of SEQ ID NOs: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 is an enzyme that has an amino acid sequence which varies from that of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 and which retains polynucleotide binding ability. This can be measured using any method known in the art. For instance, the variant can be contacted with a polynucleotide and its ability to bind to and move along the polynucleotide can be measured. The variant may include modifications that facilitate binding of the polynucleotide and/or facilitate its activity at high salt concentrations and/or room temperature. Variants may be modified such that they bind polynucleotides (i.e.
  • a variant will preferably be at least 50% homologous to that sequence based on amino acid identity. More preferably, the variant polypeptide may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 over the entire sequence.
  • the enzyme may be covalently attached to the pore. Any method may be used to covalently attach the enzyme to the pore.
  • TrwC Cba-Q594A SEQ ID NO: 25 with the mutation Q594A.
  • This variant does not function as a helicase (i.e. binds polynucleotides but does not move along them when provided with all the necessary components to facilitate movement, e.g. ATP and Mg 2+ ).
  • the polynucleotide is translocated through the pore either with or against an applied potential.
  • Exonucleases that act progressively or processively on double stranded polynucleotides can be used on the cis side of the pore to feed the remaining single strand through under an applied potential or the trans side under a reverse potential.
  • a helicase that unwinds the double stranded DNA can also be used in a similar manner.
  • a polymerase may also be used.
  • sequencing applications that require strand translocation against an applied potential, but the DNA must be first “caught” by the enzyme under a reverse or no potential.
  • the single strand DNA exonucleases or single strand DNA dependent polymerases can act as molecular motors to pull the recently translocated single strand back through the pore in a controlled stepwise manner, trans to cis, against the applied potential.
  • Helicases may work in two modes with respect to the pore.
  • the method is preferably carried out using a helicase such that it moves the polynucleotide through the pore with the field resulting from the applied voltage.
  • the helicase moves the polynucleotide into the pore such that it is passed through the pore with the field until it finally translocates through to the trans side of the membrane.
  • the method is preferably carried out such that a helicase moves the polynucleotide through the pore against the field resulting from the applied voltage.
  • the 3′ end of the polynucleotide is first captured in the pore, and the helicase moves the polynucleotide through the pore such that it is pulled out of the pore against the applied field until finally ejected back to the cis side of the membrane.
  • the method may also be carried out in the opposite direction.
  • the 3′ end of the polynucleotide may be first captured in the pore and the helicase may move the polynucleotide into the pore such that it is passed through the pore with the field until it finally translocates through to the trans side of the membrane.
  • the helicase When the helicase is not provided with the necessary components to facilitate movement or is modified to hinder or prevent its movement, it can bind to the polynucleotide and act as a brake slowing the movement of the polynucleotide when it is pulled into the pore by the applied field.
  • the inactive mode it does not matter whether the polynucleotide is captured either 3′ or 5′ down, it is the applied field which pulls the polynucleotide into the pore towards the trans side with the enzyme acting as a brake.
  • the movement control of the polynucleotide by the helicase can be described in a number of ways including ratcheting, sliding and braking. Helicase variants which lack helicase activity can also be used in this way.
  • the polynucleotide may be contacted with the polynucleotide binding protein and the pore in any order. It is preferred that, when the polynucleotide is contacted with the polynucleotide binding protein, such as a helicase, and the pore, the polynucleotide firstly forms a complex with the protein. When the voltage is applied across the pore, the polynucleotide/protein complex then forms a complex with the pore and controls the movement of the polynucleotide through the pore.
  • the polynucleotide binding protein such as a helicase
  • Any steps in the method using a polynucleotide binding protein are typically carried out in the presence of free nucleotides or free nucleotide analogues and an enzyme cofactor that facilitates the action of the polynucleotide binding protein.
  • the free nucleotides may be one or more of any of the individual nucleotides discussed above.
  • the free nucleotides include, but are not limited to, adenosine monophosphate (AMP), adenosine diphosphate (ADP), adenosine triphosphate (ATP), guanosine monophosphate (GMP), guanosine diphosphate (GDP), guanosine triphosphate (GTP), thymidine monophosphate (TMP), thymidine diphosphate (TDP), thymidine triphosphate (TTP), uridine monophosphate (UMP), uridine diphosphate (UDP), uridine triphosphate (UTP), cytidine monophosphate (CMP), cytidine diphosphate (CDP), cytidine triphosphate (CTP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP), deoxyadenosine diphosphate (dADP), deoxyaden
  • the free nucleotides are preferably selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP or dCMP.
  • the free nucleotides are preferably adenosine triphosphate (ATP).
  • the enzyme cofactor is a factor that allows the construct to function.
  • the enzyme cofactor is preferably a divalent metal cation.
  • the divalent metal cation is preferably Mg 2+ , Mn 2+ , Ca 2+ or Co 2+ .
  • the enzyme cofactor is most preferably Mg 2+ .
  • the method comprises:
  • the one or more helicases may be any of those discussed above.
  • the one or more molecular brakes may be any compound or molecule which binds to the polynucleotide and slow the movement of the polynucleotide through the pore.
  • the one or more molecular brakes preferably comprise one or more compounds which bind to the polynucleotide.
  • the one or more compounds are preferably one or more macrocycles. Suitable macrocycles include, but are not limited to, cyclodextrins, calixarenes, cyclic peptides, crown ethers, cucurbiturils, pillararenes, derivatives thereof or a combination thereof.
  • the cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A.
  • the agent is more preferably heptakis-6-amino- ⁇ -cyclodextrin (am 7 - ⁇ CD), 6-monodeoxy-6-monoamino- ⁇ -cyclodextrin (am 1 - ⁇ CD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu 7 - ⁇ CD).
  • the one or more molecular brakes are preferably not one or more single stranded binding proteins (SSB).
  • the one or more molecular brakes are more preferably not a single-stranded binding protein (SSB) comprising a carboxy-terminal (C-terminal) region which does not have a net negative charge or (ii) a modified SSB comprising one or more modifications in its C-terminal region which decreases the net negative charge of the C-terminal region.
  • the one or more molecular brakes are most preferably not any of the SSBs disclosed in International Application No. PCT/GB2013/051924 (published as WO 2014/013259).
  • the one or more molecular brakes are preferably one or more polynucleotide binding proteins.
  • the polynucleotide binding protein may be any protein that is capable of binding to the polynucleotide and controlling its movement through the pore. It is straightforward in the art to determine whether or not a protein binds to a polynucleotide.
  • the protein typically interacts with and modifies at least one property of the polynucleotide.
  • the protein may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides.
  • the moiety may modify the polynucleotide by orienting it or moving it to a specific position, i.e. controlling its movement.
  • the polynucleotide binding protein is preferably derived from a polynucleotide handling enzyme.
  • the one or more molecular brakes may be derived from any of the polynucleotide handling enzymes discussed above. Modified versions of Phi29 polymerase (SEQ ID NO: 8) which act as molecular brakes are disclosed in U.S. Pat. No. 5,576,204.
  • the one or more molecular brakes are preferably derived from a helicase.
  • any number of molecular brakes derived from a helicase may be used. For instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may be used as molecular brakes. If two or more helicases are be used as molecular brakes, the two or more helicases are typically the same helicase. The two or more helicases may be different helicases.
  • the two or more helicases may be any combination of the helicases mentioned above.
  • the two or more helicases may be two or more Dda helicases.
  • the two or more helicases may be one or more Dda helicases and one or more TrwC helicases.
  • the two or more helicases may be different variants of the same helicase.
  • the two or more helicases are preferably attached to one another.
  • the two or more helicases are more preferably covalently attached to one another.
  • the helicases may be attached in any order and using any method.
  • the one or more molecular brakes derived from helicases are preferably modified to reduce the size of an opening in the polynucleotide binding domain through which in at least one conformational state the polynucleotide can unbind from the helicase. This is disclosed in WO 2014/013260.
  • the one or more helicases may be stalled at one or more spacers as discussed in International Application No. PCT/GB2014/050175. Any configuration of one or more helicases and one or more spacers disclosed in the International Application may be used in this invention.
  • the pore of the invention may be present in a membrane.
  • the polynucleotide is typically contacted with the pore of the invention in a membrane.
  • Any membrane may be used in accordance with the invention. Suitable membranes are well-known in the art.
  • the membrane is preferably an amphiphilic layer.
  • An amphiphilic layer is a layer formed from amphiphilic molecules, such as phospholipids, which have both hydrophilic and lipophilic properties. The amphiphilic molecules may be synthetic or naturally occurring.
  • Non-naturally occurring amphiphiles and amphiphiles which form a monolayer are known in the art and include, for example, block copolymers (Gonzalez-Perez et al., Langmuir, 2009, 25, 10447-10450).
  • Block copolymers are polymeric materials in which two or more monomer sub-units that are polymerized together to create a single polymer chain. Block copolymers typically have properties that are contributed by each monomer sub-unit. However, a block copolymer may have unique properties that polymers formed from the individual sub-units do not possess.
  • Block copolymers can be engineered such that one of the monomer sub-units is hydrophobic (i.e.
  • the block copolymer may possess amphiphilic properties and may form a structure that mimics a biological membrane.
  • the block copolymer may be a diblock (consisting of two monomer sub-units), but may also be constructed from more than two monomer sub-units to form more complex arrangements that behave as amphipiles.
  • the copolymer may be a triblock, tetrablock or pentablock copolymer.
  • the membrane is preferably a triblock copolymer membrane.
  • Archaebacterial bipolar tetraether lipids are naturally occurring lipids that are constructed such that the lipid forms a monolayer membrane. These lipids are generally found in extremophiles that survive in harsh biological environments, thermophiles, halophiles and acidophiles. Their stability is believed to derive from the fused nature of the final bilayer. It is straightforward to construct block copolymer materials that mimic these biological entities by creating a triblock polymer that has the general motif hydrophilic-hydrophobic-hydrophilic. This material may form monomeric membranes that behave similarly to lipid bilayers and encompass a range of phase behaviours from vesicles through to laminar membranes. Membranes formed from these triblock copolymers hold several advantages over biological lipid membranes. Because the triblock copolymer is synthesized, the exact construction can be carefully controlled to provide the correct chain lengths and properties required to form membranes and to interact with pores and other proteins.
  • Block copolymers may also be constructed from sub-units that are not classed as lipid sub-materials; for example a hydrophobic polymer may be made from siloxane or other non-hydrocarbon based monomers.
  • the hydrophilic sub-section of block copolymer can also possess low protein binding properties, which allows the creation of a membrane that is highly resistant when exposed to raw biological samples.
  • This head group unit may also be derived from non-classical lipid head-groups.
  • Triblock copolymer membranes also have increased mechanical and environmental stability compared with biological lipid membranes, for example a much higher operational temperature or pH range.
  • the synthetic nature of the block copolymers provides a platform to customize polymer based membranes for a wide range of applications.
  • the membrane is most preferably one of the membranes disclosed in International Application No. PCT/GB2013/052766 or PCT/GB2013/052767.
  • amphiphilic molecules may be chemically-modified or functionalised to facilitate coupling of the polynucleotide.
  • the amphiphilic layer may be a monolayer or a bilayer.
  • the amphiphilic layer is typically planar.
  • the amphiphilic layer may be curved.
  • the amphiphilic layer may be supported.
  • Amphiphilic membranes are typically naturally mobile, essentially acting as two dimensional fluids with lipid diffusion rates of approximately 10 8 cm s-1. This means that the pore and coupled polynucleotide can typically move within an amphiphilic membrane.
  • the membrane may be a lipid bilayer.
  • Lipid bilayers are models of cell membranes and serve as excellent platforms for a range of experimental studies.
  • lipid bilayers can be used for in vitro investigation of membrane proteins by single-channel recording.
  • lipid bilayers can be used as biosensors to detect the presence of a range of substances.
  • the lipid bilayer may be any lipid bilayer. Suitable lipid bilayers include, but are not limited to, a planar lipid bilayer, a supported bilayer or a liposome.
  • the lipid bilayer is preferably a planar lipid bilayer. Suitable lipid bilayers are disclosed in International Application No. PCT/GB08/000563 (published as WO 2008/102121), International Application No. PCT/GB08/004127 (published as WO 2009/077734) and International Application No. PCT/GB2006/001057 (published as WO 2006/100484).
  • the polynucleotide is preferably coupled to the membrane comprising the pore of the invention.
  • the method may comprise coupling the polynucleotide to the membrane comprising the pore of the invention.
  • the polynucleotide is preferably coupled to the membrane using one or more anchors.
  • the polynucleotide may be coupled to the membrane using any known method.
  • Each anchor comprises a group which couples (or binds) to the polynucleotide and a group which couples (or binds) to the membrane.
  • Each anchor may covalently couple (or bind) to the polynucleotide and/or the membrane. If a Y adaptor and/or a hairpin loop adaptors are used, the polynucleotide is preferably coupled to the membrane using the adaptor(s).
  • the polynucleotide may be coupled to the membrane using any number of anchors, such as 2, 3, 4 or more anchors.
  • a polynucleotide may be coupled to the membrane using two anchors each of which separately couples (or binds) to both the polynucleotide and membrane.
  • the one or more anchors may comprise the one or more helicases and/or the one or more molecular brakes.
  • the one or more anchors preferably comprise a polypeptide anchor present in the membrane and/or a hydrophobic anchor present in the membrane.
  • the hydrophobic anchor is preferably a lipid, fatty acid, sterol, carbon nanotube, polypeptide, protein or amino acid, for example cholesterol, palmitate or tocopherol.
  • the one or more anchors are not the pore.
  • the components of the membrane may be chemically-modified or functionalised to form the one or more anchors. Examples of suitable chemical modifications and suitable ways of functionalising the components of the membrane are discussed in more detail below. Any proportion of the membrane components may be functionalized, for example at least 0.01%, at least 0.1%, at least 1%, at least 10%, at least 25%, at least 50% or 100%.
  • the polynucleotide may be coupled directly to the membrane.
  • the one or more anchors used to couple the polynucleotide to the membrane preferably comprise a linker.
  • the one or more anchors may comprise one or more, such as 2, 3, 4 or more, linkers.
  • One linker may be used couple more than one, such as 2, 3, 4 or more, polynucleotides to the membrane.
  • Preferred linkers include, but are not limited to, polymers, such as polynucleotides, polyethylene glycols (PEGs), polysaccharides and polypeptides. These linkers may be linear, branched or circular. For instance, the linker may be a circular polynucleotide. The polynucleotide may hybridise to a complementary sequence on the circular polynucleotide linker.
  • the coupling may be permanent or stable.
  • the coupling may be such that the polynucleotide remains coupled to the membrane when interacting with the pore.
  • the coupling may be transient.
  • the coupling may be such that the polynucleotide may decouple from the membrane when interacting with the pore.
  • the one or more anchors preferably couple the polynucleotide to the membrane via hybridisation. Hybridisation in the one or more anchors allows coupling in a transient manner as discussed above.
  • the one or more anchors may comprise a single stranded or double stranded polynucleotide. One part of the anchor may be ligated to a single stranded or double stranded polynucleotide.
  • RNA ligase I T4 RNA ligase I
  • a single stranded or double stranded polynucleotide can be ligated to a double stranded polynucleotide and then the two strands separated by thermal or chemical denaturation.
  • the one or more anchors can be incorporated during the chemical synthesis of the polynucleotide.
  • the polynucleotide can be synthesised using a primer having a reactive group attached to it.
  • the polynucleotide is coupled to the membrane without having to functionalise the polynucleotide.
  • This can be achieved by coupling the one or more anchors, such as a polynucleotide binding protein or a chemical group, to the membrane and allowing the one or more anchors to interact with the polynucleotide or by functionalizing the membrane.
  • the one or more anchors may be coupled to the membrane by any of the methods described herein.
  • the one or more anchors may comprise one or more linkers, such as maleimide functionalised linkers.
  • the polynucleotide is typically RNA, DNA, PNA, TNA or LNA and may be double or single stranded. This embodiment is particularly suited to genomic DNA polynucleotides.
  • the one or more anchors comprise a protein
  • they may be able to anchor directly into the membrane without further functonalisation, for example if it already has an external hydrophobic region which is compatible with the membrane.
  • proteins include, but are not limited to, transmembrane proteins, intramembrane proteins and membrane proteins.
  • the one or more anchors may be used to couple a polynucleotide to the membrane when the polynucleotide is attached to a leader sequence which preferentially threads into the pore.
  • Leader sequences are discussed in more detail below.
  • the polynucleotide is attached (such as ligated) to a leader sequence which preferentially threads into the pore.
  • a leader sequence may comprise a homopolymeric polynucleotide or an abasic region.
  • the leader sequence is typically designed to hybridise to the one or more anchors either directly or via one or more intermediate polynucleotides (or splints).
  • the one or more anchors typically comprise a polynucleotide sequence which is complementary to a sequence in the leader sequence or a sequence in the one or more intermediate polynucleotides (or splints).
  • the one or more splints typically comprise a polynucleotide sequence which is complementary to a sequence in the leader sequence.
  • the polynucleotide may be double stranded. If the polynucleotide is double stranded, the method preferably further comprises before the contacting step ligating a hairpin adaptor to one end of the polynucleotide.
  • the two strands of the polynucleotide may then be separated as or before the polynucleotide is contacted with the pore in accordance with the invention.
  • the two strands may be separated as the polynucleotide movement through the pore is controlled by a polynucleotide binding protein, such as a helicase, or molecular brake. This is described in International Application No. PCT/GB2012/051786 (published as WO 2013/014451). Linking and interrogating both strands on a double stranded construct in this way increases the efficiency and accuracy of characterization.
  • a target double stranded polynucleotide is provided with a hairpin loop adaptor at one end and the method comprises contacting the polynucleotide with the pore of the invention such that both strands of the polynucleotide move through the pore and taking one or more measurements as the both strands of the polynucleotide move with respect to the pore wherein the measurements are indicative of one or more characteristics of the strands of the polynucleotide and thereby characterising the target double stranded polynucleotide.
  • the method preferably comprises attaching to the polynucleotide a leader sequence which preferentially threads into the pore.
  • the leader sequence facilitates the method of the invention.
  • the leader sequence is designed to preferentially thread into the pore of the invention and thereby facilitate the movement of polynucleotide through the pore.
  • the leader sequence can also be used to link the polynucleotide to the one or more anchors as discussed above.
  • the method of the invention may involve double coupling of a double stranded polynucleotide.
  • the method of the invention comprises:
  • step (b) contacting the polynucleotide provided in step (a) with the pore the invention such that the polynucleotide moves through the pore;
  • a double stranded polynucleotide may be contacted with a MuA transposase and a population of double stranded MuA substrates, wherein a proportion of the substrates in the population are Y adaptors comprising the leader sequence and wherein a proportion of the substrates in the population are hairpin loop adaptors.
  • the transposase fragments the double stranded polynucleotide analyte and ligates MuA substrates to one or both ends of the fragments. This produces a plurality of modified double stranded polynucleotides comprising the leader sequence at one end and the hairpin loop at the other.
  • the modified double stranded polynucleotides may then be investigated using the method of the invention.
  • MuA based methods are disclosed in International Application No. PCT/GB2014/052505 (published as WO/2015/022544). They are also discussed in detail in International Application No. PCT/GB2015/050991.
  • One or more helicases may be attached to the MuA substrate Y adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
  • one or more helicases may be attached to the MuA substrate Y adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
  • One or more molecular brakes may be attached to the MuA substrate hairpin loop adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
  • one or more molecular brakes may be attached to the MuA substrate hairpin loop adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
  • the method of the invention may involve characterising multiple target polynucleotides and uncoupling of the at least the first target polynucleotide.
  • the invention involves characterising two or more target polynucleotides.
  • the method comprises:
  • the agent is preferably a cyclodextrin or a derivative thereof or a lipid.
  • the cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am. Chem. Soc. 116, 6081-6088.
  • the agent is more preferably heptakis-6-amino- ⁇ -cyclodextrin (am 7 - ⁇ CD), 6-monodeoxy-6-monoamino- ⁇ -cyclodextrin (am 1 - ⁇ CD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu 7 - ⁇ CD). Any of the lipids disclosed herein may be used.
  • a target polynucleotide may be modified by contacting the polynucleotide with a polymerase and a population of free nucleotides under conditions in which the polymerase forms a modified polynucleotide using the target polynucleotide as a template, wherein the polymerase replaces one or more of the nucleotide species in the target polynucleotide with a different nucleotide species when forming the modified polynucleotide.
  • the modified polynucleotide may then be provided with one or more helicases attached to the polynucleotide and one or more molecular brakes attached to the polynucleotide. This type of modification is described in International Application No. PCT/GB2015/050483. Any of the polymerases discussed above may be used.
  • the polymerase is preferably Klenow or 90 North.
  • the template polynucleotide is contacted with the polymerase under conditions in which the polymerase forms a modified polynucleotide using the template polynucleotide as a template.
  • Such conditions are known in the art.
  • the polynucleotide is typically contacted with the polymerase in commercially available polymerase buffer, such as buffer from New England Biolabs®.
  • the temperature is preferably from 20 to 37° C. for Klenow or from 60 to 75° C. for 90 North.
  • a primer or a 3′ hairpin is typically used as the nucleation point for polymerase extension.
  • Characterisation, such as sequencing, of a polynucleotide using a transmembrane pore typically involves analyzing polymer units made up of k nucleotides where k is a positive integer (i.e. ‘k-mers’). This is discussed in International Application No. PCT/GB2012/052343 (published as WO 2013/041878). While it is desirable to have clear separation between current measurements for different k-mers, it is common for some of these measurements to overlap. Especially with high numbers of polymer units in the k-mer, i.e. high values of k, it can become difficult to resolve the measurements produced by different k-mers, to the detriment of deriving information about the polynucleotide, for example an estimate of the underlying sequence of the polynucleotide.
  • the modified polynucleotide contains k-mers which differ from those in the target polynucleotide.
  • the different k-mers in the modified polynucleotide are capable of producing different current measurements from the k-mers in the target polynucleotide and so the modified polynucleotide provides different information from the target polynucleotide.
  • the additional information from the modified polynucleotide can make it easier to characterise the target polynucleotide.
  • the modified polynucleotide itself may be easier to characterise.
  • the modified polynucleotide may be designed to include k-mers with an increased separation or a clear separation between their current measurements or k-mers which have a decreased noise.
  • the polymerase preferably replaces two or more of the nucleotide species in the target polynucleotide with different nucleotide species when forming the modified polynucleotide.
  • the polymerase may replace each of the two or more nucleotide species in the target polynucleotide with a distinct nucleotide species.
  • the polymerase may replace each of the two or more nucleotide species in the target polynucleotide with the same nucleotide species.
  • the different nucleotide species in the modified typically comprises a nucleobase which differs from adenine, guanine, thymine, cytosine or methylcytosine and/or comprises a nucleoside which differs from deoxyadenosine, deoxyguanosine, thymidine, deoxycytidine or deoxymethylcytidine.
  • the different nucleotide species in the modified polynucleotide typically comprises a nucleobase which differs from adenine, guanine, uracil, cytosine or methylcytosine and/or comprises a nucleoside which differs from adenosine, guanosine, uridine, cytidine or methylcytidine.
  • the different nucleotide species may be any of the universal nucleotides discussed above.
  • the polymerase may replace the one or more nucleotide species with a different nucleotide species which comprises a chemical group or atom absent from the one or more nucleotide species.
  • the chemical group may be a propynyl group, a thio group, an oxo group, a methyl group, a hydroxymethyl group, a formyl group, a carboxy group, a carbonyl group, a benzyl group, a propargyl group or a propargylamine group.
  • the polymerase may replace the one or more nucleotide species with a different nucleotide species which lacks a chemical group or atom present in the one or more nucleotide species.
  • the polymerase may replace the one or more of the nucleotide species with a different nucleotide species having an altered electronegativity.
  • the different nucleotide species having an altered electronegativity preferably comprises a halogen atom.
  • the method preferably further comprises selectively removing the nucleobases from the one or more different nucleotides species in the modified polynucleotide.
  • a polynucleotide is characterised by detecting labelled species that are released as a polymerase incorporates nucleotides into the polynucleotide.
  • the polymerase uses the polynucleotide as a template. Each labelled species is specific for each nucleotide.
  • the polynucleotide is contacted with a pore of the invention, a polymerase and labelled nucleotides such that phosphate labelled species are sequentially released when nucleotides are added to the polynucleotide(s) by the polymerase, wherein the phosphate species contain a label specific for each nucleotide.
  • the polymerase may be any of those discussed above.
  • the phosphate labelled species are detected using the pore and thereby characterising the polynucleotide.
  • This type of method is disclosed in European Application No. 13187149.3 (published as EP 2682460). Any of the embodiments discussed above equally apply to this method.
  • the present invention also provides a kit for characterising a target polynucleotide.
  • the kit comprises a pore of the invention and the components of a membrane.
  • the membrane is preferably formed from the components.
  • the pore is preferably present in the membrane.
  • the kit may comprise components of any of the membranes disclosed above, such as an amphiphilic layer or a triblock copolymer membrane.
  • the kit may further comprise a polynucleotide binding protein.
  • the kit may further comprise one or more anchors for coupling the polynucleotide to the membrane.
  • the kit is preferably for characterising a double stranded polynucleotide and preferably comprises a Y adaptor and a hairpin loop adaptor.
  • the Y adaptor preferably has one or more helicases attached and the hairpin loop adaptor preferably has one or more molecular brakes attached.
  • the Y adaptor preferably comprises one or more first anchors for coupling the polynucleotide to the membrane
  • the hairpin loop adaptor preferably comprises one or more second anchors for coupling the polynucleotide to the membrane and the strength of coupling of the hairpin loop adaptor to the membrane is preferably greater than the strength of coupling of the Y adaptor to the membrane.
  • the kit of the invention may additionally comprise one or more other reagents or instruments which enable any of the embodiments mentioned above to be carried out.
  • reagents or instruments include one or more of the following: suitable buffer(s) (aqueous solutions), means to obtain a sample from a subject (such as a vessel or an instrument comprising a needle), means to amplify and/or express polynucleotides or voltage or patch clamp apparatus.
  • Reagents may be present in the kit in a dry state such that a fluid sample resuspends the reagents.
  • the kit may also, optionally, comprise instructions to enable the kit to be used in the method of the invention or details regarding for which organism the method may be used.
  • the invention also provides an apparatus for characterising a target polynucleotide.
  • the apparatus comprises a plurality of pores of the invention and a plurality of membranes.
  • the plurality of pores are preferably present in the plurality of membranes.
  • the number of pores and membranes is preferably equal.
  • a single pore is present in each membrane.
  • the apparatus preferably further comprises instructions for carrying out the method of the invention.
  • the apparatus may be any conventional apparatus for polynucleotide analysis, such as an array or a chip. Any of the embodiments discussed above with reference to the methods of the invention are equally applicable to the apparatus of the invention.
  • the apparatus may further comprise any of the features present in the kit of the invention.
  • the apparatus is preferably set up to carry out the method of the invention.
  • the apparatus preferably comprises:
  • a sensor device that is capable of supporting the plurality of pores and membranes and being operable to perform polynucleotide characterisation using the pores and membranes;
  • At least one port for delivery of the material for performing the characterisation.
  • the apparatus preferably comprises:
  • a sensor device that is capable of supporting the plurality of pores and membranes being operable to perform polynucleotide characterisation using the pores and membranes;
  • At least one reservoir for holding material for performing the characterisation.
  • the apparatus more preferably comprises:
  • a sensor device that is capable of supporting the membrane and plurality of pores and membranes and being operable to perform polynucleotide characterising using the pores and membranes;
  • At least one reservoir for holding material for performing the characterising
  • a fluidics system configured to controllably supply material from the at least one reservoir to the sensor device
  • the fluidics system being configured to supply the samples selectively from one or more containers to the sensor device.
  • the apparatus may be any of those described in International Application No. PCT/GB08/004127 (published as WO 2009/077734), PCT/GB10/000789 (published as WO 2010/122293), International Application No. PCT/GB10/002206 (published as WO 2011/067559) or International Application No. PCT/US99/25679 (published as WO 00/28312).
  • This Example describes the use of a helicase—T4 Dda—E94C/C109A/C136A/A360C (SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C) to control the movement of DNA construct X (shown in FIG. 1 ) through a number of different MspA nanopores. All of the nanopores tested exhibited changes in current as the DNA translocated through the nanopore.
  • DNA construct X or Y Prior to setting up the experiment, DNA construct X or Y (see FIGS. 1 and 2 respectively for diagram and sequences used in constructs X and Y, final concentration added to the nanopore system 0.1 nM) was pre-incubated at room temperature for five minutes with T4 Dda—E94C/C109A/C136A/A360C (final concentration added to the nanopore system 10 nM, SEQ ID NO: 24 with mutations E94C/A360C which was provided in buffer (253 mM KCl, 50 mM potassium phosphate, pH 8.0, 2 mM EDTA)).
  • TMAD 100 ⁇ M final concentration added to the nanopore system
  • MgCl2 1 or 2 mM final concentration added to the nanopore system
  • ATP 2 mM final concentration added to the nanopore system
  • KCl 500 mM final concentration added to the nanopore system
  • the enzyme (T4 Dda—E94C/C109A/C136A/A360C, 10 nM final concentration), DNA construct X or Y (0.1 nM final concentration), fuel (MgCl2 1 or 2 mM final concentration, ATP 2 mM final concentration) pre-mix (150 ⁇ L total) was then flowed into the single nanopore experimental system and the experiment run with the following protocol ⁇ 120 mV for 900 s, ⁇ 180 mV for 2 seconds, 0 mV for 2 s and then return to 120 mV for 900 s (this flip protocol was repeated 8 times) and helicase-controlled DNA movement was monitored.
  • Entry 22 shows the MspA mutant MspA—(G75S/G77 S/L88N/D90N/D91N/D93N/D118R/Q126R/D134R/E139K)8 which has substituted the aspartic acid at position 93 with a glycine.
  • Helicase-controlled DNA movement was observed when DNA translocated through this mutant.
  • entry 1 FIG. 19

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Organic Chemistry (AREA)
  • Health & Medical Sciences (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Engineering & Computer Science (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Molecular Biology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biochemistry (AREA)
  • Biophysics (AREA)
  • Biotechnology (AREA)
  • Immunology (AREA)
  • Microbiology (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Medicinal Chemistry (AREA)
  • Peptides Or Proteins (AREA)
  • Enzymes And Modification Thereof (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Apparatus Associated With Microorganisms And Enzymes (AREA)
  • Nanotechnology (AREA)

Abstract

The invention relates to mutant forms of Msp. The invention also relates to polynucleotide characterisation using Msp.

Description

    FIELD OF THE INVENTION
  • The invention relates to mutant forms of Msp. The invention also relates to polynucleotide characterisation using Msp.
    • BACKGROUND OF THE INVENTION
  • There is currently a need for rapid and cheap polynucleotide (e.g. DNA or RNA) sequencing and identification technologies across a wide range of applications. Existing technologies are slow and expensive mainly because they rely on amplification techniques to produce large volumes of polynucleotide and require a high quantity of specialist fluorescent chemicals for signal detection.
  • Transmembrane pores (nanopores) have great potential as direct, electrical biosensors for polymers and a variety of small molecules. In particular, recent focus has been given to nanopores as a potential DNA sequencing technology.
  • When a potential is applied across a nanopore, there is a change in the current flow when an analyte, such as a nucleotide, resides transiently in the barrel for a certain period of time. Nanopore detection of the nucleotide gives a current change of known signature and duration. In the strand sequencing method, a single polynucleotide strand is passed through the pore and the identities of the nucleotides are derived. Strand sequencing can involve the use of a polynucleotide binding protein to control the movement of the polynucleotide through the pore.
  • The different forms of Msp are porins from Mycobacterium smegmatis. MspA is a 157 kDa octameric porin from Mycobacterium smegmatis. Wild-type MspA does not interact with DNA in a manner that allows the DNA to be characterised or sequenced. The structure of MspA and the modifications required for it to interact with and characterise DNA have been well documented (Butler, 2007, Nanopore Analysis of Nucleic Acids, Doctor of Philosophy Dissertation, University of Washington; Gundlach, Proc Natl Acad Sci USA. 2010 Sep. 14; 107(37):16060-5. Epub 2010 Aug. 26; and International Application No. PCT/GB2012/050301 (published as WO/2012/107778). Some key residues have been identified and modified to provide observable interactions between DNA and MspA, which are essential for DNA characterisation or sequencing. In particular, Butler supra teaches that removal of negative charge from all three of positions 90, 91 and 93 is required to provide observable interactions between DNA and MspA.
    • SUMMARY OF THE INVENTION
  • The inventors have surprisingly demonstrated that novel mutants of MspA which retain a negative charge at position 93 may be used to characterise polynucleotides, such as DNA, as long as they have a decreased net negative charge in the inner lining of the cap forming region and/or the barrel forming region. The negative charge at position 93 does not affect the ability of the mutants to capture polynucleotides, interact with polynucleotides and discriminate between the nucleotides in polynucleotides.
  • Accordingly, the invention provides a mutant Msp monomer comprising a variant of the sequence shown in SEQ ID NO: 2, wherein the variant:
  • (a) does not comprise aspartic acid (D) at position 90;
  • (b) does not comprise aspartic acid (D) at position 91;
  • (c) comprises aspartic acid (D) or glutamic acid (E) at position 93; and
  • (d) comprises one or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region of the monomer.
  • The invention also provides:
      • A construct comprising two or more covalently attached MspA monomers, wherein at least one of the monomers is a mutant monomer of the invention.
      • A polynucleotide which encodes a mutant monomer of the invention or a construct of the invention.
      • A homo-oligomeric pore derived from Msp comprising identical mutant monomers of the invention or identical constructs of the invention.
      • A hetero-oligomeric pore derived from Msp comprising at least one mutant monomer of the invention or at least one construct of the invention.
      • A method of characterising a target polynucleotide, comprising:
      • a) contacting the polynucleotide with a pore of the invention such that the polynucleotide moves through the pore; and
      • b) taking one or more measurements as the polynucleotide moves with respect to the pore, wherein the measurements are indicative of one or more characteristics of the polynucleotide, and thereby characterising the target polynucleotide.
      • A kit for characterising a target polynucleotide comprising (a) a pore of the invention and (b) the components of a membrane.
      • An apparatus for characterising target polynucleotides in a sample, comprising (a) a plurality of pores of the invention and (b) a plurality of membranes.
      • A method of characterising a target polynucleotide, comprising:
      • a) contacting the polynucleotide with a pore of the invention, a polymerase and labelled nucleotides such that phosphate labelled species are sequentially released when nucleotides are added to the first polynucleotide analyte by the polymerase, wherein the phosphate species contain a label specific for each nucleotide; and
      • b) detecting the phosphate labelled species using the pore and thereby characterising the polynucleotide.
    DESCRIPTION OF THE FIGURES
  • FIG. 1 shows DNA construct X which was used in Example 1. Section a of DNA construct X corresponds to SEQ ID NO: 26. Section b corresponds to four iSpC3 spacers. C corresponds to the helicase enzyme T4 Dda—E94C/C109A/C136A/A360C (SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C) which can bind to the section labelled a. Section d corresponds to SEQ ID NO: 27. Section e corresponds to four 5′-nitroindoles. Section f corresponds to SEQ ID NO: 28. Section g corresponds to SEQ ID NO: 29 which is attached at its 3′ end to six iSp18 spacers which are attached at the opposite end to two thymines and 3′ cholesterol TEG (labelled h).
  • FIG. 2 shows DNA construct Y which was used in Example 1. Section i of DNA construct X corresponds to 25 iSpC3 spacers, which are attached to the 5′ end of SEQ ID NO: 3 (labelled j). Section j is the region of construct Y to which the helicase enzyme T4 Dda—E94C/C109A/C136A/A360C can bind (labelled c). Section k corresponds to four iSp18 spacers. Section d corresponds to SEQ ID NO: 27. Section e corresponds to four 5′-nitroindoles. Section 1 corresponds to SEQ ID NO: 4. Section g corresponds to SEQ ID NO: 29 which is attached at its 3′ end to six iSp18 spacers which are attached at the opposite end to two thymines and 3′ cholesterol TEG (labelled h).
  • FIG. 3 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 4 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for both traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct Y through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/A96D/D118R/Q126R/D134R/E139K)8. Sections B shows a zoomed in region of current trace A.
  • FIG. 5 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/N102G/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 6 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/S103A/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 7 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/N108S/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 8 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/N108P/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 9 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/A96D/N108P/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 10 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/A96D/N108A/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 11 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for both traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77 S/L88N/I89F/D90N/D91N/D118R/Q126R/D134R/E139K)8. Sections B shows a zoomed in region of current trace A.
  • FIG. 12 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/D90N/D91N/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 13 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for both traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88K/D90N/D91N/I105E/D118R/Q126R/D134R/E139K)8. Sections B shows a zoomed in region of current trace A.
  • FIG. 14 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/D118G/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 15 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/D118N/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 16 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/D118R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 17 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88K/D90N/D91N/N108E/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 18 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct Y through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/T95E/P98K/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 19 shows example current traces (y-axis label=Current (pA), x-axis label=Time (s) for all three traces) of when a helicase (T4 Dda—E94C/C109A/C136A/A360C) controls the translocation of the DNA construct X through the MspA nanopore MspA—(G75S/G77S/L88N/D90N/D91N/D93N/D118R/Q126R/D134R/E139K)8. Sections B and C show zoomed in regions of current trace A.
  • FIG. 20 shows a cartoon representation of the wild-type MspA nanopore. Region 1 corresponds to the cap forming region and includes residues 1-72 and 122-184. Region 2 corresponds to the barrel forming region and includes residues 73-82 and 112-121. Region 3 corresponds to the constriction and loops region and includes residues 83-111.
    •  DESCRIPTION OF THE SEQUENCE LISTING
  • SEQ ID NO: 1 shows the codon optimised polynucleotide sequence encoding the wild-type MspA monomer. This mutant lacks the signal sequence.
  • SEQ ID NO: 2 shows the amino acid sequence of the mature form of the wild-type MspA monomer. This mutant lacks the signal sequence.
  • SEQ ID NOs: 3 and 4 shows polynucleotide sequences used in Example 1.
  • SEQ ID NOs: 5 to 7 show the amino acid sequences of MspB, C and D.
  • SEQ ID NO: 8 shows the polynucleotide sequence encoding the Phi29 DNA polymerase.
  • SEQ ID NO: 9 shows the amino acid sequence of the Phi29 DNA polymerase.
  • SEQ ID NO: 10 shows the codon optimised polynucleotide sequence derived from the sbcB gene from E. coli. It encodes the exonuclease I enzyme (EcoExo I) from E. coli.
  • SEQ ID NO: 11 shows the amino acid sequence of exonuclease I enzyme (EcoExo I) from E. coli.
  • SEQ ID NO: 12 shows the codon optimised polynucleotide sequence derived from the xthA gene from E. coli. It encodes the exonuclease III enzyme from E. coli.
  • SEQ ID NO: 13 shows the amino acid sequence of the exonuclease III enzyme from E. coli. This enzyme performs distributive digestion of 5′ monophosphate nucleosides from one strand of double stranded DNA (dsDNA) in a 3′-5′ direction. Enzyme initiation on a strand requires a 5′ overhang of approximately 4 nucleotides.
  • SEQ ID NO: 14 shows the codon optimised polynucleotide sequence derived from the recJ gene from T. thermophilus. It encodes the RecJ enzyme from T. thermophilus (TthRecJ-cd).
  • SEQ ID NO: 15 shows the amino acid sequence of the RecJ enzyme from T thermophilus (TthRecJ-cd). This enzyme performs processive digestion of 5′ monophosphate nucleosides from ssDNA in a 5′-3′ direction. Enzyme initiation on a strand requires at least 4 nucleotides.
  • SEQ ID NO: 16 shows the codon optimised polynucleotide sequence derived from the bacteriophage lambda exo (redX) gene. It encodes the bacteriophage lambda exonuclease.
  • SEQ ID NO: 17 shows the amino acid sequence of the bacteriophage lambda exonuclease. The sequence is one of three identical subunits that assemble into a trimer. The enzyme performs highly processive digestion of nucleotides from one strand of dsDNA, in a 5′-3′ direction (http://www.neb.com/nebecomm/products/productM0262.asp). Enzyme initiation on a strand preferentially requires a 5′ overhang of approximately 4 nucleotides with a 5′ phosphate.
  • SEQ ID NO: 18 shows the amino acid sequence of Hel308 Mbu.
  • SEQ ID NO: 19 shows the amino acid sequence of Hel308 Csy.
  • SEQ ID NO: 20 shows the amino acid sequence of Hel308 Tga.
  • SEQ ID NO: 21 shows the amino acid sequence of Hel308 Mhu.
  • SEQ ID NO: 22 shows the amino acid sequence of TraI Eco.
  • SEQ ID NO: 23 shows the amino acid sequence of XPD Mbu.
  • SEQ ID NO: 24 shows the amino acid sequence of Dda 1993.
  • SEQ ID NO: 25 shows the amino acid sequence of Trwc Cba.
  • SEQ ID NO: 26-29 shows polynucleotide sequences used in Example 1.
    • DETAILED DESCRIPTION OF THE INVENTION
  • It is to be understood that different applications of the disclosed products and methods may be tailored to the specific needs in the art. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments of the invention only, and is not intended to be limiting.
  • In addition as used in this specification and the appended claims, the singular forms “a”, “an”, and “the” include plural referents unless the content clearly dictates otherwise. Thus, for example, reference to “a polynucleotide” includes two or more polynucleotides, reference to “a helicase” includes two or more helicases, reference to “a monomer” refers to two or more monomers, reference to “a pore” includes two or more pores and the like.
  • All publications, patents and patent applications cited herein, whether supra or infra, are hereby incorporated by reference in their entirety.
    • Mutant Msp Monomers
  • The present invention provides mutant Msp monomers. The mutant Msp monomers may be used to form the pores of the invention. A mutant Msp monomer is a monomer whose sequence varies from that of a wild-type Msp monomer and which retains the ability to form a pore. Methods for confirming the ability of mutant monomers to form pores are well-known in the art and are discussed in more detail below.
  • The mutant monomers have improved polynucleotide reading properties i.e. display improved polynucleotide capture and nucleotide discrimination. In particular, pores constructed from the mutant monomers capture nucleotides and polynucleotides more easily than the wild type. In addition, pores constructed from the mutant monomers display an increased current range, which makes it easier to discriminate between different nucleotides, and a reduced variance of states, which increases the signal-to-noise ratio. In addition, the number of nucleotides contributing to the current as the polynucleotide moves through pores constructed from the mutants is decreased. This makes it easier to identify a direct relationship between the observed current as the polynucleotide moves through the pore and the polynucleotide sequence.
  • A mutant monomer of the invention comprises a variant of the sequence shown in SEQ ID NO: 2. SEQ ID NO: 2 is the wild-type MspA monomer. A variant of SEQ ID NO: 2 is a polypeptide that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its ability to form a pore. The ability of a variant to form a pore can be assayed using any method known in the art. For instance, the variant may be inserted into an amphiphilic layer along with other appropriate subunits and its ability to oligomerise to form a pore may be determined. Methods are known in the art for inserting subunits into membranes, such as amphiphilic layers. For example, subunits may be suspended in a purified form in a solution containing a triblock copolymer membrane such that it diffuses to the membrane and is inserted by binding to the membrane and assembling into a functional state. Alternatively, subunits may be directly inserted into the membrane using the “pick and place” method described in M. A. Holden, H. Bayley. J. Am. Chem. Soc. 2005, 127, 6502-6503 and International Application No. PCT/GB2006/001057 (published as WO 2006/100484).
    • Positions 90 and 91
  • In wild-type MspA, amino acids 90 and 91 are both aspartic acid (D). These amino acids in each monomer form part of an inner constriction of the pore (FIG. 20). The variant does not comprise aspartic acid (D) at position 90. The variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at position 90. The variant preferably does not have a negatively charged amino acid at position 90.
  • The variant does not comprise aspartic acid (D) at position 91. The variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at position 91. The variant preferably does not have a negatively charged amino acid at position 91.
  • The variant preferably comprises serine (S), glutamine (Q), leucine (L), methionine (M), isoleucine (I), alanine (A), valine (V), glycine (G), phenylalanine (F), tryptophan (W), tyrosine (Y), histidine (H), threonine (T), arginine (R), lysine (K), asparagine (N) or cysteine (C) at position 90 and/or position 91. Any combinations of these amino acids at positions 90 and 91 are envisaged by the invention. The variant preferably comprises asparagine (N) at position 90 and/or position 91. The variant more preferably comprises asparagine (N) at position 90 and position 91. These amino acids are preferably inserted at position 90 and/or 91 by substitution.
    • Position 93
  • In wild-type MspA, amino acid 93 is aspartic acid (D). This amino acid in each monomer also forms part of an inner constriction of the pore (FIG. 20).
  • The variant comprises aspartic acid (D) or glutamic acid (E) at position 93. The variant therefore has a negative charge at position 93. The glutamic acid (E) is preferably introduced by substitution.
    • Cap Forming Region
  • In wild-type MspA, amino acids 1 to 72 and 122 to 184 form the cap of the pore (FIG. 20). Of these amino acids, V9, Q12, D13, R14, T15, W40, I49, P53, G54, D56, E57, E59, T61, E63, Y66, Q67, 168, F70, P123, 1125, Q126, E127, V128, A129, T130, F131, S132, V133, D134, S136, G137, E139, V144, H148, T150, V151, T152, F163, R165, 1167, S169, T170 and S173 face inwards into the channel of the pore.
    • Barrel Forming Region
  • In wild-type MspA, amino acids 73 to 82 and 112 to 121 form the barrel of the pore (FIG. 20). Of these amino acids, S73, G75, G77, N79, S81, G112, S114, S116, D118 and G120 face inwards into the channel of the pore. S73, G75, G77, N79, S81 face inwards in the downwards strand and G112, S114, S116, D118 and G120 face inwards in the upwards strand.
    • Decreased Net Negative Charge
  • The variant comprises one or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region of the monomer. The variant preferably comprises two or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and the barrel forming region of the monomer.
  • The variant may comprise any number of modifications, such as 1 or more, 2 or more, 3 or more, 4 or more, 5 or more, 6 or more, 7 or more, 8 or more, 9 or more, 10 or more, 15 or more, 20 or more, 30 or more, or 40 or more modifications.
  • The net negative charge may be decreased by any means known in the art. The net negative charge is decreased in a manner that does not interfere with the ability of the mutant monomer to form a pore. This can be measured as discussed above.
  • The net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region is decreased. This means that the inward facing amino acids in the cap forming region and/or the barrel forming region comprise fewer negatively charged amino acids than in SEQ ID NO: 2 and/or comprises more positively charged amino acids than in SEQ ID NO: 2. The one or more modifications may lead to a net positive charge in the inward facing amino acids in the cap forming region and/or the barrel forming region
  • The net charge can be measured using methods known in the art. For instance, the isolectric point may be used to define the net charge of the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • The one or more modifications are preferably one or more deletions of negatively charged amino acids. Removal of one or more negatively charged amino acids reduces the net negative charge of the inward facing amino acids in the cap forming region and/or barrel forming region. A negatively charged amino acid is an amino acid with a net negative charge. Negatively charged amino acids include, but are not limited to, aspartic acid (D) and glutamic acid (E). Methods for deleting amino acids from proteins, such as MspA monomers, are well known in the art.
  • The one or more modifications are preferably one or more substitutions of negatively charged amino acids with one or more positively charged, uncharged, non-polar and/or aromatic amino acids. A positively charged amino acid is an amino acid with a net positive charge. The positively charged amino acid(s) can be naturally-occurring or non-naturally-occurring. The positively charged amino acid(s) may be synthetic or modified. For instance, modified amino acids with a net positive charge may be specifically designed for use in the invention. A number of different types of modification to amino acids are well known in the art.
  • Preferred naturally-occurring positively charged amino acids include, but are not limited to, histidine (H), lysine (K) and arginine (R). Any number and combination of H, K and/or R may be substituted for the inward facing amino acids in the cap forming region and/or barrel forming region.
  • The uncharged amino acids, non-polar amino acids and/or aromatic amino acids can be naturally occurring or non-naturally-occurring. They may be synthetic or modified. Uncharged amino acids have no net charge. Suitable uncharged amino acids include, but are not limited to, cysteine (C), serine (S), threonine (T), methionine (M), asparagines (N) and glutamine (Q). Non-polar amino acids have non-polar side chains. Suitable non-polar amino acids include, but are not limited to, glycine (G), alanine (A), proline (P), isoleucine (I), leucine (L) and valine (V). Aromatic amino acids have an aromatic side chain. Suitable aromatic amino acids include, but are not limited to, histidine (H), phenylalanine (F), tryptophan (W) and tyrosine (Y). Any number and combination of these amino acids may be substituted into the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • The one or more negatively charged amino acids are preferably substituted with alanine (A), valine (V), asparagine (N) or glycine (G). Preferred substitutions include, but are not limited to, substitution of D with A, substitution of D with V, substitution of D with N and substitution of D with G.
  • The one or more modifications are preferably one or more introductions of positively charged amino acids. The introduction of positive charge decreases the net negative charge. The one or more positively charged amino acids may be introduced by addition or substitution. Any amino acid may be substituted with a positively charged amino acid. One or more uncharged amino acids, non-polar amino acids and/or aromatic amino acids may be substituted with one or more positively charged amino acids. Any number of positively charged amino acids may be introduced.
  • Wild-type MspA comprises a polar glutamine (Q) at position 126. The one or more modifications preferably reduce the net negative charge at position 126. The one or more modifications preferably increase the net positive charge at positions 126. This can be achieved by replacing the polar amino acid at position 126 or an adjacent or a nearby inward facing amino acid with a positively charged amino acid. The variant preferably comprises a positively charged amino acid at position 126. The variant preferably comprises a positively charged amino acid at one or more of positions 123, 125, 127 and 128. The variant may comprise any number and combination of positively charged amino acids at positions 123, 125, 127 and 128. The positively charged amino acid(s) may be introduced by addition or substitution.
  • The one or more modifications are preferably one or more introductions of positively charged amino acids which neutralise one or more negatively charged amino acids. The neutralisation of negative charge decreases the net negative charge. The one or more positively charged amino acids may be introduced by addition or substitution. Any amino acid may be substituted with a positively charged amino acid. One or more uncharged amino acids, non-polar amino acids and/or aromatic amino acids may be substituted with one or more positively charged amino acids. Any number of positively charged amino acids may be introduced. The number is typically the same as the number of negatively charged amino acids in the inward facing amino acids in the cap forming region and/or the barrel forming region.
  • The one or more positively charged amino acids may be introduced at any position in the cap forming region and/or the barrel forming region as long as they neutralise the negative charge of the one or more negatively charged amino acids. To effectively neutralise the negative charge, there is typically 5 or fewer amino acids in the variant between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. There is preferably 4 or fewer, 3 or fewer or 2 or fewer amino acids in the variant between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. There is more preferably two amino acids in the variant between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. Each positively charged amino acid is most preferably introduced adjacent in the variant to the negatively charged amino acid it is neutralising.
  • The one or more positively charged amino acids may be introduced at any position in the inward facing amino acids in the cap forming region and/or the barrel forming region as long as they neutralise the negative charge of the one or more negatively charged amino acids. To effectively neutralise the negative charge, there is typically 5 or fewer inward facing amino acids between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. There is preferably 4 or fewer, 3 or fewer or 2 or fewer inward facing amino acids between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. There is more preferably one inward facing amino acid between each positively charged amino acid that is introduced and the negatively charged amino acid it is neutralising. Each positively charged amino acid is most preferably introduced at the inward facing position adjacent to the negatively charged amino acid it is neutralising.
  • Wild-type MspA comprises aspartic acid (D) at positions 118 and 134 and glutamic acid (E) at position 139. Amino acid 118 in each monomer is present within the barrel of the pore (FIG. 20). The variant preferably comprises a positively charged amino acid at one or more of positions 114, 116, 120, 123, 70, 73, 75, 77 and 79. Positive charges at one or more of these positions neutralise the negative charge at position 118. Positively charged amino acids may present at any number and combination of positions 114, 116, 120, 123, 70, 73, 75, 77 and 79. The amino acids may be introduced by addition or substitution.
  • Amino acids 134 and 139 in each monomer are part of the cap (FIG. 20). The variant comprises a positively charged amino acid at one or more of positions 129, 132, 136, 137, 59, 61 and 63. Positive charges at one or more of these positions neutralise the negative charge at position 134. Positively charged amino acids may present at any number and combination of positions 129, 132, 136, 137, 59, 61 and 63. The amino acids may be introduced by addition or substitution.
  • The variant preferably comprises a positively charged amino acid at one or more of positions 137, 138, 141, 143, 45, 47, 49 and 51. Positive charges at one or more of these positions neutralise the negative charge at position 139. Positively charged amino acids may present at any number and combination of positions 137, 138, 141, 143, 45, 47, 49 and 51. The amino acids may be introduced by addition or substitution.
    • Positions 118, 126, 134 and 139
  • The one or more modifications preferably reduce the net negative charge at one or more of positions 118, 126, 134 and 139. The one or more modifications preferably reduce the net negative charge at 118; 126; 134; 139; 118 and 126; 118 and 134; 118 and 139; 126 and 134; 126 and 139; 134 and 139; 118, 126 and 134; 118, 126 and 139; 118, 134 and 139; 126, 134 and 139; or 118, 126, 134 and 139.
  • The variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at one or more of positions 118, 126, 134 and 139. The variant preferably does not comprise aspartic acid (D) or glutamic acid (E) at any of the combination of positions 118, 126, 134 and 139 disclosed above. The variant more preferably comprises arginine (R), glycine (G) or asparagine (N) at one or more of positions 118, 126, 134 and 139, such as any of the combinations of positions 118, 126, 134 and 139 disclosed above. The variant most preferably comprises D118R, Q126R, D134R and E139K.
  • Methods for introducing or substituting naturally-occurring amino acids are well known in the art. For instance, methionine (M) may be substituted with arginine (R) by replacing the codon for methionine (ATG) with a codon for arginine (CGT) at the relevant position in a polynucleotide encoding the mutant monomer. The polynucleotide can then be expressed as discussed below.
  • Methods for introducing or substituting non-naturally-occurring amino acids are also well known in the art. For instance, non-naturally-occurring amino acids may be introduced by including synthetic aminoacyl-tRNAs in the IVTT system used to express the mutant monomer. Alternatively, they may be introduced by expressing the mutant monomer in E. coli that are auxotrophic for specific amino acids in the presence of synthetic (i.e. non-naturally-occurring) analogues of those specific amino acids. They may also be produced by naked ligation if the mutant monomer is produced using partial peptide synthesis.
  • The one or more modifications are preferably one or more chemical modifications of one or more negatively charged amino acids which neutralise their negative charge. For instance, the one or more negatively charged amino acids may be reacted with a carbodiimide.
    • Other Modifications
  • The variant preferably comprises one or more of:
  • (a) serine (S) at position 75;
  • (b) serine (S) at position 77; and
  • (c) asparagine (N) or lysine (K) at position 88.
  • The variant may comprise any number and combination of (a) to (c), including (a), (b), (c), (a) and (b), (b) and (c), (a) and (c) and (a), (b) and (c). The variant preferably comprises G75S, G77S and L88N.
  • The variant most preferably comprises G75S, G77S, L88N, D90N, D91N, D118R, Q126R, D134R and E139K.
  • The variant preferably further comprises one or more of:
  • (d) phenylalanine (F) at position 89;
  • (e) glutamic acid (E) at position 95 and lysine (K) at position 98;
  • (f) aspartic acid (D) at position 96;
  • (g) glycine (G) at position 102;
  • (h) alanine (A) at position 103; and
  • (i) alanine (A), serine (S) or proline (P) at position 108.
  • The may comprise any number and combination of (d) to (i).
    • Variants
  • In addition to the specific mutations discussed above, the variant may include other mutations. Over the entire length of the amino acid sequence of SEQ ID NO: 2, a variant will preferably be at least 50% homologous to that sequence based on amino acid identity. More preferably, the variant may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95%, amino acid identity over a stretch of 100 or more, for example 125, 150, 175 or 200 or more, contiguous amino acids (“hard homology”).
  • Standard methods in the art may be used to determine homology. For example the UWGCG Package provides the BESTFIT program which can be used to calculate homology, for example used on its default settings (Devereux et at (1984) Nucleic Acids Research 12, p387-395). The PILEUP and BLAST algorithms can be used to calculate homology or line up sequences (such as identifying equivalent residues or corresponding sequences (typically on their default settings)), for example as described in Altschul S. F. (1993) J Mol Evol 36:290-300; Altschul, S. F et at (1990) J Mol Biol 215:403-10. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/).
  • SEQ ID NO: 2 is the mature form of the wild-type MspA monomer. The variant may comprise any of the mutations in the MspB, C or D monomers compared with MspA. The mature forms of MspB, C and D are shown in SEQ ID NOs: 5 to 7. In particular, the variant may comprise the following substitution present in MspB: A138P. The variant may comprise one or more of the following substitutions present in MspC: A96G, N102E and A138P. The variant may comprise one or more of the following mutations present in MspD: Deletion of G1, L2V, E5Q, L8V, D13G, W21A, D22E, K47T, I49H, 168V, D91G, A96Q, N102D, S103T, V1041, S136K and G141A. The variant may comprise combinations of one or more of the mutations and substitutions from Msp B, C and D.
  • Amino acid substitutions may be made to the amino acid sequence of SEQ ID NO: 2 in addition to those discussed above, for example up to 1, 2, 3, 4, 5, 10, 20 or 30 substitutions. Conservative substitutions replace amino acids with other amino acids of similar chemical structure, similar chemical properties or similar side-chain volume. The amino acids introduced may have similar polarity, hydrophilicity, hydrophobicity, basicity, acidity, neutrality or charge to the amino acids they replace. Alternatively, the conservative substitution may introduce another amino acid that is aromatic or aliphatic in the place of a pre-existing aromatic or aliphatic amino acid. Conservative amino acid changes are well-known in the art and may be selected in accordance with the properties of the 20 main amino acids as defined in Table 1 below. Where amino acids have similar polarity, this can also be determined by reference to the hydropathy scale for amino acid side chains in Table 1.
  • TABLE 1
    Chemical properties of amino acids
    Ala aliphatic, hydrophobic, Met hydrophobic, neutral
    neutral
    Cys polar, hydrophobic, Asn polar, hydrophilic,
    neutral neutral
    Asp polar, hydrophilic, Pro hydrophobic, neutral
    charged (−)
    Glu polar, hydrophilic, Gln polar, hydrophilic,
    charged (−) neutral
    Phe aromatic, hydrophobic, Arg polar, hydrophilic,
    neutral charged (+)
    Gly aliphatic, neutral Ser polar, hydrophilic,
    neutral
    His aromatic, polar, Thr polar, hydrophilic,
    hydrophilic, charged (+) neutral
    Ile aliphatic, hydrophobic, Val aliphatic, hydrophobic,
    neutral neutral
    Lys polar, hydrophilic, Trp aromatic, hydrophobic,
    charged(+) neutral
    Leu aliphatic, hydrophobic, Tyr aromatic, polar,
    neutral hydrophobic
  • TABLE 2
    Hydropathy scale
    Side Chain Hydropathy
    Ile 4.5
    Val 4.2
    Leu 3.8
    Phe 2.8
    Cys 2.5
    Met 1.9
    Ala 1.8
    Gly −0.4
    Thr −0.7
    Ser −0.8
    Trp −0.9
    Tyr −1.3
    Pro −1.6
    His −3.2
    Glu −3.5
    Gln −3.5
    Asp −3.5
    Asn −3.5
    Lys −3.9
    Arg −4.5
  • One or more amino acid residues of the amino acid sequence of SEQ ID NO: 2 may additionally be deleted from the polypeptides described above. Up to 1, 2, 3, 4, 5, 10, 20 or 30 residues may be deleted, or more.
  • Variants may include fragments of SEQ ID NO: 2. Such fragments retain pore forming activity. Fragments may be at least 50, 100, 150 or 200 amino acids in length. Such fragments may be used to produce the pores. A fragment preferably comprises the pore forming domain of SEQ ID NO: 2. Fragments must include one of residues 88, 90, 91, 105, 118 and 134 of SEQ ID NO: 2. Typically, fragments include all of residues 88, 90, 91, 105, 118 and 134 of SEQ ID NO: 2.
  • One or more amino acids may be alternatively or additionally added to the polypeptides described above. An extension may be provided at the amino terminal or carboxy terminal of the amino acid sequence of SEQ ID NO: 2 or polypeptide variant or fragment thereof. The extension may be quite short, for example from 1 to 10 amino acids in length. Alternatively, the extension may be longer, for example up to 50 or 100 amino acids. A carrier protein may be fused to an amino acid sequence according to the invention. Other fusion proteins are discussed in more detail below.
  • As discussed above, a variant is a polypeptide that has an amino acid sequence which varies from that of SEQ ID NO: 2 and which retains its ability to form a pore. A variant typically contains the regions of SEQ ID NO: 2 that are responsible for pore formation. The pore forming ability of Msp, which contains a β-barrel, is provided by β-sheets in each subunit. A variant of SEQ ID NO: 2 typically comprises the regions in SEQ ID NO: 2 that form β-sheets. One or more modifications can be made to the regions of SEQ ID NO: 2 that form β-sheets as long as the resulting variant retains its ability to form a pore. A variant of SEQ ID NO: 2 preferably includes one or more modifications, such as substitutions, additions or deletions, within its α-helices and/or loop regions.
  • The monomers derived from Msp may be modified to assist their identification or purification, for example by the addition of a streptavidin tag or by the addition of a signal sequence to promote their secretion from a cell where the monomer does not naturally contain such a sequence. Other suitable tags are discussed in more detail below. The monomer may be labelled with a revealing label. The revealing label may be any suitable label which allows the monomer to be detected. Suitable labels are described below.
  • The monomer derived from Msp may also be produced using D-amino acids. For instance, the monomer derived from Msp may comprise a mixture of L-amino acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.
  • The monomer derived from Msp contains one or more specific modifications to facilitate nucleotide discrimination. The monomer derived from Msp may also contain other non-specific modifications as long as they do not interfere with pore formation. A number of non-specific side chain modifications are known in the art and may be made to the side chains of the monomer derived from Msp. Such modifications include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed by reduction with NaBH4, amidination with methylacetimidate or acylation with acetic anhydride.
  • The monomer derived from Msp can be produced using standard methods known in the art. The monomer derived from Msp may be made synthetically or by recombinant means. For example, the monomer may be synthesized by in vitro translation and transcription (IVTT). Suitable methods for producing pores and monomers are discussed in International Application Nos. PCT/GB09/001690 (published as WO 2010/004273), PCT/GB09/001679 (published as WO 2010/004265) or PCT/GB10/000133 (published as WO 2010/086603).
  • In some embodiments, the mutant monomer is chemically modified. The mutant monomer can be chemically modified in any way and at any site. The mutant monomer is preferably chemically modified by attachment of a molecule to one or more cysteines (cysteine linkage), attachment of a molecule to one or more lysines, attachment of a molecule to one or more non-natural amino acids, enzyme modification of an epitope or modification of a terminus. Suitable methods for carrying out such modifications are well-known in the art. The mutant monomer may be chemically modified by the attachment of any molecule. For instance, the mutant monomer may be chemically modified by attachment of a dye or a fluorophore.
  • In some embodiments, the mutant monomer is chemically modified with a molecular adaptor that facilitates the interaction between a pore comprising the monomer and a target nucleotide or target polynucleotide sequence. The presence of the adaptor improves the host-guest chemistry of the pore and the nucleotide or polynucleotide sequence and thereby improves the sequencing ability of pores formed from the mutant monomer. The principles of host-guest chemistry are well-known in the art. The adaptor has an effect on the physical or chemical properties of the pore that improves its interaction with the nucleotide or polynucleotide sequence. The adaptor may alter the charge of the barrel or channel of the pore or specifically interact with or bind to the nucleotide or polynucleotide sequence thereby facilitating its interaction with the pore.
  • The molecular adaptor is preferably a cyclic molecule, a cyclodextrin, a species that is capable of hybridization, a DNA binder or interchelator, a peptide or peptide analogue, a synthetic polymer, an aromatic planar molecule, a small positively-charged molecule or a small molecule capable of hydrogen-bonding.
  • The adaptor may be cyclic. A cyclic adaptor preferably has the same symmetry as the pore. The adaptor preferably has eight-fold symmetry since Msp typically has eight subunits around a central axis. This is discussed in more detail below.
  • The adaptor typically interacts with the nucleotide or polynucleotide sequence via host-guest chemistry. The adaptor is typically capable of interacting with the nucleotide or polynucleotide sequence. The adaptor comprises one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence. The one or more chemical groups preferably interact with the nucleotide or polynucleotide sequence by non-covalent interactions, such as hydrophobic interactions, hydrogen bonding, Van der Waal's forces, π-cation interactions and/or electrostatic forces. The one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence are preferably positively charged. The one or more chemical groups that are capable of interacting with the nucleotide or polynucleotide sequence more preferably comprise amino groups. The amino groups can be attached to primary, secondary or tertiary carbon atoms. The adaptor even more preferably comprises a ring of amino groups, such as a ring of 6, 7 or 8 amino groups. The adaptor most preferably comprises a ring of eight amino groups. A ring of protonated amino groups may interact with negatively charged phosphate groups in the nucleotide or polynucleotide sequence.
  • The correct positioning of the adaptor within the pore can be facilitated by host-guest chemistry between the adaptor and the pore comprising the mutant monomer. The adaptor preferably comprises one or more chemical groups that are capable of interacting with one or more amino acids in the pore. The adaptor more preferably comprises one or more chemical groups that are capable of interacting with one or more amino acids in the pore via non-covalent interactions, such as hydrophobic interactions, hydrogen bonding, Van der Waal's forces, π-cation interactions and/or electrostatic forces. The chemical groups that are capable of interacting with one or more amino acids in the pore are typically hydroxyls or amines. The hydroxyl groups can be attached to primary, secondary or tertiary carbon atoms. The hydroxyl groups may form hydrogen bonds with uncharged amino acids in the pore. Any adaptor that facilitates the interaction between the pore and the nucleotide or polynucleotide sequence can be used.
  • Suitable adaptors include, but are not limited to, cyclodextrins, cyclic peptides and cucurbiturils. The adaptor is preferably a cyclodextrin or a derivative thereof. The cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am. Chem. Soc. 116, 6081-6088. The adaptor is more preferably heptakis-6-amino-β-cyclodextrin (am7-βCD), 6-monodeoxy-6-monoamino-β-cyclodextrin (am1-βCD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu7-βCD). The guanidino group in gu7-βCD has a much higher pKa than the primary amines in am7-βCD and so it more positively charged. This gu7-βCD adaptor may be used to increase the dwell time of the nucleotide in the pore, to increase the accuracy of the residual current measured, as well as to increase the base detection rate at high temperatures or low data acquisition rates.
  • If a succinimidyl 3-(2-pyridyldithio)propionate (SPDP) crosslinker is used as discussed in more detail below, the adaptor is preferably heptakis(6-deoxy-6-amino)-6-N-mono(2-pyridyl)dithiopropanoyl-β-cyclodextrin (am6amPDP1-βCD).
  • More suitable adaptors include γ-cyclodextrins, which comprise 8 sugar units (and therefore have eight-fold symmetry). The γ-cyclodextrin may contain a linker molecule or may be modified to comprise all or more of the modified sugar units used in the β-cyclodextrin examples discussed above.
  • The molecular adaptor is preferably covalently attached to the mutant monomer. The adaptor can be covalently attached to the pore using any method known in the art. The adaptor is typically attached via chemical linkage. If the molecular adaptor is attached via cysteine linkage, the one or more cysteines have preferably been introduced to the mutant by substitution. The mutant monomers of the invention can of course comprise a cysteine residue at one or more of positions 88, 90, 91, 103 and 105. The mutant monomer may be chemically modified by attachment of a molecular adaptor to one or more, such as 2, 3, 4 or 5, of these cysteines. Alternatively, the mutant monomer may be chemically modified by attachment of a molecule to one or more cysteines introduced at other positions. The molecular adaptor is preferably attached to one or more of positions 90, 91 and 103 of SEQ ID NO: 2.
  • The reactivity of cysteine residues may be enhanced by modification of the adjacent residues. For instance, the basic groups of flanking arginine, histidine or lysine residues will change the pKa of the cysteines thiol group to that of the more reactive S− group. The reactivity of cysteine residues may be protected by thiol protective groups such as dTNB. These may be reacted with one or more cysteine residues of the mutant monomer before a linker is attached. The molecule may be attached directly to the mutant monomer. The molecule is preferably attached to the mutant monomer using a linker, such as a chemical crosslinker or a peptide linker.
  • Suitable chemical crosslinkers are well-known in the art. Preferred crosslinkers include 2,5-dioxopyrrolidin-1-yl 3-(pyridin-2-yldisulfanyl)propanoate, 2,5-dioxopyrrolidin-1-yl 4-(pyridin-2-yldisulfanyl)butanoate and 2,5-dioxopyrrolidin-1-yl 8-(pyridin-2-yldisulfanyl)octananoate. The most preferred crosslinker is succinimidyl 3-(2-pyridyldithio)propionate (SPDP). Typically, the molecule is covalently attached to the bifunctional crosslinker before the molecule/crosslinker complex is covalently attached to the mutant monomer but it is also possible to covalently attach the bifunctional crosslinker to the monomer before the bifunctional crosslinker/monomer complex is attached to the molecule.
  • The linker is preferably resistant to dithiothreitol (DTT). Suitable linkers include, but are not limited to, iodoacetamide-based and Maleimide-based linkers.
  • In other embodiment, the monomer may be attached to a polynucleotide binding protein. This forms a modular sequencing system that may be used in the methods of sequencing of the invention. Polynucleotide binding proteins are discussed below.
  • The polynucleotide binding protein is preferably covalently attached to the mutant monomer. The protein can be covalently attached to the monomer using any method known in the art. The monomer and protein may be chemically fused or genetically fused. The monomer and protein are genetically fused if the whole construct is expressed from a single polynucleotide sequence. Genetic fusion of a monomer to a polynucleotide binding protein is discussed in International Application No. PCT/GB09/001679 (published as WO 2010/004265).
  • If the polynucleotide binding protein is attached via cysteine linkage, the one or more cysteines have preferably been introduced to the mutant by substitution. The mutant monomers of the invention can of course comprise cysteine residues at one or more of positions 10 to 15, 51 to 60, 136 to 139 and 168 to 172. These positions are present in loop regions which have low conservation amongst homologues indicating that mutations or insertions may be tolerated. They are therefore suitable for attaching a polynucleotide binding protein. The reactivity of cysteine residues may be enhanced by modification as described above.
  • The polynucleotide binding protein may be attached directly to the mutant monomer or via one or more linkers. The molecule may be attached to the mutant monomer using the hybridization linkers described in International Application No. PCT/GB10/000132 (published as WO 2010/086602). Alternatively, peptide linkers may be used. Peptide linkers are amino acid sequences. The length, flexibility and hydrophilicity of the peptide linker are typically designed such that it does not to disturb the functions of the monomer and molecule. Preferred flexible peptide linkers are stretches of 2 to 20, such as 4, 6, 8, 10 or 16, serine and/or glycine amino acids. More preferred flexible linkers include (SG)1, (SG)2, (SG)3, (SG)4, (SG)5 and (SG)8 wherein S is serine and G is glycine. Preferred rigid linkers are stretches of 2 to 30, such as 4, 6, 8, 16 or 24, proline amino acids. More preferred rigid linkers include (P)12 wherein P is proline.
  • The mutant monomer may be chemically modified with a molecular adaptor and a polynucleotide binding protein.
  • The reactivity of cysteine residues may be enhanced by modification of the adjacent residues. For instance, the basic groups of flanking arginine, histidine or lysine residues will change the pKa of the cysteines thiol group to that of the more reactive S− group. The reactivity of cysteine residues may be protected by thiol protective groups such as dTNB. These may be reacted with one or more cysteine residues of the monomer before a linker is attached.
  • The molecule (with which the monomer is chemically modified) may be attached directly to the monomer or attached via a linker as disclosed in International Application Nos. PCT/GB09/001690 (published as WO 2010/004273), PCT/GB09/001679 (published as WO 2010/004265) or PCT/GB10/000133 (published as WO 2010/086603).
  • Any of the proteins described herein, such as the mutant monomers and pores of the invention, may be modified to assist their identification or purification, for example by the addition of histidine residues (a his tag), aspartic acid residues (an asp tag), a streptavidin tag, a flag tag, a SUMO tag, a GST tag or a MBP tag, or by the addition of a signal sequence to promote their secretion from a cell where the polypeptide does not naturally contain such a sequence. An alternative to introducing a genetic tag is to chemically react a tag onto a native or engineered position on the protein. An example of this would be to react a gel-shift reagent to a cysteine engineered on the outside of the protein. This has been demonstrated as a method for separating hemolysin hetero-oligomers (Chem Biol. 1997 July; 4(7):497-505).
  • Any of the proteins described herein, such as the mutant monomers and pores of the invention, may be labelled with a revealing label. The revealing label may be any suitable label which allows the protein to be detected. Suitable labels include, but are not limited to, fluorescent molecules, radioisotopes e.g. 125I, 35S, enzymes, antibodies, antigens, polynucleotides and ligands such as biotin.
  • Any of the proteins described herein, such as the monomers or pores of the invention, may be made synthetically or by recombinant means. For example, the protein may be synthesized by in vitro translation and transcription (IVTT). The amino acid sequence of the protein may be modified to include non-naturally occurring amino acids or to increase the stability of the protein. When a protein is produced by synthetic means, such amino acids may be introduced during production. The protein may also be altered following either synthetic or recombinant production.
  • Proteins may also be produced using D-amino acids. For instance, the protein may comprise a mixture of L-amino acids and D-amino acids. This is conventional in the art for producing such proteins or peptides.
  • The protein may also contain other non-specific modifications as long as they do not interfere with the function of the protein. A number of non-specific side chain modifications are known in the art and may be made to the side chains of the protein(s). Such modifications include, for example, reductive alkylation of amino acids by reaction with an aldehyde followed by reduction with NaBH4, amidination with methylacetimidate or acylation with acetic anhydride.
  • Any of the proteins described herein, including the monomers and pores of the invention, can be produced using standard methods known in the art. Polynucleotide sequences encoding a protein may be derived and replicated using standard methods in the art. Polynucleotide sequences encoding a protein may be expressed in a bacterial host cell using standard techniques in the art. The protein may be produced in a cell by in situ expression of the polypeptide from a recombinant expression vector. The expression vector optionally carries an inducible promoter to control the expression of the polypeptide. These methods are described in Sambrook, J. and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • Proteins may be produced in large scale following purification by any protein liquid chromatography system from protein producing organisms or after recombinant expression. Typical protein liquid chromatography systems include FPLC, AKTA systems, the Bio-Cad system, the Bio-Rad BioLogic system and the Gilson HPLC system.
    • Constructs
  • The invention also provides a construct comprising two or more covalently attached MspA monomers, wherein at least one of the monomers is a mutant monomer of the invention. The construct of the invention retains its ability to form a pore. This may be determined as discussed above. One or more constructs of the invention may be used to form pores for characterising, such as sequencing, polynucleotides. The construct may comprise at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9 or at least 10 monomers. The construct preferably comprises two monomers. The two or more monomers may be the same or different.
  • The construct may comprise one or more monomers which are not mutant monomers of the invention. MspA mutant monomers which are non mutant monomers of the invention comprise comparative variants of SEQ ID NO: 2. At least one monomer in the construct may comprise a comparative variant of the sequence shown in SEQ ID NO: 2 which comprises D90N, D91N, D93N, D118R, D134R and E139K. At least one monomer in the construct may be any of the monomers disclosed in International Application No. PCT/GB2012/050301 (published as WO/2012/107778), including those comprising a comparative variant of the sequence shown in SEQ ID NO: 2 which comprises G75S, G77S, L88N, D90N, D91N, D93N, D118R, Q126R, D134R and E139K. A comparative variant of SEQ ID NO: 2 is at least 50% homologous to SEQ ID NO: 2 over its entire sequence based on amino acid identity. More preferably, the comparative variant may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 2 over the entire sequence.
  • At least one monomer in the construct is a mutant monomer of the invention. All of the monomers in the construct may be a mutant monomer of the invention. The mutant monomers may be the same or different. In a more preferred embodiment, the construct comprises two monomers of the invention.
  • The monomers in the construct are preferably genetically fused. Monomers are genetically fused if the whole construct is expressed from a single polynucleotide sequence. The coding sequences of the monomers may be combined in any way to form a single polynucleotide sequence encoding the construct.
  • The monomers may be genetically fused in any configuration. The monomers may be fused via their terminal amino acids. For instance, the amino terminus of the one monomer may be fused to the carboxy terminus of another monomer. The second and subsequent monomers in the construct (in the amino to carboxy direction) may comprise a methionine at their amino terminal ends (each of which is fused to the carboxy terminus of the previous monomer). For instance, if M is a monomer (without an amino terminal methionine) and mM is a monomer with an amino terminal methionine, the construct may comprise the sequence M-mM, M-mM-mM or M-mM-mM-mM. The presences of these methionines typically results from the expression of the start codons (i.e. ATGs) at the 5′ end of the polynucleotides encoding the second or subsequent monomers within the polynucleotide encoding entire construct. The first monomer in the construct (in the amino to carboxy direction) may also comprise a methionine (e.g. mM-mM, mM-mM-mM or mM-mM-mM-mM).
  • The two or more monomers may be genetically fused directly together. The monomers are preferably genetically fused using a linker. The linker may be designed to constrain the mobility of the monomers. Preferred linkers are amino acid sequences (i.e. peptide linkers). Any of the peptide linkers discussed above may be used.
  • In another preferred embodiment, the monomers are chemically fused. Two monomers are chemically fused if the two parts are chemically attached, for instance via a chemical crosslinker. Any of the chemical crosslinkers discussed above may be used. The linker may be attached to one or more cysteine residues introduced into a mutant monomer of the invention. Alternatively, the linker may be attached to a terminus of one of the monomers in the construct.
  • If a construct contains different monomers, crosslinkage of monomers to themselves may be prevented by keeping the concentration of linker in a vast excess of the monomers. Alternatively, a “lock and key” arrangement may be used in which two linkers are used. Only one end of each linker may react together to form a longer linker and the other ends of the linker each react with a different monomers. Such linkers are described in International Application No. PCT/GB10/000132 (published as WO 2010/086602).
    • Polynucleotides
  • The present invention also provides polynucleotide sequences which encode a mutant monomer of the invention. The mutant monomer may be any of those discussed above. The polynucleotide sequence preferably comprises a sequence at least 50%, 60%, 70%, 80%, 90% or 95% homologous based on nucleotide identity to the sequence of SEQ ID NO: 1 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95% nucleotide identity over a stretch of 300 or more, for example 375, 450, 525 or 600 or more, contiguous nucleotides (“hard homology”). Homology may be calculated as described above. The polynucleotide sequence may comprise a sequence that differs from SEQ ID NO: 1 on the basis of the degeneracy of the genetic code.
  • The present invention also provides polynucleotide sequences which encode any of the genetically fused constructs of the invention. The polynucleotide preferably comprises two or more variants of the sequence shown in SEQ ID NO: 1. The polynucleotide sequence preferably comprises two or more sequences having at least 50%, 60%, 70%, 80%, 90% or 95% homology to SEQ ID NO: 1 based on nucleotide identity over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95% nucleotide identity over a stretch of 600 or more, for example 750, 900, 1050 or 1200 or more, contiguous nucleotides (“hard homology”). Homology may be calculated as described above.
  • Polynucleotide sequences may be derived and replicated using standard methods in the art. Chromosomal DNA encoding wild-type Msp may be extracted from a pore producing organism, such as Mycobacterium smegmatis. The gene encoding the pore subunit may be amplified using PCR involving specific primers. The amplified sequence may then undergo site-directed mutagenesis. Suitable methods of site-directed mutagenesis are known in the art and include, for example, combine chain reaction. Polynucleotides encoding a construct of the invention can be made using well-known techniques, such as those described in Sambrook, J. and Russell, D. (2001). Molecular Cloning: A Laboratory Manual, 3rd Edition. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
  • The resulting polynucleotide sequence may then be incorporated into a recombinant replicable vector such as a cloning vector. The vector may be used to replicate the polynucleotide in a compatible host cell. Thus polynucleotide sequences may be made by introducing a polynucleotide into a replicable vector, introducing the vector into a compatible host cell, and growing the host cell under conditions which bring about replication of the vector. The vector may be recovered from the host cell. Suitable host cells for cloning of polynucleotides are known in the art and described in more detail below.
  • The polynucleotide sequence may be cloned into suitable expression vector. In an expression vector, the polynucleotide sequence is typically operably linked to a control sequence which is capable of providing for the expression of the coding sequence by the host cell. Such expression vectors can be used to express a pore subunit.
  • The term “operably linked” refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner. A control sequence “operably linked” to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences. Multiple copies of the same or different polynucleotide sequences may be introduced into the vector.
  • The expression vector may then be introduced into a suitable host cell. Thus, a mutant monomer or construct of the invention can be produced by inserting a polynucleotide sequence into an expression vector, introducing the vector into a compatible bacterial host cell, and growing the host cell under conditions which bring about expression of the polynucleotide sequence. The recombinantly-expressed monomer or construct may self-assemble into a pore in the host cell membrane. Alternatively, the recombinant pore produced in this manner may be removed from the host cell and inserted into another membrane. When producing pores comprising at least two different monomers or constructs, the different monomers or constructs may be expressed separately in different host cells as described above, removed from the host cells and assembled into a pore in a separate membrane, such as a rabbit cell membrane.
  • The vectors may be for example, plasmid, virus or phage vectors provided with an origin of replication, optionally a promoter for the expression of the said polynucleotide sequence and optionally a regulator of the promoter. The vectors may contain one or more selectable marker genes, for example a tetracycline resistance gene. Promoters and other expression regulation signals may be selected to be compatible with the host cell for which the expression vector is designed. A T7, trc, lac, ara or λL promoter is typically used.
  • The host cell typically expresses the monomer or construct at a high level. Host cells transformed with a polynucleotide sequence will be chosen to be compatible with the expression vector used to transform the cell. The host cell is typically bacterial and preferably Escherichia coli. Any cell with a λ DE3 lysogen, for example C41 (DE3), BL21 (DE3), JM109 (DE3), B834 (DE3), TUNER, Origami and Origami B, can express a vector comprising the T7 promoter. In addition to the conditions listed above any of the methods cited in Proc Natl Acad Sci USA. 2008 Dec. 30; 105(52):20647-52 may be used to express the Msp proteins.
  • The invention also comprises a method of producing a mutant monomer of the invention or a construct of the invention. The method comprises expressing a polynucleotide of the invention in a suitable host cell. The polynucleotide is preferably part of a vector and is preferably operably linked to a promoter.
    • Pores
  • The invention also provides various pores. The pores of the invention are ideal for characterising, such as sequencing, polynucleotide sequences because they can discriminate between different nucleotides with a high degree of sensitivity. The pores can surprisingly distinguish between the four nucleotides in DNA and RNA. The pores of the invention can even distinguish between methylated and unmethylated nucleotides. The base resolution of pores of the invention is surprisingly high. The pores show almost complete separation of all four DNA nucleotides. The pores further discriminate between deoxycytidine monophosphate (dCMP) and methyl-dCMP based on the dwell time in the pore and the current flowing through the pore.
  • The pores of the invention can also discriminate between different nucleotides under a range of conditions. In particular, the pores will discriminate between nucleotides under conditions that are favourable to the characterising, such as sequencing, of nucleic acids. The extent to which the pores of the invention can discriminate between different nucleotides can be controlled by altering the applied potential, the salt concentration, the buffer, the temperature and the presence of additives, such as urea, betaine and DTT. This allows the function of the pores to be fine-tuned, particularly when sequencing. This is discussed in more detail below. The pores of the invention may also be used to identify polynucleotide polymers from the interaction with one or more monomers rather than on a nucleotide by nucleotide basis.
  • A pore of the invention may be isolated, substantially isolated, purified or substantially purified. A pore of the invention is isolated or purified if it is completely free of any other components, such as lipids or other pores. A pore is substantially isolated if it is mixed with carriers or diluents which will not interfere with its intended use. For instance, a pore is substantially isolated or substantially purified if it is present in a form that comprises less than 10%, less than 5%, less than 2% or less than 1% of other components, such as triblock copolymers, lipids or other pores. Alternatively, a pore of the invention may be present in a membrane. Suitable membranes are discussed below.
  • A pore of the invention may be present as an individual or single pore. Alternatively, a pore of the invention may be present in a homologous or heterologous population of two or more pores.
    • Homo-Oligomeric Pores
  • The invention also provides a homo-oligomeric pore derived from Msp comprising identical mutant monomers of the invention. The homo-oligomeric pore may comprise any of the mutants of the invention. The homo-oligomeric pore of the invention is ideal for characterising, such as sequencing, polynucleotides. The homo-oligomeric pore of the invention may have any of the advantages discussed above.
  • The homo-oligomeric pore may contain any number of mutant monomers. The pore typically comprises at least 7, at least 8, at least 9 or at least 10 identical mutant monomers, such as 7, 8, 9 or 10 mutant monomers. The pore preferably comprises eight identical mutant monomers. One or more, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10, of the mutant monomers is preferably chemically modified as discussed above.
  • Methods for making pores are discussed in more detail below.
    • Hetero-Oligomeric Pores
  • The invention also provides a hetero-oligomeric pore derived from Msp comprising at least one mutant monomer of the invention. The hetero-oligomeric pore of the invention is ideal for characterising, such as sequencing, polynucleotides. Hetero-oligomeric pores can be made using methods known in the art (e.g. Protein Sci. 2002 July; 11(7):1813-24).
  • The hetero-oligomeric pore contains sufficient monomers to form the pore. The monomers may be of any type. The pore typically comprises at least 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9 or 10 monomers. The pore preferably comprises eight monomers.
  • In a preferred embodiment, all of the monomers (such as 10, 9, 8 or 7 of the monomers) are mutant monomers of the invention and at least one of them differs from the others. In a more preferred embodiment, the pore comprises eight mutant monomers of the invention and at least one of them differs from the others. They may all differ from one another.
  • In another preferred embodiment, at least one of the mutant monomers is not a mutant monomer of the invention. In this embodiment, the remaining monomers are preferably mutant monomers of the invention. Hence, the pore may comprise 9, 8, 7, 6, 5, 4, 3, 2 or 1 mutant monomers of the invention. Any number of the monomers in the pore may not be a mutant monomer of the invention. The pore preferably comprises seven mutant monomers of the invention and a monomer which is not a monomer of the invention, such as a monomer comprising a comparative variant as discussed above. The mutant monomers of the invention may be the same or different.
  • In all the embodiments discussed above, one or more, such as 2, 3, 4, 5, 6, 7, 8, 9 or 10, of the mutant monomers is preferably chemically modified as discussed above.
  • Methods for making pores are discussed in more detail below.
    • Construct-Containing Pores
  • The invention also provides a pore comprising at least one construct of the invention. A construct of the invention comprises two or more covalently attached monomers derived from Msp wherein at least one of the monomers is a mutant monomer of the invention. In other words, a construct must contain more than one monomer. The pore contains sufficient constructs and, if necessary, monomers to form the pore. For instance, an octameric pore may comprise (a) four constructs each comprising two constructs, (b) two constructs each comprising four monomers or (b) one construct comprising two monomers and six monomers that do not form part of a construct. Other combinations of constructs and monomers can be envisaged by the skilled person.
  • At least two of the monomers in the pore are in the form of a construct of the invention. The construct, and hence the pore, comprises at least one mutant monomer of the invention. The pore typically comprises at least 7, at least 8, at least 9 or at least 10 monomers, such as 7, 8, 9 or 10 monomers, in total (at least two of which must be in a construct). The pore preferably comprises eight monomers (at least two of which must be in a construct).
  • The construct containing pore may be a homo-oligomer (i.e. include identical constructs) or be a hetero-oligomer (i.e. where at least one construct differs from the others).
  • A pore typically contains (a) one construct comprising two monomers and (b) 5, 6, 7 or 8 monomers. The construct may be any of those discussed above. The monomers may be any of those discussed above, including mutant monomers of the invention and mutant monomers comprising a comparative variant of SEQ ID NO: 2 as discussed above.
  • Another typical pore comprises more than one construct of the invention, such as two, three or four constructs of the invention. If necessary, such pores further comprise sufficient additional monomers or constructs to form the pore. The additional monomer(s) may be any of those discussed above, including mutant monomers of the invention and mutant monomers comprising a comparative variant of SEQ ID NO: 2 as discussed above. The additional construct(s) may be any of those discussed above or may be a construct comprising two or more covalently attached MspA monomers each comprising a comparative variant of SEQ ID NO: 2 as discussed above.
  • A further pore of the invention comprises only constructs comprising 2 monomers, for example a pore may comprise 4, 5, 6, 7 or 8 constructs comprising 2 monomers. At least one construct is a construct of the invention, i.e. at least one monomer in the at least one construct, and preferably each monomer in the at least one construct, is a mutant monomer of the invention. All of the constructs comprising 2 monomers may be constructs of the invention.
  • A specific pore according to the invention comprises four constructs of the invention each comprising two monomers, wherein at least one monomer in each construct, and preferably each monomer in each construct, is a mutant monomer of the invention. The constructs may oligomerise into a pore with a structure such that only one monomer of each construct contributes to the channel of the pore. Typically the other monomers of the construct will be on the outside of the channel of the pore. For example, pores of the invention may comprise 5, 6, 7 or 8 constructs comprising 2 monomers where the channel comprises 8 monomers.
  • Mutations can be introduced into the construct as described above. The mutations may be alternating, i.e. the mutations are different for each monomer within a two monomer construct and the constructs are assembled as a homo-oligomer resulting in alternating modifications. In other words, monomers comprising MutA and MutB are fused and assembled to form an A-B:A-B:A-B:A-B pore. Alternatively, the mutations may be neighbouring, i.e. identical mutations are introduced into two monomers in a construct and this is then oligomerised with different mutant monomers or constructs. In other words, monomers comprising MutA are fused follow by oligomerisation with MutB-containing monomers to form A-A:B:B:B:B:B:B.
  • One or more of the monomers of the invention in a construct-containing pore may be chemically-modified as discussed above.
    • Polynucleotide Characterisation
  • The invention provides a method of characterising a target polynucleotide. The method involves measuring one or more characteristics of the target polynucleotide. The target polynucleotide may also be called the template polynucleotide or the polynucleotide of interest.
    • Polynucleotide
  • A polynucleotide, such as a nucleic acid, is a macromolecule comprising two or more nucleotides. The polynucleotide or nucleic acid may comprise any combination of any nucleotides. The nucleotides can be naturally occurring or artificial. One or more nucleotides in the polynucleotide can be oxidized or methylated. One or more nucleotides in the polynucleotide may be damaged. For instance, the polynucleotide may comprise a pyrimidine dimer. Such dimers are typically associated with damage by ultraviolet light and are the primary cause of skin melanomas. One or more nucleotides in the polynucleotide may be modified, for instance with a label or a tag. Suitable labels are described below. The polynucleotide may comprise one or more spacers.
  • A nucleotide typically contains a nucleobase, a sugar and at least one phosphate group. The nucleobase and sugar form a nucleoside.
  • The nucleobase is typically heterocyclic. Nucleobases include, but are not limited to, purines and pyrimidines and more specifically adenine (A), guanine (G), thymine (T), uracil (U) and cytosine (C).
  • The sugar is typically a pentose sugar. Nucleotide sugars include, but are not limited to, ribose and deoxyribose. The sugar is preferably a deoxyribose.
  • The polynucleotide preferably comprises the following nucleosides: deoxyadenosine (dA), deoxyuridine (dU) and/or thymidine (dT), deoxyguanosine (dG) and deoxycytidine (dC).
  • The nucleotide is typically a ribonucleotide or deoxyribonucleotide. The nucleotide typically contains a monophosphate, diphosphate or triphosphate. The nucleotide may comprise more than three phosphates, such as 4 or 5 phosphates. Phosphates may be attached on the 5′ or 3′ side of a nucleotide. Nucleotides include, but are not limited to, adenosine monophosphate (AMP), guanosine monophosphate (GMP), thymidine monophosphate (TMP), uridine monophosphate (UMP), 5-methylcytidine monophosphate, 5-hydroxymethylcytidine monophosphate, cytidine monophosphate (CMP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxythymidine monophosphate (dTMP), deoxyuridine monophosphate (dUMP), deoxycytidine monophosphate (dCMP) and deoxymethylcytidine monophosphate. The nucleotides are preferably selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP, dCMP and dUMP.
  • A nucleotide may be abasic (i.e. lack a nucleobase). A nucleotide may also lack a nucleobase and a sugar (i.e. is a C3 spacer).
  • The nucleotides in the polynucleotide may be attached to each other in any manner. The nucleotides are typically attached by their sugar and phosphate groups as in nucleic acids. The nucleotides may be connected via their nucleobases as in pyrimidine dimers.
  • The polynucleotide may be single stranded or double stranded. At least a portion of the polynucleotide is preferably double stranded.
  • The polynucleotide can be a nucleic acid, such as deoxyribonucleic acid (DNA) or ribonucleic acid (RNA). The polynucleotide can comprise one strand of RNA hybridised to one strand of DNA. The polynucleotide may be any synthetic nucleic acid known in the art, such as peptide nucleic acid (PNA), glycerol nucleic acid (GNA), threose nucleic acid (TNA), locked nucleic acid (LNA) or other synthetic polymers with nucleotide side chains. The PNA backbone is composed of repeating N-(2-aminoethyl)-glycine units linked by peptide bonds. The GNA backbone is composed of repeating glycol units linked by phosphodiester bonds. The TNA backbone is composed of repeating threose sugars linked together by phosphodiester bonds. LNA is formed from ribonucleotides as discussed above having an extra bridge connecting the 2′ oxygen and 4′ carbon in the ribose moiety.
  • The polynucleotide is most preferably ribonucleic nucleic acid (RNA) or deoxyribonucleic acid (DNA).
  • The polynucleotide can be any length. For example, the polynucleotide can be at least 10, at least 50, at least 100, at least 150, at least 200, at least 250, at least 300, at least 400 or at least 500 nucleotides or nucleotide pairs in length. The polynucleotide can be 1000 or more nucleotides or nucleotide pairs, 5000 or more nucleotides or nucleotide pairs in length or 100000 or more nucleotides or nucleotide pairs in length.
  • Any number of polynucleotides can be investigated. For instance, the method of the invention may concern characterising 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 50, 100 or more polynucleotides. If two or more polynucleotides are characterized, they may be different polynucleotides or two instances of the same polynucleotide.
  • The polynucleotide can be naturally occurring or artificial. For instance, the method may be used to verify the sequence of a manufactured oligonucleotide. The method is typically carried out in vitro.
    • Sample
  • Each analyte is typically present in any suitable sample. The invention is typically carried out on two or more samples that are known to contain or suspected to contain the analytes. Alternatively, the invention may be carried out on two or more samples to confirm the identity of two or more analytes whose presence in the samples is known or expected.
  • The first sample and/or second sample may be a biological sample. The invention may be carried out in vitro using at least one sample obtained from or extracted from any organism or microorganism. The first sample and/or second sample may be a non-biological sample. The non-biological sample is preferably a fluid sample. Examples of non-biological samples include surgical fluids, water such as drinking water, sea water or river water, and reagents for laboratory tests.
  • The first sample and/or second sample is typically processed prior to being used in the invention, for example by centrifugation or by passage through a membrane that filters out unwanted molecules or cells, such as red blood cells. The first sample and/or second sample may be measured immediately upon being taken. The first sample and/or second sample may also be typically stored prior to assay, preferably below −70° C.
    • Characterisation
  • The method may involve measuring two, three, four or five or more characteristics of the polynucleotide. The one or more characteristics are preferably selected from (i) the length of the polynucleotide, (ii) the identity of the polynucleotide, (iii) the sequence of the polynucleotide, (iv) the secondary structure of the polynucleotide and (v) whether or not the polynucleotide is modified. Any combination of (i) to (v) may be measured in accordance with the invention, such as {i}, {ii}, {iii}, {iv}, {v}, {i,ii}, {i,iii}, {i,iv}, {i,v}, {ii,iii}, {ii,iv}, {ii,v}, {iii,iv}, {iii,v}, {iv,v}, {i,ii,iv}, {i,ii,v}, {i,iii,iv}, {i,iii,v}, {i,iv,v}, {ii,iii,iv}, {ii,iii,v}, {ii,iv,v}, {iii,iv,v}, {i,ii,iii,iv}, {i,ii,iii,v}, {i,ii,iv,v}, {i,iii,iv,v}, {ii,iii,iv,v} or {i,ii,iii,iv,v}. Different combinations of (i) to (v) may be measured for the first polynucleotide compared with the second polynucleotide, including any of those combinations listed above.
  • For (i), the length of the polynucleotide may be measured for example by determining the number of interactions between the polynucleotide and the pore or the duration of interaction between the polynucleotide and the pore.
  • For (ii), the identity of the polynucleotide may be measured in a number of ways. The identity of the polynucleotide may be measured in conjunction with measurement of the sequence of the polynucleotide or without measurement of the sequence of the polynucleotide. The former is straightforward; the polynucleotide is sequenced and thereby identified. The latter may be done in several ways. For instance, the presence of a particular motif in the polynucleotide may be measured (without measuring the remaining sequence of the polynucleotide). Alternatively, the measurement of a particular electrical and/or optical signal in the method may identify the polynucleotide as coming from a particular source.
  • For (iii), the sequence of the polynucleotide can be determined as described previously. Suitable sequencing methods, particularly those using electrical measurements, are described in Stoddart D et al., Proc Natl Acad Sci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc. 2010; 132(50):17961-72, and International Application WO 2000/28312.
  • For (iv), the secondary structure may be measured in a variety of ways. For instance, if the method involves an electrical measurement, the secondary structure may be measured using a change in dwell time or a change in current flowing through the pore. This allows regions of single-stranded and double-stranded polynucleotide to be distinguished.
  • For (v), the presence or absence of any modification may be measured. The method preferably comprises determining whether or not the polynucleotide is modified by methylation, by oxidation, by damage, with one or more proteins or with one or more labels, tags or spacers. Specific modifications will result in specific interactions with the pore which can be measured using the methods described below. For instance, methylcyotsine may be distinguished from cytosine on the basis of the current flowing through the pore during its interaction with each nucleotide.
  • The target polynucleotide is contacted with a pore of the invention. The pore is typically present in a membrane. Suitable membranes are discussed below. The method may be carried out using any apparatus that is suitable for investigating a membrane/pore system in which a pore is present in a membrane. The method may be carried out using any apparatus that is suitable for transmembrane pore sensing. For example, the apparatus comprises a chamber comprising an aqueous solution and a barrier that separates the chamber into two sections. The barrier typically has an aperture in which the membrane containing the pore is formed. Alternatively the barrier forms the membrane in which the pore is present.
  • The method may be carried out using the apparatus described in International Application No. PCT/GB08/000562 (WO 2008/102120).
  • A variety of different types of measurements may be made. This includes without limitation: electrical measurements and optical measurements. Possible electrical measurements include: current measurements, impedance measurements, tunnelling measurements (Ivanov A P et al., Nano Lett. 2011 Jan. 12; 11(1):279-85), and FET measurements (International Application WO 2005/124888). Optical measurements may be combined with electrical measurements (Soni G V et al., Rev Sci Instrum. 2010 January; 81(1):014301). The measurement may be a transmembrane current measurement such as measurement of ionic current flowing through the pore.
  • Electrical measurements may be made using standard single channel recording equipment as describe in Stoddart D et al., Proc Natl Acad Sci, 12; 106(19):7702-7, Lieberman K R et al, J Am Chem Soc. 2010; 132(50):17961-72, and International Application WO 2000/28312. Alternatively, electrical measurements may be made using a multi-channel system, for example as described in International Application WO 2009/077734 and International Application WO 2011/067559.
  • The method is preferably carried out with a potential applied across the membrane. The applied potential may be a voltage potential. Alternatively, the applied potential may be a chemical potential. An example of this is using a salt gradient across a membrane, such as an amphiphilic layer. A salt gradient is disclosed in Holden et al., J Am Chem Soc. 2007 Jul. 11; 129(27):8650-5. In some instances, the current passing through the pore as a polynucleotide moves with respect to the pore is used to estimate or determine the sequence of the polynucleotide. This is strand sequencing.
  • The method may involve measuring the current passing through the pore as the polynucleotide moves with respect to the pore. Therefore the apparatus used in the method may also comprise an electrical circuit capable of applying a potential and measuring an electrical signal across the membrane and pore. The methods may be carried out using a patch clamp or a voltage clamp. The methods preferably involve the use of a voltage clamp.
  • The method of the invention may involve the measuring of a current passing through the pore as the polynucleotide moves with respect to the pore. Suitable conditions for measuring ionic currents through transmembrane protein pores are known in the art and disclosed in the Example. The method is typically carried out with a voltage applied across the membrane and pore. The voltage used is typically from +5 V to −5 V, such as from +4 V to −4 V, +3 V to −3 V or +2 V to −2 V. The voltage used is typically from −600 mV to +600 mV or −400 mV to +400 mV. The voltage used is preferably in a range having a lower limit selected from −400 mV, −300 mV, −200 mV, −150 mV, −100 mV, −50 mV, −20 mV and 0 mV and an upper limit independently selected from +10 mV, +20 mV, +50 mV, +100 mV, +150 mV, +200 mV, +300 mV and +400 mV. The voltage used is more preferably in the range 100 mV to 240 mV and most preferably in the range of 120 mV to 220 mV. It is possible to increase discrimination between different nucleotides by a pore by using an increased applied potential.
  • The method is typically carried out in the presence of any charge carriers, such as metal salts, for example alkali metal salt, halide salts, for example chloride salts, such as alkali metal chloride salt. Charge carriers may include ionic liquids or organic salts, for example tetramethyl ammonium chloride, trimethylphenyl ammonium chloride, phenyltrimethyl ammonium chloride, or 1-ethyl-3-methyl imidazolium chloride. In the exemplary apparatus discussed above, the salt is present in the aqueous solution in the chamber. Potassium chloride (KCl), sodium chloride (NaCl), caesium chloride (CsCl) or a mixture of potassium ferrocyanide and potassium ferricyanide is typically used. KCl, NaCl and a mixture of potassium ferrocyanide and potassium ferricyanide are preferred. The charge carriers may be asymmetric across the membrane. For instance, the type and/or concentration of the charge carriers may be different on each side of the membrane.
  • The salt concentration may be at saturation. The salt concentration may be 3 M or lower and is typically from 0.1 to 2.5 M, from 0.3 to 1.9 M, from 0.5 to 1.8 M, from 0.7 to 1.7 M, from 0.9 to 1.6 M or from 1 M to 1.4 M. The salt concentration is preferably from 150 mM to 1 M. The method is preferably carried out using a salt concentration of at least 0.3 M, such as at least 0.4 M, at least 0.5 M, at least 0.6 M, at least 0.8 M, at least 1.0 M, at least 1.5 M, at least 2.0 M, at least 2.5 M or at least 3.0 M. High salt concentrations provide a high signal to noise ratio and allow for currents indicative of the presence of a nucleotide to be identified against the background of normal current fluctuations.
  • The method is typically carried out in the presence of a buffer. In the exemplary apparatus discussed above, the buffer is present in the aqueous solution in the chamber. Any buffer may be used in the method of the invention. Typically, the buffer is phosphate buffer. Other suitable buffers are HEPES and Tris-HCl buffer. The methods are typically carried out at a pH of from 4.0 to 12.0, from 4.5 to 10.0, from 5.0 to 9.0, from 5.5 to 8.8, from 6.0 to 8.7 or from 7.0 to 8.8 or 7.5 to 8.5. The pH used is preferably about 7.5.
  • The method may be carried out at from 0° C. to 100° C., from 15° C. to 95° C., from 16° C. to 90° C., from 17° C. to 85° C., from 18° C. to 80° C., 19° C. to 70° C., or from 20° C. to 60° C. The methods are typically carried out at room temperature. The methods are optionally carried out at a temperature that supports enzyme function, such as about 37° C.
    • Polynucleotide Binding Protein
  • Step (a) preferably comprises contacting the polynucleotide with a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore.
  • More preferably, the method comprises (a) contacting the polynucleotide with the pore of the invention and a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore and (b) taking one or more measurements as the polynucleotide moves with respect to the pore, wherein the measurements are indicative of one or more characteristics of the polynucleotide, and thereby characterising the polynucleotide.
  • More preferably, the method comprises (a) contacting the polynucleotide with the pore of the invention and a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore and (b) measuring the current through the pore as the polynucleotide moves with respect to the pore, wherein the current is indicative of one or more characteristics of the polynucleotide, and thereby characterising the polynucleotide.
  • The polynucleotide binding protein may be any protein that is capable of binding to the polynucleotide and controlling its movement through the pore. It is straightforward in the art to determine whether or not a protein binds to a polynucleotide. The protein typically interacts with and modifies at least one property of the polynucleotide. The protein may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides. The protein may modify the polynucleotide by orienting it or moving it to a specific position, i.e. controlling its movement.
  • The polynucleotide binding protein is preferably derived from a polynucleotide handling enzyme. A polynucleotide handling enzyme is a polypeptide that is capable of interacting with and modifying at least one property of a polynucleotide. The enzyme may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides. The enzyme may modify the polynucleotide by orienting it or moving it to a specific position. The polynucleotide handling enzyme does not need to display enzymatic activity as long as it is capable of binding the polynucleotide and controlling its movement through the pore. For instance, the enzyme may be modified to remove its enzymatic activity or may be used under conditions which prevent it from acting as an enzyme. Such conditions are discussed in more detail below.
  • The polynucleotide handling enzyme is preferably derived from a nucleolytic enzyme. The polynucleotide handling enzyme used in the construct of the enzyme is more preferably derived from a member of any of the Enzyme Classification (EC) groups 3.1.11, 3.1.13, 3.1.14, 3.1.15, 3.1.16, 3.1.21, 3.1.22, 3.1.25, 3.1.26, 3.1.27, 3.1.30 and 3.1.31. The enzyme may be any of those disclosed in International Application No. PCT/GB10/000133 (published as WO 2010/086603).
  • Preferred enzymes are polymerases, exonucleases, helicases and topoisomerases, such as gyrases. Suitable enzymes include, but are not limited to, exonuclease I from E. coli (SEQ ID NO: 11), exonuclease III enzyme from E. coli (SEQ ID NO: 13), RecJ from T. thermophilus (SEQ ID NO: 15) and bacteriophage lambda exonuclease (SEQ ID NO: 17) and variants thereof. Three subunits comprising the sequence shown in SEQ ID NO: 15 or a variant thereof interact to form a trimer exonuclease. The enzyme is preferably Phi29 DNA polymerase (SEQ ID NO: 9) or a variant thereof. The topoisomerase is preferably a member of any of the Moiety Classification (EC) groups 5.99.1.2 and 5.99.1.3.
  • The enzyme is most preferably derived from a helicase, such as Hel308 Mbu (SEQ ID NO: 18), Hel308 Csy (SEQ ID NO: 19), Hel308 Mhu (SEQ ID NO: 21), TraI Eco (SEQ ID NO: 22), XPD Mbu (SEQ ID NO: 23) or a variant thereof. Any helicase may be used in the invention. The helicase may be or be derived from a Hel308 helicase, a RecD helicase, such as TraI helicase or a TrwC helicase, a XPD helicase or a Dda helicase. The helicase may be any of the helicases, modified helicases or helicase constructs disclosed in International Application Nos. PCT/GB2012/052579 (published as WO 2013/057495); PCT/GB2012/053274 (published as WO 2013/098562); PCT/GB2012/053273 (published as WO2013098561); PCT/GB2013/051925 (published as WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259) and PCT/GB2013/051928 (published as WO 2014/013262); and in PCT/GB2014/052736 (published as WO/2015/055981).
  • The helicase preferably comprises the sequence shown in SEQ ID NO: 25 (Trwc Cba) or as variant thereof, the sequence shown in SEQ ID NO: 18 (Hel308 Mbu) or a variant thereof or the sequence shown in SEQ ID NO: 24 (Dda) or a variant thereof. Variants may differ from the native sequences in any of the ways discussed below for transmembrane pores. A preferred variant of SEQ ID NO: 8 comprises E94C/A360C and then (ΔM1)G1G2 (i.e. deletion of M1 and then addition G1 and G2).
  • Any number of helicases may be used in accordance with the invention. For instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may be used. In some embodiments, different numbers of helicases may be used.
  • The method of the invention preferably comprises contacting the polynucleotide with two or more helicases. The two or more helicases are typically the same helicase. The two or more helicases may be different helicases.
  • The two or more helicases may be any combination of the helicases mentioned above. The two or more helicases may be two or more Dda helicases. The two or more helicases may be one or more Dda helicases and one or more TrwC helicases. The two or more helicases may be different variants of the same helicase.
  • The two or more helicases are preferably attached to one another. The two or more helicases are more preferably covalently attached to one another. The helicases may be attached in any order and using any method. Preferred helicase constructs for use in the invention are described in International Application Nos. PCT/GB2013/051925 (published as WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259) and PCT/GB2013/051928 (published as WO 2014/013262); and in PCT/GB2014/052736 (published as WO/2015/055981).
  • A variant of SEQ ID NOs: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 is an enzyme that has an amino acid sequence which varies from that of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 and which retains polynucleotide binding ability. This can be measured using any method known in the art. For instance, the variant can be contacted with a polynucleotide and its ability to bind to and move along the polynucleotide can be measured. The variant may include modifications that facilitate binding of the polynucleotide and/or facilitate its activity at high salt concentrations and/or room temperature. Variants may be modified such that they bind polynucleotides (i.e. retain polynucleotide binding ability) but do not function as a helicase (i.e. do not move along polynucleotides when provided with all the necessary components to facilitate movement, e.g. ATP and Mg2+). Such modifications are known in the art. For instance, modification of the Mg2+ binding domain in helicases typically results in variants which do not function as helicases. These types of variants may act as molecular brakes (see below).
  • Over the entire length of the amino acid sequence of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25, a variant will preferably be at least 50% homologous to that sequence based on amino acid identity. More preferably, the variant polypeptide may be at least 55%, at least 60%, at least 65%, at least 70%, at least 75%, at least 80%, at least 85%, at least 90% and more preferably at least 95%, 97% or 99% homologous based on amino acid identity to the amino acid sequence of SEQ ID NO: 9, 11, 13, 15, 17, 18, 19, 20, 21, 22, 23, 24 or 25 over the entire sequence. There may be at least 80%, for example at least 85%, 90% or 95%, amino acid identity over a stretch of 200 or more, for example 230, 250, 270, 280, 300, 400, 500, 600, 700, 800, 900 or 1000 or more, contiguous amino acids (“hard homology”). Homology is determined as described above. The variant may differ from the wild-type sequence in any of the ways discussed above with reference to SEQ ID NO: 2 and 4 above. The enzyme may be covalently attached to the pore. Any method may be used to covalently attach the enzyme to the pore.
  • A preferred molecular brake is TrwC Cba-Q594A (SEQ ID NO: 25 with the mutation Q594A). This variant does not function as a helicase (i.e. binds polynucleotides but does not move along them when provided with all the necessary components to facilitate movement, e.g. ATP and Mg2+).
  • In strand sequencing, the polynucleotide is translocated through the pore either with or against an applied potential. Exonucleases that act progressively or processively on double stranded polynucleotides can be used on the cis side of the pore to feed the remaining single strand through under an applied potential or the trans side under a reverse potential. Likewise, a helicase that unwinds the double stranded DNA can also be used in a similar manner. A polymerase may also be used. There are also possibilities for sequencing applications that require strand translocation against an applied potential, but the DNA must be first “caught” by the enzyme under a reverse or no potential. With the potential then switched back following binding the strand will pass cis to trans through the pore and be held in an extended conformation by the current flow. The single strand DNA exonucleases or single strand DNA dependent polymerases can act as molecular motors to pull the recently translocated single strand back through the pore in a controlled stepwise manner, trans to cis, against the applied potential.
  • Any helicase may be used in the method. Helicases may work in two modes with respect to the pore. First, the method is preferably carried out using a helicase such that it moves the polynucleotide through the pore with the field resulting from the applied voltage. In this mode the 5′ end of the polynucleotide is first captured in the pore, and the helicase moves the polynucleotide into the pore such that it is passed through the pore with the field until it finally translocates through to the trans side of the membrane. Alternatively, the method is preferably carried out such that a helicase moves the polynucleotide through the pore against the field resulting from the applied voltage. In this mode the 3′ end of the polynucleotide is first captured in the pore, and the helicase moves the polynucleotide through the pore such that it is pulled out of the pore against the applied field until finally ejected back to the cis side of the membrane.
  • The method may also be carried out in the opposite direction. The 3′ end of the polynucleotide may be first captured in the pore and the helicase may move the polynucleotide into the pore such that it is passed through the pore with the field until it finally translocates through to the trans side of the membrane.
  • When the helicase is not provided with the necessary components to facilitate movement or is modified to hinder or prevent its movement, it can bind to the polynucleotide and act as a brake slowing the movement of the polynucleotide when it is pulled into the pore by the applied field. In the inactive mode, it does not matter whether the polynucleotide is captured either 3′ or 5′ down, it is the applied field which pulls the polynucleotide into the pore towards the trans side with the enzyme acting as a brake. When in the inactive mode, the movement control of the polynucleotide by the helicase can be described in a number of ways including ratcheting, sliding and braking. Helicase variants which lack helicase activity can also be used in this way.
  • The polynucleotide may be contacted with the polynucleotide binding protein and the pore in any order. It is preferred that, when the polynucleotide is contacted with the polynucleotide binding protein, such as a helicase, and the pore, the polynucleotide firstly forms a complex with the protein. When the voltage is applied across the pore, the polynucleotide/protein complex then forms a complex with the pore and controls the movement of the polynucleotide through the pore.
  • Any steps in the method using a polynucleotide binding protein are typically carried out in the presence of free nucleotides or free nucleotide analogues and an enzyme cofactor that facilitates the action of the polynucleotide binding protein. The free nucleotides may be one or more of any of the individual nucleotides discussed above. The free nucleotides include, but are not limited to, adenosine monophosphate (AMP), adenosine diphosphate (ADP), adenosine triphosphate (ATP), guanosine monophosphate (GMP), guanosine diphosphate (GDP), guanosine triphosphate (GTP), thymidine monophosphate (TMP), thymidine diphosphate (TDP), thymidine triphosphate (TTP), uridine monophosphate (UMP), uridine diphosphate (UDP), uridine triphosphate (UTP), cytidine monophosphate (CMP), cytidine diphosphate (CDP), cytidine triphosphate (CTP), cyclic adenosine monophosphate (cAMP), cyclic guanosine monophosphate (cGMP), deoxyadenosine monophosphate (dAMP), deoxyadenosine diphosphate (dADP), deoxyadenosine triphosphate (dATP), deoxyguanosine monophosphate (dGMP), deoxyguanosine diphosphate (dGDP), deoxyguanosine triphosphate (dGTP), deoxythymidine monophosphate (dTMP), deoxythymidine diphosphate (dTDP), deoxythymidine triphosphate (dTTP), deoxyuridine monophosphate (dUMP), deoxyuridine diphosphate (dUDP), deoxyuridine triphosphate (dUTP), deoxycytidine monophosphate (dCMP), deoxycytidine diphosphate (dCDP) and deoxycytidine triphosphate (dCTP). The free nucleotides are preferably selected from AMP, TMP, GMP, CMP, UMP, dAMP, dTMP, dGMP or dCMP. The free nucleotides are preferably adenosine triphosphate (ATP). The enzyme cofactor is a factor that allows the construct to function. The enzyme cofactor is preferably a divalent metal cation. The divalent metal cation is preferably Mg2+, Mn2+, Ca2+ or Co2+. The enzyme cofactor is most preferably Mg2+.
    • Helicase(s) and Molecular Brake(s)
  • In a preferred embodiment, the method comprises:
      • (a) providing the polynucleotide with one or more helicases and one or more molecular brakes attached to the polynucleotide;
      • (b) contacting the polynucleotide with a pore of the invention and applying a potential across the pore such that the one or more helicases and the one or more molecular brakes are brought together and both control the movement of the polynucleotide through the pore;
      • (c) taking one or more measurements as the polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the polynucleotide and thereby characterising the polynucleotide. This type of method is discussed in detail in International Application No. PCT/GB2014/052737.
  • The one or more helicases may be any of those discussed above. The one or more molecular brakes may be any compound or molecule which binds to the polynucleotide and slow the movement of the polynucleotide through the pore. The one or more molecular brakes preferably comprise one or more compounds which bind to the polynucleotide. The one or more compounds are preferably one or more macrocycles. Suitable macrocycles include, but are not limited to, cyclodextrins, calixarenes, cyclic peptides, crown ethers, cucurbiturils, pillararenes, derivatives thereof or a combination thereof. The cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am. Chem. Soc. 116, 6081-6088. The agent is more preferably heptakis-6-amino-β-cyclodextrin (am7-βCD), 6-monodeoxy-6-monoamino-β-cyclodextrin (am1-βCD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu7-βCD).
  • The one or more molecular brakes are preferably not one or more single stranded binding proteins (SSB). The one or more molecular brakes are more preferably not a single-stranded binding protein (SSB) comprising a carboxy-terminal (C-terminal) region which does not have a net negative charge or (ii) a modified SSB comprising one or more modifications in its C-terminal region which decreases the net negative charge of the C-terminal region. The one or more molecular brakes are most preferably not any of the SSBs disclosed in International Application No. PCT/GB2013/051924 (published as WO 2014/013259).
  • The one or more molecular brakes are preferably one or more polynucleotide binding proteins. The polynucleotide binding protein may be any protein that is capable of binding to the polynucleotide and controlling its movement through the pore. It is straightforward in the art to determine whether or not a protein binds to a polynucleotide. The protein typically interacts with and modifies at least one property of the polynucleotide. The protein may modify the polynucleotide by cleaving it to form individual nucleotides or shorter chains of nucleotides, such as di- or trinucleotides. The moiety may modify the polynucleotide by orienting it or moving it to a specific position, i.e. controlling its movement.
  • The polynucleotide binding protein is preferably derived from a polynucleotide handling enzyme. The one or more molecular brakes may be derived from any of the polynucleotide handling enzymes discussed above. Modified versions of Phi29 polymerase (SEQ ID NO: 8) which act as molecular brakes are disclosed in U.S. Pat. No. 5,576,204. The one or more molecular brakes are preferably derived from a helicase.
  • Any number of molecular brakes derived from a helicase may be used. For instance, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more helicases may be used as molecular brakes. If two or more helicases are be used as molecular brakes, the two or more helicases are typically the same helicase. The two or more helicases may be different helicases.
  • The two or more helicases may be any combination of the helicases mentioned above. The two or more helicases may be two or more Dda helicases. The two or more helicases may be one or more Dda helicases and one or more TrwC helicases. The two or more helicases may be different variants of the same helicase.
  • The two or more helicases are preferably attached to one another. The two or more helicases are more preferably covalently attached to one another. The helicases may be attached in any order and using any method. The one or more molecular brakes derived from helicases are preferably modified to reduce the size of an opening in the polynucleotide binding domain through which in at least one conformational state the polynucleotide can unbind from the helicase. This is disclosed in WO 2014/013260.
  • Preferred helicase constructs for use in the invention are described in International Application Nos. PCT/GB2013/051925 (published as WO 2014/013260); PCT/GB2013/051924 (published as WO 2014/013259) and PCT/GB2013/051928 (published as WO 2014/013262); and in PCT/GB2014/052736 (published as WO/2015/055981).
    • Spacers
  • The one or more helicases may be stalled at one or more spacers as discussed in International Application No. PCT/GB2014/050175. Any configuration of one or more helicases and one or more spacers disclosed in the International Application may be used in this invention.
    • Membrane
  • The pore of the invention may be present in a membrane. In the method of the invention, the polynucleotide is typically contacted with the pore of the invention in a membrane. Any membrane may be used in accordance with the invention. Suitable membranes are well-known in the art. The membrane is preferably an amphiphilic layer. An amphiphilic layer is a layer formed from amphiphilic molecules, such as phospholipids, which have both hydrophilic and lipophilic properties. The amphiphilic molecules may be synthetic or naturally occurring. Non-naturally occurring amphiphiles and amphiphiles which form a monolayer are known in the art and include, for example, block copolymers (Gonzalez-Perez et al., Langmuir, 2009, 25, 10447-10450). Block copolymers are polymeric materials in which two or more monomer sub-units that are polymerized together to create a single polymer chain. Block copolymers typically have properties that are contributed by each monomer sub-unit. However, a block copolymer may have unique properties that polymers formed from the individual sub-units do not possess. Block copolymers can be engineered such that one of the monomer sub-units is hydrophobic (i.e. lipophilic), whilst the other sub-unit(s) are hydrophilic whilst in aqueous media. In this case, the block copolymer may possess amphiphilic properties and may form a structure that mimics a biological membrane. The block copolymer may be a diblock (consisting of two monomer sub-units), but may also be constructed from more than two monomer sub-units to form more complex arrangements that behave as amphipiles. The copolymer may be a triblock, tetrablock or pentablock copolymer. The membrane is preferably a triblock copolymer membrane.
  • Archaebacterial bipolar tetraether lipids are naturally occurring lipids that are constructed such that the lipid forms a monolayer membrane. These lipids are generally found in extremophiles that survive in harsh biological environments, thermophiles, halophiles and acidophiles. Their stability is believed to derive from the fused nature of the final bilayer. It is straightforward to construct block copolymer materials that mimic these biological entities by creating a triblock polymer that has the general motif hydrophilic-hydrophobic-hydrophilic. This material may form monomeric membranes that behave similarly to lipid bilayers and encompass a range of phase behaviours from vesicles through to laminar membranes. Membranes formed from these triblock copolymers hold several advantages over biological lipid membranes. Because the triblock copolymer is synthesized, the exact construction can be carefully controlled to provide the correct chain lengths and properties required to form membranes and to interact with pores and other proteins.
  • Block copolymers may also be constructed from sub-units that are not classed as lipid sub-materials; for example a hydrophobic polymer may be made from siloxane or other non-hydrocarbon based monomers. The hydrophilic sub-section of block copolymer can also possess low protein binding properties, which allows the creation of a membrane that is highly resistant when exposed to raw biological samples. This head group unit may also be derived from non-classical lipid head-groups.
  • Triblock copolymer membranes also have increased mechanical and environmental stability compared with biological lipid membranes, for example a much higher operational temperature or pH range. The synthetic nature of the block copolymers provides a platform to customize polymer based membranes for a wide range of applications.
  • The membrane is most preferably one of the membranes disclosed in International Application No. PCT/GB2013/052766 or PCT/GB2013/052767.
  • The amphiphilic molecules may be chemically-modified or functionalised to facilitate coupling of the polynucleotide.
  • The amphiphilic layer may be a monolayer or a bilayer. The amphiphilic layer is typically planar. The amphiphilic layer may be curved. The amphiphilic layer may be supported.
  • Amphiphilic membranes are typically naturally mobile, essentially acting as two dimensional fluids with lipid diffusion rates of approximately 108 cm s-1. This means that the pore and coupled polynucleotide can typically move within an amphiphilic membrane.
  • The membrane may be a lipid bilayer. Lipid bilayers are models of cell membranes and serve as excellent platforms for a range of experimental studies. For example, lipid bilayers can be used for in vitro investigation of membrane proteins by single-channel recording. Alternatively, lipid bilayers can be used as biosensors to detect the presence of a range of substances. The lipid bilayer may be any lipid bilayer. Suitable lipid bilayers include, but are not limited to, a planar lipid bilayer, a supported bilayer or a liposome. The lipid bilayer is preferably a planar lipid bilayer. Suitable lipid bilayers are disclosed in International Application No. PCT/GB08/000563 (published as WO 2008/102121), International Application No. PCT/GB08/004127 (published as WO 2009/077734) and International Application No. PCT/GB2006/001057 (published as WO 2006/100484).
    • Coupling
  • The polynucleotide is preferably coupled to the membrane comprising the pore of the invention. The method may comprise coupling the polynucleotide to the membrane comprising the pore of the invention. The polynucleotide is preferably coupled to the membrane using one or more anchors. The polynucleotide may be coupled to the membrane using any known method.
  • Each anchor comprises a group which couples (or binds) to the polynucleotide and a group which couples (or binds) to the membrane. Each anchor may covalently couple (or bind) to the polynucleotide and/or the membrane. If a Y adaptor and/or a hairpin loop adaptors are used, the polynucleotide is preferably coupled to the membrane using the adaptor(s).
  • The polynucleotide may be coupled to the membrane using any number of anchors, such as 2, 3, 4 or more anchors. For instance, a polynucleotide may be coupled to the membrane using two anchors each of which separately couples (or binds) to both the polynucleotide and membrane.
  • The one or more anchors may comprise the one or more helicases and/or the one or more molecular brakes.
  • If the membrane is an amphiphilic layer, such as a copolymer membrane or a lipid bilayer, the one or more anchors preferably comprise a polypeptide anchor present in the membrane and/or a hydrophobic anchor present in the membrane. The hydrophobic anchor is preferably a lipid, fatty acid, sterol, carbon nanotube, polypeptide, protein or amino acid, for example cholesterol, palmitate or tocopherol. In preferred embodiments, the one or more anchors are not the pore.
  • The components of the membrane, such as the amphiphilic molecules, copolymer or lipids, may be chemically-modified or functionalised to form the one or more anchors. Examples of suitable chemical modifications and suitable ways of functionalising the components of the membrane are discussed in more detail below. Any proportion of the membrane components may be functionalized, for example at least 0.01%, at least 0.1%, at least 1%, at least 10%, at least 25%, at least 50% or 100%.
  • The polynucleotide may be coupled directly to the membrane. The one or more anchors used to couple the polynucleotide to the membrane preferably comprise a linker. The one or more anchors may comprise one or more, such as 2, 3, 4 or more, linkers. One linker may be used couple more than one, such as 2, 3, 4 or more, polynucleotides to the membrane.
  • Preferred linkers include, but are not limited to, polymers, such as polynucleotides, polyethylene glycols (PEGs), polysaccharides and polypeptides. These linkers may be linear, branched or circular. For instance, the linker may be a circular polynucleotide. The polynucleotide may hybridise to a complementary sequence on the circular polynucleotide linker.
  • The coupling may be permanent or stable. In other words, the coupling may be such that the polynucleotide remains coupled to the membrane when interacting with the pore.
  • The coupling may be transient. In other words, the coupling may be such that the polynucleotide may decouple from the membrane when interacting with the pore.
  • Coupling of polynucleotides to a linker or to a functionalised membrane can also be achieved by a number of other means provided that a complementary reactive group or an anchoring group can be added to the polynucleotide. The addition of reactive groups to either end of a polynucleotide has been reported previously. The one or more anchors preferably couple the polynucleotide to the membrane via hybridisation. Hybridisation in the one or more anchors allows coupling in a transient manner as discussed above. The one or more anchors may comprise a single stranded or double stranded polynucleotide. One part of the anchor may be ligated to a single stranded or double stranded polynucleotide. Ligation of short pieces of ssDNA have been reported using T4 RNA ligase I (Troutt, A. B., M. G. McHeyzer-Williams, et al. (1992). “Ligation-anchored PCR: a simple amplification technique with single-sided specificity.” Proc Natl Acad Sci USA 89(20): 9823-5). Alternatively, either a single stranded or double stranded polynucleotide can be ligated to a double stranded polynucleotide and then the two strands separated by thermal or chemical denaturation. If the polynucleotide is a synthetic strand, the one or more anchors can be incorporated during the chemical synthesis of the polynucleotide. For instance, the polynucleotide can be synthesised using a primer having a reactive group attached to it.
  • Ideally, the polynucleotide is coupled to the membrane without having to functionalise the polynucleotide. This can be achieved by coupling the one or more anchors, such as a polynucleotide binding protein or a chemical group, to the membrane and allowing the one or more anchors to interact with the polynucleotide or by functionalizing the membrane. The one or more anchors may be coupled to the membrane by any of the methods described herein. In particular, the one or more anchors may comprise one or more linkers, such as maleimide functionalised linkers.
  • In this embodiment, the polynucleotide is typically RNA, DNA, PNA, TNA or LNA and may be double or single stranded. This embodiment is particularly suited to genomic DNA polynucleotides.
  • Where the one or more anchors comprise a protein, they may be able to anchor directly into the membrane without further functonalisation, for example if it already has an external hydrophobic region which is compatible with the membrane. Examples of such proteins include, but are not limited to, transmembrane proteins, intramembrane proteins and membrane proteins.
  • According to a preferred embodiment, the one or more anchors may be used to couple a polynucleotide to the membrane when the polynucleotide is attached to a leader sequence which preferentially threads into the pore. Leader sequences are discussed in more detail below. Preferably, the polynucleotide is attached (such as ligated) to a leader sequence which preferentially threads into the pore. Such a leader sequence may comprise a homopolymeric polynucleotide or an abasic region. The leader sequence is typically designed to hybridise to the one or more anchors either directly or via one or more intermediate polynucleotides (or splints). In such instances, the one or more anchors typically comprise a polynucleotide sequence which is complementary to a sequence in the leader sequence or a sequence in the one or more intermediate polynucleotides (or splints). In such instances, the one or more splints typically comprise a polynucleotide sequence which is complementary to a sequence in the leader sequence.
    • Double Stranded Polynucleotide
  • The polynucleotide may be double stranded. If the polynucleotide is double stranded, the method preferably further comprises before the contacting step ligating a hairpin adaptor to one end of the polynucleotide. The two strands of the polynucleotide may then be separated as or before the polynucleotide is contacted with the pore in accordance with the invention. The two strands may be separated as the polynucleotide movement through the pore is controlled by a polynucleotide binding protein, such as a helicase, or molecular brake. This is described in International Application No. PCT/GB2012/051786 (published as WO 2013/014451). Linking and interrogating both strands on a double stranded construct in this way increases the efficiency and accuracy of characterization.
    • Round the Corner Sequencing
  • In a preferred embodiment, a target double stranded polynucleotide is provided with a hairpin loop adaptor at one end and the method comprises contacting the polynucleotide with the pore of the invention such that both strands of the polynucleotide move through the pore and taking one or more measurements as the both strands of the polynucleotide move with respect to the pore wherein the measurements are indicative of one or more characteristics of the strands of the polynucleotide and thereby characterising the target double stranded polynucleotide. Any of the embodiments discussed above equally apply to this embodiment.
    • Leader Sequence
  • Before the contacting step, the method preferably comprises attaching to the polynucleotide a leader sequence which preferentially threads into the pore. The leader sequence facilitates the method of the invention. The leader sequence is designed to preferentially thread into the pore of the invention and thereby facilitate the movement of polynucleotide through the pore. The leader sequence can also be used to link the polynucleotide to the one or more anchors as discussed above.
    • Double Coupling
  • The method of the invention may involve double coupling of a double stranded polynucleotide. In a preferred embodiment, the method of the invention comprises:
  • (a) providing the double stranded polynucleotide with a Y adaptor at one end and a hairpin loop adaptor at the other end, wherein the Y adaptor comprises one or more first anchors for coupling the polynucleotide to the membrane, wherein the hairpin loop adaptor comprises one or more second anchors for coupling the polynucleotide to the membrane and wherein the strength of coupling of the hairpin loop adaptor to the membrane is greater than the strength of coupling of the Y adaptor to the membrane;
  • (b) contacting the polynucleotide provided in step (a) with the pore the invention such that the polynucleotide moves through the pore; and
  • (c) taking one or more measurements as the polynucleotide moves with respect to the pore, wherein the measurements are indicative of one or more characteristics of the polynucleotide, and thereby characterising the target polynucleotide. This type of method is discussed in detail in International Application No. PCT/GB2015/050991.
    • Adding Hairpin Loops and Leader Sequences
  • Before provision, a double stranded polynucleotide may be contacted with a MuA transposase and a population of double stranded MuA substrates, wherein a proportion of the substrates in the population are Y adaptors comprising the leader sequence and wherein a proportion of the substrates in the population are hairpin loop adaptors. The transposase fragments the double stranded polynucleotide analyte and ligates MuA substrates to one or both ends of the fragments. This produces a plurality of modified double stranded polynucleotides comprising the leader sequence at one end and the hairpin loop at the other. The modified double stranded polynucleotides may then be investigated using the method of the invention. These MuA based methods are disclosed in International Application No. PCT/GB2014/052505 (published as WO/2015/022544). They are also discussed in detail in International Application No. PCT/GB2015/050991.
  • One or more helicases may be attached to the MuA substrate Y adaptors before they are contacted with the double stranded polynucleotide and MuA transposase. Alternatively, one or more helicases may be attached to the MuA substrate Y adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
  • One or more molecular brakes may be attached to the MuA substrate hairpin loop adaptors before they are contacted with the double stranded polynucleotide and MuA transposase. Alternatively, one or more molecular brakes may be attached to the MuA substrate hairpin loop adaptors before they are contacted with the double stranded polynucleotide and MuA transposase.
    • Uncoupling
  • The method of the invention may involve characterising multiple target polynucleotides and uncoupling of the at least the first target polynucleotide.
  • In a preferred embodiment, the invention involves characterising two or more target polynucleotides. The method comprises:
      • (a) providing a first polynucleotide in a first sample;
      • (b) providing a second polynucleotide in a second sample;
      • (c) coupling the first polynucleotide in the first sample to a membrane using one or more anchors;
      • (d) contacting the first polynucleotide with the pore of the invention such that the polynucleotide moves through the pore;
      • (e) taking one or more measurements as the first polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the first polynucleotide and thereby characterising the first polynucleotide;
      • (f) uncoupling the first polynucleotide from the membrane;
      • (g) coupling the second polynucleotide in the second sample to the membrane using one or more anchors;
      • (h) contacting the second polynucleotide with the pore of the invention such that the second polynucleotide moves through the pore; and
      • (i) taking one or more measurements as the second polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the second polynucleotide and thereby characterising the second polynucleotide.
  • This type of method is discussed in detail in International Application No. PCT/GB2015/050992.
  • If one or more anchors comprise a hydrophobic anchor, such as cholesterol, the agent is preferably a cyclodextrin or a derivative thereof or a lipid. The cyclodextrin or derivative thereof may be any of those disclosed in Eliseev, A. V., and Schneider, H-J. (1994) J. Am. Chem. Soc. 116, 6081-6088. The agent is more preferably heptakis-6-amino-β-cyclodextrin (am7-βCD), 6-monodeoxy-6-monoamino-β-cyclodextrin (am1-βCD) or heptakis-(6-deoxy-6-guanidino)-cyclodextrin (gu7-βCD). Any of the lipids disclosed herein may be used.
    • Modified Polynucleotides
  • Before characterisation, a target polynucleotide may be modified by contacting the polynucleotide with a polymerase and a population of free nucleotides under conditions in which the polymerase forms a modified polynucleotide using the target polynucleotide as a template, wherein the polymerase replaces one or more of the nucleotide species in the target polynucleotide with a different nucleotide species when forming the modified polynucleotide. The modified polynucleotide may then be provided with one or more helicases attached to the polynucleotide and one or more molecular brakes attached to the polynucleotide. This type of modification is described in International Application No. PCT/GB2015/050483. Any of the polymerases discussed above may be used. The polymerase is preferably Klenow or 90 North.
  • The template polynucleotide is contacted with the polymerase under conditions in which the polymerase forms a modified polynucleotide using the template polynucleotide as a template. Such conditions are known in the art. For instance, the polynucleotide is typically contacted with the polymerase in commercially available polymerase buffer, such as buffer from New England Biolabs®. The temperature is preferably from 20 to 37° C. for Klenow or from 60 to 75° C. for 90 North. A primer or a 3′ hairpin is typically used as the nucleation point for polymerase extension.
  • Characterisation, such as sequencing, of a polynucleotide using a transmembrane pore typically involves analyzing polymer units made up of k nucleotides where k is a positive integer (i.e. ‘k-mers’). This is discussed in International Application No. PCT/GB2012/052343 (published as WO 2013/041878). While it is desirable to have clear separation between current measurements for different k-mers, it is common for some of these measurements to overlap. Especially with high numbers of polymer units in the k-mer, i.e. high values of k, it can become difficult to resolve the measurements produced by different k-mers, to the detriment of deriving information about the polynucleotide, for example an estimate of the underlying sequence of the polynucleotide.
  • By replacing one or more nucleotide species in the target polynucleotide with different nucleotide species in the modified polynucleotide, the modified polynucleotide contains k-mers which differ from those in the target polynucleotide. The different k-mers in the modified polynucleotide are capable of producing different current measurements from the k-mers in the target polynucleotide and so the modified polynucleotide provides different information from the target polynucleotide. The additional information from the modified polynucleotide can make it easier to characterise the target polynucleotide. In some instances, the modified polynucleotide itself may be easier to characterise. For instance, the modified polynucleotide may be designed to include k-mers with an increased separation or a clear separation between their current measurements or k-mers which have a decreased noise.
  • The polymerase preferably replaces two or more of the nucleotide species in the target polynucleotide with different nucleotide species when forming the modified polynucleotide. The polymerase may replace each of the two or more nucleotide species in the target polynucleotide with a distinct nucleotide species. The polymerase may replace each of the two or more nucleotide species in the target polynucleotide with the same nucleotide species.
  • If the target polynucleotide is DNA, the different nucleotide species in the modified typically comprises a nucleobase which differs from adenine, guanine, thymine, cytosine or methylcytosine and/or comprises a nucleoside which differs from deoxyadenosine, deoxyguanosine, thymidine, deoxycytidine or deoxymethylcytidine. If the target polynucleotide is RNA, the different nucleotide species in the modified polynucleotide typically comprises a nucleobase which differs from adenine, guanine, uracil, cytosine or methylcytosine and/or comprises a nucleoside which differs from adenosine, guanosine, uridine, cytidine or methylcytidine. The different nucleotide species may be any of the universal nucleotides discussed above.
  • The polymerase may replace the one or more nucleotide species with a different nucleotide species which comprises a chemical group or atom absent from the one or more nucleotide species. The chemical group may be a propynyl group, a thio group, an oxo group, a methyl group, a hydroxymethyl group, a formyl group, a carboxy group, a carbonyl group, a benzyl group, a propargyl group or a propargylamine group.
  • The polymerase may replace the one or more nucleotide species with a different nucleotide species which lacks a chemical group or atom present in the one or more nucleotide species. The polymerase may replace the one or more of the nucleotide species with a different nucleotide species having an altered electronegativity. The different nucleotide species having an altered electronegativity preferably comprises a halogen atom.
  • The method preferably further comprises selectively removing the nucleobases from the one or more different nucleotides species in the modified polynucleotide.
    • Other Characterisation Method
  • In another embodiment, a polynucleotide is characterised by detecting labelled species that are released as a polymerase incorporates nucleotides into the polynucleotide. The polymerase uses the polynucleotide as a template. Each labelled species is specific for each nucleotide. The polynucleotide is contacted with a pore of the invention, a polymerase and labelled nucleotides such that phosphate labelled species are sequentially released when nucleotides are added to the polynucleotide(s) by the polymerase, wherein the phosphate species contain a label specific for each nucleotide. The polymerase may be any of those discussed above. The phosphate labelled species are detected using the pore and thereby characterising the polynucleotide. This type of method is disclosed in European Application No. 13187149.3 (published as EP 2682460). Any of the embodiments discussed above equally apply to this method.
    • Kits
  • The present invention also provides a kit for characterising a target polynucleotide. The kit comprises a pore of the invention and the components of a membrane. The membrane is preferably formed from the components. The pore is preferably present in the membrane. The kit may comprise components of any of the membranes disclosed above, such as an amphiphilic layer or a triblock copolymer membrane.
  • The kit may further comprise a polynucleotide binding protein.
  • The kit may further comprise one or more anchors for coupling the polynucleotide to the membrane.
  • The kit is preferably for characterising a double stranded polynucleotide and preferably comprises a Y adaptor and a hairpin loop adaptor. The Y adaptor preferably has one or more helicases attached and the hairpin loop adaptor preferably has one or more molecular brakes attached. The Y adaptor preferably comprises one or more first anchors for coupling the polynucleotide to the membrane, the hairpin loop adaptor preferably comprises one or more second anchors for coupling the polynucleotide to the membrane and the strength of coupling of the hairpin loop adaptor to the membrane is preferably greater than the strength of coupling of the Y adaptor to the membrane.
  • The kit of the invention may additionally comprise one or more other reagents or instruments which enable any of the embodiments mentioned above to be carried out. Such reagents or instruments include one or more of the following: suitable buffer(s) (aqueous solutions), means to obtain a sample from a subject (such as a vessel or an instrument comprising a needle), means to amplify and/or express polynucleotides or voltage or patch clamp apparatus. Reagents may be present in the kit in a dry state such that a fluid sample resuspends the reagents. The kit may also, optionally, comprise instructions to enable the kit to be used in the method of the invention or details regarding for which organism the method may be used.
    • Apparatus
  • The invention also provides an apparatus for characterising a target polynucleotide. The apparatus comprises a plurality of pores of the invention and a plurality of membranes. The plurality of pores are preferably present in the plurality of membranes. The number of pores and membranes is preferably equal. Preferably, a single pore is present in each membrane.
  • The apparatus preferably further comprises instructions for carrying out the method of the invention. The apparatus may be any conventional apparatus for polynucleotide analysis, such as an array or a chip. Any of the embodiments discussed above with reference to the methods of the invention are equally applicable to the apparatus of the invention. The apparatus may further comprise any of the features present in the kit of the invention.
  • The apparatus is preferably set up to carry out the method of the invention.
  • The apparatus preferably comprises:
  • a sensor device that is capable of supporting the plurality of pores and membranes and being operable to perform polynucleotide characterisation using the pores and membranes; and
  • at least one port for delivery of the material for performing the characterisation.
  • Alternatively, the apparatus preferably comprises:
  • a sensor device that is capable of supporting the plurality of pores and membranes being operable to perform polynucleotide characterisation using the pores and membranes; and
  • at least one reservoir for holding material for performing the characterisation.
  • The apparatus more preferably comprises:
  • a sensor device that is capable of supporting the membrane and plurality of pores and membranes and being operable to perform polynucleotide characterising using the pores and membranes;
  • at least one reservoir for holding material for performing the characterising;
  • a fluidics system configured to controllably supply material from the at least one reservoir to the sensor device; and
  • one or more containers for receiving respective samples, the fluidics system being configured to supply the samples selectively from one or more containers to the sensor device.
  • The apparatus may be any of those described in International Application No. PCT/GB08/004127 (published as WO 2009/077734), PCT/GB10/000789 (published as WO 2010/122293), International Application No. PCT/GB10/002206 (published as WO 2011/067559) or International Application No. PCT/US99/25679 (published as WO 00/28312).
  • The following Example illustrates the invention.
    • Example 1
  • This Example describes the use of a helicase—T4 Dda—E94C/C109A/C136A/A360C (SEQ ID NO: 24 with mutations E94C/C109A/C136A/A360C) to control the movement of DNA construct X (shown in FIG. 1) through a number of different MspA nanopores. All of the nanopores tested exhibited changes in current as the DNA translocated through the nanopore.
    • Materials and Methods
  • Prior to setting up the experiment, DNA construct X or Y (see FIGS. 1 and 2 respectively for diagram and sequences used in constructs X and Y, final concentration added to the nanopore system 0.1 nM) was pre-incubated at room temperature for five minutes with T4 Dda—E94C/C109A/C136A/A360C (final concentration added to the nanopore system 10 nM, SEQ ID NO: 24 with mutations E94C/A360C which was provided in buffer (253 mM KCl, 50 mM potassium phosphate, pH 8.0, 2 mM EDTA)). After five minutes, TMAD (100 μM final concentration added to the nanopore system) was added to the pre-mix and the mixture incubated for a further 5 minutes. Finally, MgCl2 (1 or 2 mM final concentration added to the nanopore system), ATP (2 mM final concentration added to the nanopore system) and KCl (500 mM final concentration added to the nanopore system) were added to the pre-mix.
  • Electrical measurements were acquired from single MspA nanopores (please see table 5 below for those tested) inserted in block co-polymer in buffer (500 mM KCl, 25 mM potassium phosphate pH 8.0). After achieving a single pore inserted in the block co-polymer, then buffer (1 mL, 500 mM KCl, 25 mM potassium phosphate) was flowed through the system to remove any excess MspA nanopores. The enzyme (T4 Dda—E94C/C109A/C136A/A360C, 10 nM final concentration), DNA construct X or Y (0.1 nM final concentration), fuel ( MgCl2 1 or 2 mM final concentration, ATP 2 mM final concentration) pre-mix (150 μL total) was then flowed into the single nanopore experimental system and the experiment run with the following protocol −120 mV for 900 s, −180 mV for 2 seconds, 0 mV for 2 s and then return to 120 mV for 900 s (this flip protocol was repeated 8 times) and helicase-controlled DNA movement was monitored.
    • Results
  • The MspA nanopores which were tested are shown in the table 3 below. Helicase controlled DNA movement was observed for DNA constructs X and Y (FIGS. 1 and 2 respectively) using T4 Dda—E94C/C109A/C136A/A360C (see table 5 for which figures correspond to which nanopore mutants tested).
  • TABLE 3
    Mutant MspA Nanopore Final Mg2+
    (SEQ ID NO: 2 with the specified DNA concentration Figure
    Entry mutations) Construct (mM) Number
    1 MspA - (G75S/G77S/L88N/D90N/ X 1 3
    D91N/D118R/Q126R/D134R/E139K)8
    2 MspA - (G75S/G77S/L88N/D90N/ Y 2 4
    D91N/A96D/D118R/Q126R/D134R/E139K)8
    3 MspA - (G75S/G77S/L88N/D90N/ X 1 5
    D91N/N102G/D118R/Q126R/D134R/E139K)8
    4 MspA - (G75S/G77S/L88N/D90N/ X 1 6
    D91N/S103A/D118R/Q126R/D134R/E139K)8
    5 MspA - (G75S/G77S/L88N/D90N/ X 1 7
    D91N/N108S/D118R/Q126R/D134R/E139K)8
    6 MspA - (G75S/G77S/L88N/D90N/ X 1 8
    D91N/N108P/D118R/Q126R/D134R/E139K)8
    7 MspA - (G75S/G77S/L88N/D90N/D9IN/ X 1 9
    A96D/N108P/D118R/Q126R/D134R/E139K)8
    8 MspA - (G75S/G77S/L88N/D90N/D9IN/ X 1 10
    A96D/N108A/D118R/Q126R/D134R/E139K)8
    9 MspA - (G75S/G77S/L88N/I89F/ X 1 11
    D90N/D91N/D118R/Q126R/D134R/E139K)8
    10 MspA - (G75S/G77S/D90N/D91N/ X 1 12
    D118R/Q126R/D134R/E139K)8
    11 MspA - (G75S/G77S/L88K/D90N/ X 1 13
    D91N/I105E/D118R/Q126R/D134R/E139K)8
    12 MspA - (G75S/G77S/L88N/D90N/ X 1 14
    D91N/D118G/Q126R/D134R/E139K)8
    13 MspA - (G75S/G77S/L88N/D90N/ X 1 15
    D91N/D118N/Q126R/D134R/E139K)8
    14 MspA - (G75S/G77S/L88N/D90N/ X 1 16
    D91N/D118R/D134R/E139K)8
    19 MspA - (G75S/G77S/L88K/D90N/D9IN/ X 1 17
    N108E/D118R/Q126R/D134R/E139K)8
    21 MspA - (G75S/G77S/L88N/D90N/D9IN/ Y 2 18
    T95E/P98K/D118R/Q126R/D134R/E139K)8
    22 MspA - (G75S/G77S/L88N/D90N/ X 1 19
    D91N/D93N/D118R/Q126R/D134R/E139K)8
  • Entry 22 (FIG. 19) shows the MspA mutant MspA—(G75S/G77 S/L88N/D90N/D91N/D93N/D118R/Q126R/D134R/E139K)8 which has substituted the aspartic acid at position 93 with a glycine. Helicase-controlled DNA movement was observed when DNA translocated through this mutant. However, entry 1 (FIG. 3) has position 93 changed back to an aspartic acid MspA—(G75S/G77 S/L88N/D90N/D91N/D118R/Q126R/D134R/E139K)8 (which is the same amino acid that is present in the wild-type MspA) and this also exhibited helicase-controlled DNA movement. Therefore, it was possible to put the aspartic acid back into the nanopore amino acid sequence and helicase-controlled DNA movement was still observed.

Claims (24)

1. A mutant Msp monomer comprising a variant of the sequence shown in SEQ ID NO: 2, wherein the variant:
(a) does not comprise aspartic acid (D) at position 90;
(b) does not comprise aspartic acid (D) at position 91;
(c) comprises aspartic acid (D) or glutamic acid (E) at position 93; and
(d) comprises one or more modifications which decrease the net negative charge of the inward facing amino acids in the cap forming region and/or the barrel forming region of the monomer.
2. A mutant monomer according to claim 1, wherein the cap forming region comprises amino acids 1 to 72 and 122 to 184 of SEQ ID NO: 2.
3. A mutant monomer according to claim 1, wherein the barrel forming region comprises amino acids 73 to 82 and 112 to 121 of SEQ ID NO: 2.
4. A mutant monomer according to claim 1, wherein the inward facing amino acids in the cap forming region are V9, Q12, D13, R14, T15, W40, I49, P53, G54, D56, E57, E59, T61, E63, Y66, Q67, I68, F70, P123, I125, Q126, E127, V128, A129, T130, F131, S132, V133, D134, S136, G137, E139, V144, H148, T150, V151, T152, F163, R165, I167, S169, T170 and S173.
5. A mutant monomer according to claim 1, wherein the inward facing amino acids in the barrel forming region are S73, G75, G77, N79, S81, G112, S114, S116, D118 and G120.
6. A mutant monomer according to claim 1, wherein the one or more modifications are one or more deletions of negatively charged amino acids or one or more substitutions of negatively charged amino acids with one or more positively charged, uncharged, non-polar and/or aromatic amino acids.
7. A mutant monomer according to claim 6, wherein the one or more negatively charged amino acids are substituted with alanine (A), valine (V), asparagine (N) or glycine (G).
8. A mutant monomer according to claim 1, wherein the one or more modifications are one or more introductions of positively charged amino acids.
9. A mutant monomer according to claim 6, wherein the one or more positively charged amino acids are histidine (H), lysine (K) and/or arginine (R).
10. A mutant monomer according to claim 1, wherein the one or more modifications are one or more chemical modifications of one or more negatively charged amino acids which neutralise their negative charge.
11. A mutant monomer according to claim 1, wherein the one or more modifications reduce the net negative charge at one or more of positions 118, 126, 134 and 139.
12. A mutant monomer according to claim 1, wherein
(i) the variant comprises a positively charged amino acid at one or more of positions 114, 116, 120, 123, 70, 73, 75, 77 and 79,
(ii) the variant comprises a positively charged amino acid at one or more of positions 123, 125, 127 and 128;
(iii) the variant comprises a positively charged amino acid at one or more of positions 129, 132, 136, 137, 59, 61 and 63;
(iv) the variant comprises a positively charged amino acid at one or more of positions 137, 138, 141, 143, 45, 47, 49 and 51;
(v) the variant does not comprise aspartic acid (D) or glutamic acid (E) at one or more of positions 118, 126, 134 and 139;
(vi) the variant comprises arginine (R), glycine (G) or asparagine (N) at one or more of positions 118, 126, 134 and 139;
(vii) the variant comprises D118R, Q126R, D134R and E139K;
(viii) the variant comprises serine (S), glutamine (Q), leucine (L), methionine (M), isoleucine (I), alanine (A), valine (V), glycine (G), phenylalanine (F), tryptophan (W), tyrosine (Y), histidine (H), threonine (T), arginine (R), lysine (K), asparagine (N) or cysteine (C) at position 90 and/or position 91;
(ix) the variant comprises asparagine (N) at position 90 and/or position 91;
(x) the variant comprises one or more of:
(e) serine (S) at position 75;
(f) serine (S) at position 77; and
(g) asparagine (N) or lysine (K) at position 88;
(xi) the variant comprises G75S, G77S and L88K or G75S, G77S and L88N;
(xii) the variant comprises G75S, G77S, L88N, D90N, D91N, D118R, Q126R, D134R and E139K; and/or
(xiii) the variant further comprises one or more of:
(h) phenylalanine (F) at position 89;
(i) glutamic acid (E) at position 95 and lysine (K) at position 98;
(j) aspartic acid (D) at position 96;
(k) glycine (G) at position 102;
(l) alanine (A) at position 103; and
(m) alanine (A), serine (S) or proline (P) at position 108.
13-32. (canceled)
33. A pore derived from Msp comprising at least one mutant monomer according to claim 1.
34. A pore according to claim 33, wherein the pore comprises eight mutant monomers according to claim 1 and wherein at least one of them differs from the others.
35. A method of characterising a target polynucleotide, comprising:
a) contacting the polynucleotide with a pore according to claim 31 such that the polynucleotide moves through the pore; and
b) taking one or more measurements as the polynucleotide moves with respect to the pore, wherein the measurements are indicative of one or more characteristics of the polynucleotide, and thereby characterising the target polynucleotide.
36. A method according to claim 35, wherein the one or more characteristics are selected from (i) the length of the polynucleotide, (ii) the identity of the polynucleotide, (iii) the sequence of the polynucleotide, (iv) the secondary structure of the polynucleotide and (v) whether or not the polynucleotide is modified.
37. A method according to claim 35, wherein the one or more characteristics of the polynucleotide are measured by electrical measurement and/or optical measurement.
38. (canceled)
39. A method according to claim 35, wherein step a) further comprises contacting the polynucleotide with a polynucleotide binding protein such that the protein controls the movement of the polynucleotide through the pore.
40. (canceled)
41. A method according to claim 39, wherein the polynucleotide binding protein is a helicase or is derived from a helicase.
42-51. (canceled)
52. A pore according to claim 33, wherein the pore comprises eight identical mutant monomers according to claim 1.
US15/308,206 2014-05-02 2015-05-01 Mutant pores Active US10167503B2 (en)

Applications Claiming Priority (7)

Application Number Priority Date Filing Date Title
GB1407809.1 2014-05-02
GB201407809A GB201407809D0 (en) 2014-05-02 2014-05-02 Method
GBGB1417712.5A GB201417712D0 (en) 2014-10-07 2014-10-07 Method
GB1417712.5 2014-10-07
GB201417708A GB201417708D0 (en) 2014-10-07 2014-10-07 Mutant pores
GB1417708.3 2014-10-07
PCT/GB2015/051290 WO2015166275A1 (en) 2014-05-02 2015-05-01 Mutant pores

Publications (3)

Publication Number Publication Date
US20170058337A1 US20170058337A1 (en) 2017-03-02
US20170356037A9 true US20170356037A9 (en) 2017-12-14
US10167503B2 US10167503B2 (en) 2019-01-01

Family

ID=53052882

Family Applications (5)

Application Number Title Priority Date Filing Date
US15/308,206 Active US10167503B2 (en) 2014-05-02 2015-05-01 Mutant pores
US15/308,252 Active US10443097B2 (en) 2014-05-02 2015-05-01 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US16/572,869 Active US10844432B2 (en) 2014-05-02 2019-09-17 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US17/075,017 Active 2036-04-12 US11739377B2 (en) 2014-05-02 2020-10-20 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US18/341,906 Pending US20240060126A1 (en) 2014-05-02 2023-06-27 Method

Family Applications After (4)

Application Number Title Priority Date Filing Date
US15/308,252 Active US10443097B2 (en) 2014-05-02 2015-05-01 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US16/572,869 Active US10844432B2 (en) 2014-05-02 2019-09-17 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US17/075,017 Active 2036-04-12 US11739377B2 (en) 2014-05-02 2020-10-20 Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US18/341,906 Pending US20240060126A1 (en) 2014-05-02 2023-06-27 Method

Country Status (4)

Country Link
US (5) US10167503B2 (en)
EP (2) EP3137490B1 (en)
CN (2) CN106459159B (en)
WO (2) WO2015166276A1 (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020043653A2 (en) 2018-08-28 2020-03-05 F. Hoffmann-La Roche Ag Ruthenium-containing electrodes
WO2020131759A1 (en) 2018-12-19 2020-06-25 Roche Diagnostics Gmbh 3' protected nucleotides

Families Citing this family (42)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CA2774710C (en) 2008-09-22 2016-08-02 University Of Washington Msp nanopores and related methods
GB0905140D0 (en) 2009-03-25 2009-05-06 Isis Innovation Method
KR20140090633A (en) 2011-10-21 2014-07-17 옥스포드 나노포어 테크놀로지즈 리미티드 Method of characterizing a target polynucleotide using a pore and a hel308 helicase
JP6271505B2 (en) 2012-04-10 2018-01-31 オックスフォード ナノポール テクノロジーズ リミテッド Mutant lysenin pore
WO2014013260A1 (en) 2012-07-19 2014-01-23 Oxford Nanopore Technologies Limited Modified helicases
GB201313477D0 (en) 2013-07-29 2013-09-11 Univ Leuven Kath Nanopore biosensors for detection of proteins and nucleic acids
JP6677640B2 (en) 2013-10-18 2020-04-08 オックスフォード ナノポール テクノロジーズ リミテッド Modification enzyme
CN111534504B (en) 2014-01-22 2024-06-21 牛津纳米孔科技公开有限公司 Method of ligating one or more polynucleotide binding proteins to a target polynucleotide
ES2895625T3 (en) 2014-04-16 2022-02-22 Uab Res Found MSP nanopores and uses thereof
GB201417712D0 (en) 2014-10-07 2014-11-19 Oxford Nanopore Tech Ltd Method
CN106459159B (en) * 2014-05-02 2021-11-30 牛津纳米孔技术公司 Abrupt change hole
CN114605507A (en) 2014-09-01 2022-06-10 弗拉芒区生物技术研究所 Mutant CSGG pore
US10266885B2 (en) 2014-10-07 2019-04-23 Oxford Nanopore Technologies Ltd. Mutant pores
GB201502809D0 (en) 2015-02-19 2015-04-08 Oxford Nanopore Tech Ltd Mutant pore
GB201502810D0 (en) 2015-02-19 2015-04-08 Oxford Nanopore Tech Ltd Method
CN107735686B (en) 2015-04-14 2021-06-11 鲁汶天主教大学 Nanopores with internal protein adaptors
CA3011830A1 (en) * 2015-12-08 2017-06-15 Katholieke Universiteit Leuven Ku Leuven Research & Development Modified nanopores, compositions comprising the same, and uses thereof
WO2017149317A1 (en) 2016-03-02 2017-09-08 Oxford Nanopore Technologies Limited Mutant pore
CN118256605A (en) 2016-04-06 2024-06-28 牛津纳米孔科技公开有限公司 Mutant wells
JP7383480B2 (en) 2017-02-10 2023-11-20 オックスフォード ナノポール テクノロジーズ ピーエルシー Modified nanopores, compositions containing the same, and uses thereof
GB201707122D0 (en) 2017-05-04 2017-06-21 Oxford Nanopore Tech Ltd Pore
GB201707140D0 (en) 2017-05-04 2017-06-21 Oxford Nanopore Tech Ltd Method
SG11201913174PA (en) 2017-06-30 2020-01-30 Vib Vzw Novel protein pores
WO2019157365A1 (en) * 2018-02-09 2019-08-15 Ohio State Innovation Foundation Bacteriophage-derived nanopore sensors
GB201809323D0 (en) 2018-06-06 2018-07-25 Oxford Nanopore Tech Ltd Method
CN112805393A (en) * 2018-09-28 2021-05-14 北京齐碳科技有限公司 Helicase and application thereof
CN109473144B (en) * 2018-10-30 2021-07-09 中国石油大学(华东) Method for constructing full-atom model of polymer and supercritical carbon dioxide mixed system
CA3118808A1 (en) * 2018-11-08 2020-05-14 Oxford Nanopore Technologies Limited Pore
US20220366313A1 (en) * 2019-02-14 2022-11-17 University Of Washington Systems and methods for improved nanopore-based analysis of nucleic acids
US11926819B2 (en) 2019-05-28 2024-03-12 The Regents Of The University Of California Methods of adding polymers to ribonucleic acids
WO2021056599A1 (en) * 2019-09-29 2021-04-01 北京齐碳科技有限公司 Mnep monomer variant and application thereof
CN111164097B (en) * 2019-09-29 2021-02-19 北京齐碳科技有限公司 Mnep monomer variant and application thereof
WO2022126304A1 (en) * 2020-12-14 2022-06-23 北京齐碳科技有限公司 Modified helicase and application thereof
CN114450400B (en) * 2021-01-25 2022-10-04 Cj第一制糖株式会社 Novel copper-transporting P-type ATPase A variants and methods of producing L-tryptophan using same
CN113480620B (en) * 2021-08-18 2024-02-06 成都齐碳科技有限公司 Mutant of porin monomer, protein hole and application thereof
WO2023049682A1 (en) * 2021-09-22 2023-03-30 Illumina, Inc. Sequencing polynucleotides using nanopores
CN113735948B (en) * 2021-09-28 2024-02-02 成都齐碳科技有限公司 Mutant of porin monomer, protein hole and application thereof
CN113912683B (en) * 2021-10-12 2024-02-06 成都齐碳科技有限公司 Mutant of porin monomer, protein hole and application thereof
WO2023125605A1 (en) * 2021-12-30 2023-07-06 深圳华大生命科学研究院 Single molecule nanopore sequencing method
CN118234741A (en) * 2021-12-31 2024-06-21 深圳华大生命科学研究院 Nanoporous proteins and related applications in sequencing
GB202205617D0 (en) 2022-04-14 2022-06-01 Oxford Nanopore Tech Plc Novel modified protein pores and enzymes
GB202216905D0 (en) 2022-11-11 2022-12-28 Oxford Nanopore Tech Plc Novel pore monomers and pores

Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9751915B2 (en) * 2011-02-11 2017-09-05 Oxford Nanopore Technologies Ltd. Mutant pores

Family Cites Families (150)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
FI82266C (en) 1982-10-19 1991-02-11 Cetus Corp Process for Preparation of IL-2 Mutein
US5198543A (en) 1989-03-24 1993-03-30 Consejo Superior Investigaciones Cientificas PHI29 DNA polymerase
US5777078A (en) 1993-04-28 1998-07-07 Worcester Foundation For Experimental Biology Triggered pore-forming agents
CA2160909A1 (en) 1993-04-28 1994-11-10 Hagan Bayley Cell-targeted lytic pore-forming agents
DE4320201A1 (en) 1993-06-18 1995-01-12 Asta Medica Ag Use of Cetrorelix and other nona and decapeptides for the manufacture of a medicament for combating AIDS and for growth stimulation
US5386373A (en) 1993-08-05 1995-01-31 Pavilion Technologies, Inc. Virtual continuous emission monitoring system with sensor validation
US5561043A (en) 1994-01-31 1996-10-01 Trustees Of Boston University Self-assembling multimeric nucleic acid constructs
US7569341B2 (en) 1994-01-31 2009-08-04 Trustees Of Boston University Nucleic acid directed immobilization arrays and methods of assembly
US5795782A (en) 1995-03-17 1998-08-18 President & Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
US6362002B1 (en) 1995-03-17 2002-03-26 President And Fellows Of Harvard College Characterization of individual polymer molecules based on monomer-interface interactions
JP3891620B2 (en) 1996-11-14 2007-03-14 株式会社アイシン・コスモス研究所 Nucleic acid probe molecule having a hairpin structure, and nucleic acid detection method using the nucleic acid probe molecule
US20020197614A1 (en) 1997-05-16 2002-12-26 Mosaic Technologies, Inc. Electrophoretic analysis of target molecules using adapter molecules
WO1999005167A1 (en) 1997-07-25 1999-02-04 University Of Massachusetts Designed protein pores as components for biosensors
US6087099A (en) 1997-09-08 2000-07-11 Myriad Genetics, Inc. Method for sequencing both strands of a double stranded DNA in a single sequencing reaction
US6127166A (en) 1997-11-03 2000-10-03 Bayley; Hagan Molluscan ligament polypeptides and genes encoding them
JPH11137260A (en) 1997-11-06 1999-05-25 Soyaku Gijutsu Kenkyusho:Kk Anti-influenza viral cyclic dumbbell type rna-dna chimera compound and anti-influenza viral agent
US6123819A (en) 1997-11-12 2000-09-26 Protiveris, Inc. Nanoelectrode arrays
DE19826758C1 (en) 1998-06-15 1999-10-21 Soft Gene Gmbh Production of closed, double-stranded DNA molecules for use in gene therapy or genetic vaccination
US6743605B1 (en) 1998-06-24 2004-06-01 Enzo Life Sciences, Inc. Linear amplification of specific nucleic acid sequences
US7155344B1 (en) 1998-07-27 2006-12-26 Caliper Life Sciences, Inc. Distributed database for analytical instruments
US6150112A (en) 1998-09-18 2000-11-21 Yale University Methods for identifying DNA sequences for use in comparison of DNA samples by their lack of polymorphism using Y shape adaptors
US6267872B1 (en) 1998-11-06 2001-07-31 The Regents Of The University Of California Miniature support for thin films containing single channels or nanopores and methods for using same
US6426231B1 (en) 1998-11-18 2002-07-30 The Texas A&M University System Analyte sensing mediated by adapter/carrier molecules
NO986133D0 (en) 1998-12-23 1998-12-23 Preben Lexow Method of DNA Sequencing
US6627067B1 (en) 1999-06-22 2003-09-30 President And Fellows Of Harvard College Molecular and atomic scale evaluation of biopolymers
WO2001002425A2 (en) 1999-06-29 2001-01-11 University Health Network Peptide conjugates for the stabilization of membrane proteins and interactions with biological membranes
JP2003508054A (en) 1999-08-31 2003-03-04 ニーデルバイス，ミヒャエル Method for producing channel-forming protein
US6498023B1 (en) 1999-12-02 2002-12-24 Molecular Staging, Inc. Generation of single-strand circular DNA from linear self-annealing segments
US6916665B2 (en) 2000-02-11 2005-07-12 The Texas A&M University System Biosensor compositions and methods of use
US7078501B2 (en) 2000-02-25 2006-07-18 Invitrogen Corporation Topoisomerase linker-mediated amplification methods
WO2001070174A2 (en) 2000-03-21 2001-09-27 Curagen Corporation Vegf-modulated genes and methods employing them
US20020098540A1 (en) 2000-03-22 2002-07-25 Diane Pennica Novel polypeptides, and nucleic acids encoding the same
US7001792B2 (en) 2000-04-24 2006-02-21 Eagle Research & Development, Llc Ultra-fast nucleic acid sequencing device and a method for making and using the same
WO2002025934A2 (en) 2000-09-25 2002-03-28 Sensovation Ag Image sensor device, apparatus and method for optical measurements
AU2002239284A1 (en) 2000-11-27 2002-06-03 The Regents Of The University Of California Methods and devices for characterizing duplex nucleic acid molecules
US20030087232A1 (en) 2001-01-25 2003-05-08 Fred Christians Methods for screening polypeptides
US7807408B2 (en) 2001-03-19 2010-10-05 President & Fellows Of Harvard College Directed evolution of proteins
US6995236B2 (en) 2001-05-08 2006-02-07 Riken Sphingomyelin detecting probe
JP2002355035A (en) 2001-05-08 2002-12-10 Inst Of Physical & Chemical Res Sphingomyelin-detecting probe
US6863833B1 (en) 2001-06-29 2005-03-08 The Board Of Trustees Of The Leland Stanford Junior University Microfabricated apertures for supporting bilayer lipid membranes
WO2003004992A2 (en) 2001-07-03 2003-01-16 The Regents Of The University Of California Mammalian sweet and amino acid heterodimeric taste receptors
MXPA04001719A (en) 2001-08-31 2004-05-31 Gentex Corp Vehicle lamp assembly with heat sink.
EP1487978B1 (en) 2002-03-15 2008-11-19 Nuevolution A/S An improved method for synthesising templated molecules
EP1504114B1 (en) 2002-05-10 2017-07-12 The Texas A & M University System Stochastic sensing through covalent interactions
US20040209299A1 (en) 2003-03-07 2004-10-21 Rubicon Genomics, Inc. In vitro DNA immortalization and whole genome amplification using libraries generated from randomly fragmented DNA
DE602004025801D1 (en) 2003-03-25 2010-04-15 Stratagene California DNA POLYMERASE FUSIONS AND ITS USES
US7163658B2 (en) 2003-04-23 2007-01-16 Rouvain Bension Rapid sequencing of polymers
US7344882B2 (en) 2003-05-12 2008-03-18 Bristol-Myers Squibb Company Polynucleotides encoding variants of the TRP channel family member, LTRPC3
AU2003904237A0 (en) 2003-08-08 2003-08-21 Garvan Institute Of Medical Research Novel translocation assay
WO2005056750A2 (en) 2003-12-11 2005-06-23 Quark Biotech, Inc. Inversion-duplication of nucleic acids and libraries prepared thereby
EP1721283B1 (en) 2004-02-06 2022-11-30 Council of Scientific and Industrial Research Computational method for identifying adhesin and adhesin-like proteins of therapeutic potential
WO2006028508A2 (en) 2004-03-23 2006-03-16 President And Fellows Of Harvard College Methods and apparatus for characterizing polynucleotides
WO2005124888A1 (en) 2004-06-08 2005-12-29 President And Fellows Of Harvard College Suspended carbon nanotube field effect transistor
EP1784754A4 (en) 2004-08-13 2009-05-27 Harvard College An ultra high-throughput opti-nanopore dna readout platform
US20060105461A1 (en) 2004-10-22 2006-05-18 May Tom-Moy Nanopore analysis system
WO2007084103A2 (en) 2004-12-21 2007-07-26 The Texas A & M University System High temperature ion channels and pores
GB0505971D0 (en) 2005-03-23 2005-04-27 Isis Innovation Delivery of molecules to a lipid bilayer
US7272518B2 (en) 2005-07-01 2007-09-18 Square D Company Automated hierarchy classification in utility monitoring systems
WO2007024997A2 (en) 2005-08-22 2007-03-01 Fermalogic, Inc. Methods of increasing production of secondary metabolites
US7877154B2 (en) 2005-09-30 2011-01-25 Fisher-Rosemount Systems, Inc. Method and system for controlling a batch process
KR100730350B1 (en) 2005-10-17 2007-06-19 삼성전자주식회사 Method for short DNA detection using surface functionalized nanopore, and Detection Apparatus therefor
GB0523282D0 (en) 2005-11-15 2005-12-21 Isis Innovation Methods using pores
EP1963530B1 (en) 2005-12-22 2011-07-27 Pacific Biosciences of California, Inc. Active surface coupled polymerases
US7932029B1 (en) 2006-01-04 2011-04-26 Si Lok Methods for nucleic acid mapping and identification of fine-structural-variations in nucleic acids and utilities
US7849581B2 (en) 2006-05-05 2010-12-14 University Of Utah Research Foundation Nanopore electrode, nanopore membrane, methods of preparation and surface modification, and use thereof
WO2008030968A2 (en) 2006-09-06 2008-03-13 Phase Bioscience, Inc. Fusion peptide therapeutic compositions
US7638034B2 (en) 2006-09-21 2009-12-29 Los Alamos National Security, Llc Electrochemical detection of single molecules using abiotic nanopores having electrically tunable dimensions
US20100311602A1 (en) 2006-10-13 2010-12-09 J. Craig Venter Institute, Inc. Sequencing method
US8594848B2 (en) 2006-11-28 2013-11-26 Lester F. Ludwig Reconfigurable chemical process systems
US20110121840A1 (en) 2007-02-20 2011-05-26 Gurdial Singh Sanghera Lipid Bilayer Sensor System
CA2684801C (en) 2007-04-04 2017-10-10 The Regents Of The University Of California Compositions, devices, systems, and methods for using a nanopore
US8158344B2 (en) 2007-06-29 2012-04-17 Duke University Methods and compositions for correlating genetic markers with multiple sclerosis
GB0716005D0 (en) 2007-08-16 2007-09-26 Imp Innovations Ltd Single molecule spectroscopy using nanoporpus membranes
GB0716264D0 (en) 2007-08-21 2007-09-26 Isis Innovation Bilayers
EP2195648B1 (en) 2007-09-12 2019-05-08 President and Fellows of Harvard College High-resolution molecular graphene sensor comprising an aperture in the graphene layer
GB2453377A (en) 2007-10-05 2009-04-08 Isis Innovation Transmembrane protein pores and molecular adapters therefore.
WO2009052214A2 (en) 2007-10-15 2009-04-23 Complete Genomics, Inc. Sequence analysis using decorated nucleic acids
GB0724736D0 (en) 2007-12-19 2008-01-30 Oxford Nanolabs Ltd Formation of layers of amphiphilic molecules
WO2009084721A1 (en) 2007-12-31 2009-07-09 Fujirebio Inc. Clusters of microresonators for cavity mode optical sensing
US8231969B2 (en) 2008-03-26 2012-07-31 University Of Utah Research Foundation Asymmetrically functionalized nanoparticles
CA2991818C (en) 2008-03-28 2022-10-11 Pacific Biosciences Of California, Inc. Compositions and methods for nucleic acid sequencing
US8772041B2 (en) 2008-05-22 2014-07-08 The Regents Of The University Of California Membrane precursors and membranes formed therefrom
US8652771B2 (en) 2008-05-28 2014-02-18 University of Souther California Measurement of succinate in urine samples as a biomarker of kidney damage in diabetic subjects
CA2730068A1 (en) 2008-07-07 2010-01-14 Oxford Nanopore Technologies Limited Base-detecting pore
CN102245760A (en) 2008-07-07 2011-11-16 牛津纳米孔技术有限公司 Enzyme-pore constructs
CA2774710C (en) * 2008-09-22 2016-08-02 University Of Washington Msp nanopores and related methods
US9080211B2 (en) 2008-10-24 2015-07-14 Epicentre Technologies Corporation Transposon end compositions and methods for modifying nucleic acids
GB0820927D0 (en) 2008-11-14 2008-12-24 Isis Innovation Method
EP2359289A4 (en) 2008-11-26 2015-11-11 Illumina Inc Methods and systems for analysis of sequencing data
CA2750879C (en) 2009-01-30 2018-05-22 Oxford Nanopore Technologies Limited Adaptors for nucleic acid constructs in transmembrane sequencing
CN102482330A (en) 2009-01-30 2012-05-30 牛津纳米孔技术有限公司 Enzyme mutant
US8399219B2 (en) 2009-02-23 2013-03-19 Cytomx Therapeutics, Inc. Protease activatable interferon alpha proprotein
FR2943656A1 (en) 2009-03-25 2010-10-01 Air Liquide HYDROGEN PRODUCTION METHOD AND PLANT USING A THERMOCINETIC COMPRESSOR
GB0905140D0 (en) 2009-03-25 2009-05-06 Isis Innovation Method
AU2010240670B2 (en) 2009-04-20 2015-08-20 Oxford Nanopore Technologies Limited Lipid bilayer sensor array
US9127313B2 (en) 2009-12-01 2015-09-08 Oxford Nanopore Technologies Limited Biochemical analysis instrument
FR2955773B1 (en) 2010-02-01 2017-05-26 Commissariat A L'energie Atomique MOLECULAR COMPLEX FOR TARGETING ANTIGENS TO ANTIGEN-PRESENTING CELLS AND ITS APPLICATIONS FOR VACCINATION
EP3933402A1 (en) * 2010-02-23 2022-01-05 University of Washington Method of making unsupported artificial mycolic acid membranes
WO2011125015A2 (en) 2010-04-05 2011-10-13 Bar-Ilan University Protease-activatable pore-forming polypeptides
EP2622343B1 (en) 2010-10-01 2016-01-20 Oxford Nanopore Technologies Limited Biochemical analysis apparatus using nanopores
CN102116783B (en) 2010-12-31 2013-05-29 北京普源精电科技有限公司 Waveform display method
GB201100516D0 (en) 2011-01-12 2011-02-23 Isis Innovation Method using fluorinated amphiphiles
CN102174554A (en) 2011-01-24 2011-09-07 内蒙古民族大学 Double-control double-regulation prokaryotic expression vector system and construction method and application thereof
SG10201604316WA (en) 2011-05-27 2016-07-28 Oxford Nanopore Tech Ltd Coupling method
US9580480B2 (en) 2011-05-31 2017-02-28 Massachusetts Institute Of Technology Cell-directed synthesis of multifunctional nanopatterns and nanomaterials
KR20140050067A (en) 2011-07-25 2014-04-28 옥스포드 나노포어 테크놀로지즈 리미티드 Hairpin loop method for double strand polynucleotide sequencing using transmembrane pores
EP2758545B1 (en) 2011-09-23 2017-07-26 Oxford Nanopore Technologies Limited Analysis of a polymer comprising polymer units
KR20140090633A (en) 2011-10-21 2014-07-17 옥스포드 나노포어 테크놀로지즈 리미티드 Method of characterizing a target polynucleotide using a pore and a hel308 helicase
AU2012360244B2 (en) 2011-12-29 2018-08-23 Oxford Nanopore Technologies Limited Enzyme method
US9617591B2 (en) 2011-12-29 2017-04-11 Oxford Nanopore Technologies Ltd. Method for characterising a polynucleotide by using a XPD helicase
EP2807476A4 (en) 2012-01-20 2015-12-09 Genia Technologies Inc Nanopore based molecular detection and sequencing
US10739341B2 (en) 2012-02-15 2020-08-11 Oxford Nanopore Technologies Limited Aptamer method
JP6271505B2 (en) 2012-04-10 2018-01-31 オックスフォード ナノポール テクノロジーズ リミテッド Mutant lysenin pore
TWI655213B (en) 2012-07-13 2019-04-01 目立康股份有限公司 Method for producing self-organizing peptide derivative
WO2014013260A1 (en) 2012-07-19 2014-01-23 Oxford Nanopore Technologies Limited Modified helicases
AU2013291765C1 (en) 2012-07-19 2019-08-08 Oxford Nanopore Technologies Limited Enzyme construct
WO2014013259A1 (en) 2012-07-19 2014-01-23 Oxford Nanopore Technologies Limited Ssb method
JP6375301B2 (en) 2012-10-26 2018-08-15 オックスフォード ナノポール テクノロジーズ リミテッド Droplet interface
GB201313121D0 (en) 2013-07-23 2013-09-04 Oxford Nanopore Tech Ltd Array of volumes of polar medium
WO2014071250A1 (en) 2012-11-01 2014-05-08 University Of Washington Through Its Center For Commercialization Methods for detecting and mapping modifications to nucleic acid polymers using nanopore systems
US9683230B2 (en) 2013-01-09 2017-06-20 Illumina Cambridge Limited Sample preparation on a solid support
US20140206842A1 (en) 2013-01-22 2014-07-24 Muhammed Majeed Peptides Modified with Triterpenoids and Small Organic Molecules: Synthesis and use in Cosmeceutical
CN105074458B (en) 2013-02-07 2019-06-28 耶路撒冷希伯来大学伊森姆研究发展有限公司 Hybridized nanometer hole and its purposes for testing and analyzing object
CN105209634B (en) 2013-03-08 2020-05-12 牛津纳米孔技术公司 Enzyme arrest method
GB201314695D0 (en) 2013-08-16 2013-10-02 Oxford Nanopore Tech Ltd Method
WO2014142850A1 (en) 2013-03-13 2014-09-18 Illumina, Inc. Methods and compositions for nucleic acid sequencing
US10613076B2 (en) 2013-03-14 2020-04-07 The Trustees Of Boston University Optoelectronic control of solid-state nanopores
GB201313477D0 (en) 2013-07-29 2013-09-11 Univ Leuven Kath Nanopore biosensors for detection of proteins and nucleic acids
EP3825415B1 (en) 2013-05-24 2024-08-28 Illumina Cambridge Limited Pyrophosphorolytic sequencing using nanopores
WO2015051378A1 (en) 2013-10-04 2015-04-09 University Of Washington Through Its Center For Commercialization Systems and methods for nanopore-based analysis of nucleic acids
GB201406151D0 (en) 2014-04-04 2014-05-21 Oxford Nanopore Tech Ltd Method
JP6677640B2 (en) 2013-10-18 2020-04-08 オックスフォード ナノポール テクノロジーズ リミテッド Modification enzyme
LT3074534T (en) 2013-11-26 2019-08-26 Illumina, Inc. Methods for polynucleotide sequencing
US20160326220A1 (en) 2013-12-24 2016-11-10 Vib Vzw Secretion and functional display of chimeric polypeptides
CN111534504B (en) 2014-01-22 2024-06-21 牛津纳米孔科技公开有限公司 Method of ligating one or more polynucleotide binding proteins to a target polynucleotide
GB201406155D0 (en) 2014-04-04 2014-05-21 Oxford Nanopore Tech Ltd Method
GB201403096D0 (en) 2014-02-21 2014-04-09 Oxford Nanopore Tech Ltd Sample preparation method
US10337060B2 (en) 2014-04-04 2019-07-02 Oxford Nanopore Technologies Ltd. Method for characterising a double stranded nucleic acid using a nano-pore and anchor molecules at both ends of said nucleic acid
CN106459159B (en) 2014-05-02 2021-11-30 牛津纳米孔技术公司 Abrupt change hole
FR3023394B1 (en) 2014-07-02 2017-12-29 Adn Access Data Networks DEVICE FOR FACILITATING THE TEACHING OF THE AMBARIC LANGUAGE AND NORMALIZING THE WRITING
CN114605507A (en) 2014-09-01 2022-06-10 弗拉芒区生物技术研究所 Mutant CSGG pore
US10266885B2 (en) 2014-10-07 2019-04-23 Oxford Nanopore Technologies Ltd. Mutant pores
GB201502810D0 (en) 2015-02-19 2015-04-08 Oxford Nanopore Tech Ltd Method
GB201502809D0 (en) 2015-02-19 2015-04-08 Oxford Nanopore Tech Ltd Mutant pore
CN107735686B (en) 2015-04-14 2021-06-11 鲁汶天主教大学 Nanopores with internal protein adaptors
CA3011830A1 (en) 2015-12-08 2017-06-15 Katholieke Universiteit Leuven Ku Leuven Research & Development Modified nanopores, compositions comprising the same, and uses thereof
WO2017149317A1 (en) 2016-03-02 2017-09-08 Oxford Nanopore Technologies Limited Mutant pore
CN118256605A (en) 2016-04-06 2024-06-28 牛津纳米孔科技公开有限公司 Mutant wells
GB201707122D0 (en) 2017-05-04 2017-06-21 Oxford Nanopore Tech Ltd Pore
SG11201913174PA (en) 2017-06-30 2020-01-30 Vib Vzw Novel protein pores

Patent Citations (1)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9751915B2 (en) * 2011-02-11 2017-09-05 Oxford Nanopore Technologies Ltd. Mutant pores

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2020043653A2 (en) 2018-08-28 2020-03-05 F. Hoffmann-La Roche Ag Ruthenium-containing electrodes
WO2020131759A1 (en) 2018-12-19 2020-06-25 Roche Diagnostics Gmbh 3' protected nucleotides

Also Published As

Publication number Publication date
US20200224262A1 (en) 2020-07-16
US20210139972A1 (en) 2021-05-13
CN106574300A (en) 2017-04-19
WO2015166276A1 (en) 2015-11-05
US10844432B2 (en) 2020-11-24
EP3137490A1 (en) 2017-03-08
US20170058337A1 (en) 2017-03-02
US10167503B2 (en) 2019-01-01
US10443097B2 (en) 2019-10-15
WO2015166275A1 (en) 2015-11-05
CN106459159B (en) 2021-11-30
CN106459159A (en) 2017-02-22
EP3137627A1 (en) 2017-03-08
US11739377B2 (en) 2023-08-29
EP3137490B1 (en) 2021-01-27
US20240060126A1 (en) 2024-02-22
US20170058338A1 (en) 2017-03-02

Similar Documents

Publication Publication Date Title
US11739377B2 (en) Method of improving the movement of a target polynucleotide with respect to a transmembrane pore
US10266885B2 (en) Mutant pores
US10472673B2 (en) Hetero-pores
US11685949B2 (en) Mutant pore
US12024541B2 (en) Transmembrane pore consisting of two CsgG pores

Legal Events

Date Code Title Description
AS Assignment

Owner name: OXFORD NANOPORE TECHNOLOGIES LTD., UNITED KINGDOM

Free format text: ASSIGNMENT OF ASSIGNORS INTEREST;ASSIGNORS:CLARKE, JAMES ANTHONY;HERON, ANDREW JOHN;JAYASINGHE, LAKMAL;AND OTHERS;SIGNING DATES FROM 20161213 TO 20161214;REEL/FRAME:040769/0846

STCF Information on status: patent grant

Free format text: PATENTED CASE

CC Certificate of correction
FEPP Fee payment procedure

Free format text: ENTITY STATUS SET TO UNDISCOUNTED (ORIGINAL EVENT CODE: BIG.); ENTITY STATUS OF PATENT OWNER: LARGE ENTITY

MAFP Maintenance fee payment

Free format text: PAYMENT OF MAINTENANCE FEE, 4TH YEAR, LARGE ENTITY (ORIGINAL EVENT CODE: M1551); ENTITY STATUS OF PATENT OWNER: LARGE ENTITY

Year of fee payment: 4