SSB method
The invention relates to a method of characterising a target polynucleotide using a single-stranded binding protein (SSB). The SSB is either an SSB comprising a carboxy-terminal (C-terminal) region which does not have a net negative charge or a modified SSB comprising one or more modifications in its C-terminal region which decreases the net negative charge of the C-terminal region.
1. A method of characterising a target polynucleotide, comprising:
a) contacting the target polynucleotide with a transmembrane pore and a single-stranded binding protein (SSB) such that the target polynucleotide moves through the pore and the SSB does not move through the pore, wherein the SSB comprises one or more amino acid substitutions in its C-terminal region relative to a wild-type SSB that decreases the net negative charge of the C-terminal region relative to the wild-type SSB and the decrease in the net negative charge of the C-terminal region reduces blockage of the pore relative to the wild-type SSB, wherein the one or more amino acid substitutions are 1) one or more substitutions of negatively charged amino acids with one or more positively charged, uncharged, non-polar and/or aromatic amino acids, or 2) one or more substitutions of uncharged, non-polar and/or aromatic amino acids with one or more positively charged amino acids; 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 target polynucleotide and thereby characterising the target polynucleotide.
2. A method according to claim 1 , wherein the C-terminal region comprises about the last 10 to about the last 60 amino acids of the C-terminal end.
3. A method according to claim 1 , wherein the one or more negatively charged amino acids are substituted with alanine (A), valine (V), asparagine (N) or glycine (G).
4. A method according to claim 1 , wherein the one or more positively charged amino acids are histidine (H), lysine (K) and/or arginine (R).
5. A method according to claim 1 , wherein
the SSB is (a) derived from the SSB of E. coli , the SSB of Mycobacterium tuberculosis , the SSB of Deinococcus radiodurans , the SSB of Thermus thermophiles , the SSB from Sulfolobus solfataricus , the human replication protein A 32 kDa subunit (RPA32) fragment, the CDC13 SSB from Saccharomyces cerevisiae , the Primosomal replication protein N (PriB) from E. coli , the PriB from Arabidopsis thaliana , the hypothetical protein At4g28440, the SSB from T4, the SSB from RB69, the SSB from T7 or a variant thereof; or (b) derived from the sequence shown in SEQ ID NO: 65 or a variant thereof and comprises the following modification(s):
a) substitution of one or more of amino acids 170, 172, 173 and 174 in SEQ ID NO: 65 with a positively charged, uncharged, non-polar or aromatic amino acid;
b) substitution of one or more of amino acids 168, 169, 171, 175, 176 and 177 in SEQ ID NO: 65 with a positively charged amino acid; or
c) comprises the sequence set forth in SEQ ID NO: 66 or 67.
6. A method according to claim 1 , wherein the one or more characteristics are selected from (i) the length of the target polynucleotide, (ii) the identity of the target polynucleotide, (iii) the sequence of the target polynucleotide, (iv) the secondary structure of the target polynucleotide, (v) whether or not the target polynucleotide is modified or whether or not the target polynucleotide is modified by methylation, by oxidation, by damage, with one or more proteins or with one or more labels, tags or spacers.
7. A method according to claim 1 , wherein step (a) further comprises contacting the polynucleotide with a transport control protein such that the transport control protein controls the movement of the target polynucleotide through the pore and wherein the transport control protein does not move through the pore.
8. A method according to claim 7 , wherein the transport control protein is derived from an exonuclease, polymerase, helicase and topoisomerase.
9. A method according to claim 8 , wherein the SSB is attached to the transport control protein and the resulting construct has the ability to control the movement of the target polynucleotide.
10. A method according to claim 1 , wherein at least a portion of the polynucleotide is single stranded.
11. A method according to claim 1 , wherein the target polynucleotide is contacted with the pore and the SSB on the same side of the membrane.
12. A method according to claim 1 , wherein the pore is a transmembrane protein pore, wherein the protein is selected from hemolysin, leukocidin, Mycobacterium smegmatis porin A (MspA), MspB, MspC, MspD, outer membrane phospholipase A, Neisseria autotransporter lipoprotein (NaIP) and WZA.
13. A method according to claim 1 , wherein the barrel or channel of the pore has a diameter of less than 7 nm at its narrowest point.
14. A method of characterising a target polynucleotide, comprising:
a) contacting the target polynucleotide with a transmembrane pore and a single-stranded binding protein (SSB) such that the target polynucleotide moves through the pore and the SSB does not move through the pore, wherein the SSB comprises one or more amino acid deletions in its C-terminal region relative to a wild-type SSB that decreases the net negative charge of the C-terminal region relative to the wild-type SSB and the decrease in the net negative charge of the C-terminal region reduces blockage of the pore relative to the wild-type SSB; 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 target polynucleotide and thereby characterising the target polynucleotide.
15. A method according to claim 14 , wherein the C-terminal region comprises about the last 10 to about the last 60 amino acids of the C-terminal end.
16. A method according to claim 14 , wherein the SSB is (a) derived from the SSB of E. coli , the SSB of Mycobacterium tuberculosis , the SSB of Deinococcus radiodurans , the SSB of Thermus thermophiles , the SSB from Sulfolobus solfataricus , the human replication protein A 32 kDa subunit (RPA32) fragment, the CDC13 SSB from Saccharomyces cerevisiae , the Primosomal replication protein N (PriB) from E. coli , the PriB from Arabidopsis thaliana , the hypothetical protein At4g28440, the SSB from T4, the SSB from RB69, the SSB from T7 or a variant thereof; or (b) derived from the sequence shown in SEQ ID NO: 65 or a variant thereof and comprises the following modification(s):
a) deletion of one or more of amino acids 170, 172, 173 and 174 in SEQ ID NO: 65;
b) deletion of amino acids 168 to 177 of SEQ ID NO: 65; or
c) comprises the sequence set forth in any one of SEQ ID NOs: 59, 60, 68, and 69.
17. A method according to claim 14 , wherein the one or more deletions are one or more deletions of negatively charged amino acids or deletion of the C-terminal region.