Polynucleotide modification methods

• US 10,501,767 B2
• Filed: 08/14/2014
• Issued: 12/10/2019
• Est. Priority Date: 08/16/2013
• Status: Active Grant

• Current Assignee: Oxford Nanopore Technologies Limited
• Original Assignee: Oxford Nanopore Technologies Limited
• Inventors: Stoddart, David Jackson, White, James
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US14/911,853
• Publication Number:
  US 20160194677A1
• Time in Patent Office: 1,944 Days
• Field of Search: 435 912, 435 61
• CPC Class Codes: C12N 9/1241 Nucleotidyltransferases (2.7.7)
• CPC Class Codes: C12P 19/34 Polynucleotides, e.g. nucleic acids, oligoribonucleotides
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: C12Y 207/07 Nucleotidyltransferases (2.7.7)

Abstract

The invention relates to a method for modifying a template double stranded polynucleotide, especially for characterization using nanopore sequencing. The method produces from the template a plurality of modified double stranded polynucleotides. These modified polynucleotides can then be characterized.

Claims

1. A method for modifying a template double stranded polynucleotide, comprising:

(a) contacting a double stranded template polynucleotide with a MuA transposase and a population of double stranded MuA substrates each comprising at least one overhang of universal nucleotides, such that the transposase fragments the template polynucleotide into two or more double-stranded fragments, and ligates a substrate to an end of each of the double stranded fragments, thereby producing a plurality of fragment/substrate constructs; and

(b) ligating the overhangs to the fragments in the constructs and thereby producing a plurality of modified double stranded polynucleotides.

2. A method according to claim 1, wherein the universal nucleotide is selected from the group consisting of hypoxanthine, 4-nitroindole, 5-nitroindole, 6-nitroindole, 3-nitropyrrole, nitroimidazole, 4-nitropyrazole, 4-nitrobenzimidazole, 5-nitroindazole, 4-aminobenzimidazole or phenyl (C6-aromatic ring.

3. A method according to claim 2, wherein the universal nucleotide is selected from the group consisting of 2′

-deoxyinosine, inosine, 7-deaza-2′

-deoxyinosine, 7-deaza-inosine, 2-aza-deoxyinosine, 2-aza-inosine, 4-nitroindole 2′

-deoxyribonucleoside, 4-nitroindole ribonucleoside, 5-nitroindole 2′

-deoxyribonucleoside, 5-nitroindole ribonucleoside, 6-nitroindole 2′

-deoxyribonucleoside, 6-nitroindole ribonucleoside, 3-nitropyrrole 2′

-deoxyribonucleoside, 3-nitropyrrole ribonucleoside, an acyclic sugar analogue of hypoxanthine, nitroimidazole 2′

-deoxyribonucleoside, nitroimidazole ribonucleoside, 4-nitropyrazole 2′

-deoxyribonucleoside, 4-nitropyrazole ribonucleoside, 4-nitrobenzimidazole 2′

-deoxyribonucleoside, 4-nitrobenzimidazole ribonucleoside, 5-nitroindazole 2′

-deoxyribonucleoside, 5-nitroindazole ribonucleoside, 4-aminobenzimidazole 2′

-deoxyribonucleoside, 4-aminobenzimidazole ribonucleoside, phenyl C-ribonucleoside or phenyl C-2′

-deoxyribosyl nucleoside.

4. A method according to claim 1, wherein the overhang is five nucleotides in length.

5. A method according to claim 1, wherein

(a) each substrate comprises an overhang at one end and a hairpin loop at the other end and wherein the two strands of the modified double stranded polynucleotides produced by the method are linked by the hairpin loop at one end;

or

(b) a proportion of the substrates in the population comprise an overhang at one end and a hairpin loop at the other end and a proportion of the substrates in the population are Y substrates with an overhang at one end and a region that is not complementary at the other end and wherein at least some of the modified double stranded polynucleotides produced by the method have the hairpin loop at one end and the non-complementary region at the other end.

6. A method according to claim 1, wherein each substrate is a Y substrate with an overhang at one end and a region that is not complementary at the other end and wherein the modified double stranded polynucleotides produced by the method have the non-complementary region at one or both ends.

7. A method according to claim 1, wherein the substrate comprises a selectable binding moiety.

8. A method according to claim 5, wherein the method further comprises separating the two strands of at least one modified double stranded polynucleotide to produce at least one single stranded polynucleotide comprising one strand of the modified double stranded polynucleotide linked to the other strand of the modified double stranded polynucleotide.

9. A method of characterising at least one polynucleotide modified using a method according to claim 1, comprising:

a) contacting the modified polynucleotide with a transmembrane pore such that at least one strand of the polynucleotide moves through the pore; and

b) taking one or more measurements as the at least one strand moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the at least one strand and thereby characterising the modified polynucleotide.

10. A method of characterising a template polynucleotide, comprising:

a) modifying the template polynucleotide using a method according to claim 1 to produce a plurality of modified polynucleotides;

b) contacting each modified polynucleotide with a transmembrane pore such that at least one strand of each polynucleotide moves through the pore; and

c) taking one or more measurements as the at least one strand of each polynucleotide moves with respect to the pore wherein the measurements are indicative of one or more characteristics of the at least one strand of each polynucleotide and thereby characterising the template polynucleotide.

11. A method according to claim 10, 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.

12. A method according to claim 10, wherein step (b) further comprises contacting each modified polynucleotide with a polynucleotide binding protein such that the protein controls the movement of the at least one strand of each polynucleotide through the pore.

13. A method according to claim 12, wherein the method comprises (a) contacting each modified polynucleotide with a transmembrane pore and a polynucleotide binding protein such that at least one strand of each polynucleotide moves through the pore and the protein controls the movement of the at least one strand of each polynucleotide through the pore;

and

(b) measuring the current passing through the pore as the at least one strand of each polynucleotide moves with respect to the pore wherein the current is indicative of one or more characteristics of the at least one strand of each polynucleotide and thereby characterising the template polynucleotide.

14. A method according to claim 12, wherein the polynucleotide binding protein is derived from a helicase.