Method of nanopore sequencing of concatenated nucleic acids

Patent metadata

Field	Value
Publication number	US-11098355-B2
Application number	US-201716304101-A
Country	US
Kind code	B2
Filing date	May 25, 2017
Priority date	May 25, 2016
Publication date	Aug 24, 2021
Grant date	Aug 24, 2021

Abstract

The invention relates to a new method of characterising two or more target polynucleotides using a pore. The method involves sequentially attaching to a first polynucleotide one or more subsequent polynucleotides to form a concatenated polynucleotide.

First claim

The invention claimed is:

1. A method of characterising two or more target polynucleotides, comprising:
(a) contacting a first target polynucleotide with a transmembrane pore in a membrane such that the first target polynucleotide moves through the pore;
(b) sequentially attaching to the first target polynucleotide one or more subsequent target polynucleotides to provide a concatenated polynucleotide within which the target polynucleotides move through the pore in attachment order, wherein a subsequent target polynucleotide is selectively attached to the preceding target polynucleotide in the attachment order as the preceding target polynucleotide moves through the pore; and
(c) taking one or more measurements which are indicative of one or more characteristics of the concatenated polynucleotide as it moves with respect to the pore.

2. The method according to claim 1 , wherein 2 or more, 5 or more, 10 or more, 20 or more, 50 or more, 100 or more, 500 or more, 1,000 or more, 5,000 or more, 10,000 or more, 50,000 or more, 100,000 or more, 500,000 or more, 1,000,000 or more or 5,000,000 or more subsequent target polynucleotides are attached to the first target polynucleotide.

3. The method according to claim 1 , wherein a part of the preceding target polynucleotide is initially protected from attachment to the subsequent target polynucleotide and is revealed for attachment as the preceding target polynucleotide moves through the pore.

4. The method according to claim 1 , wherein a part of the subsequent target polynucleotide selectively hybridises to a part of the preceding polynucleotide and further wherein the part of the preceding target polynucleotide is initially protected from hybridisation to the part of the subsequent target polynucleotide and is revealed for hybridisation as the preceding target polynucleotide moves through the pore.

5. The method according to claim 1 , wherein a part of the subsequent target polynucleotide selectively hybridises to a part of the preceding polynucleotide and the preceding target polynucleotide is double stranded, wherein the part of the preceding target polynucleotide is in one strand and is hybridised to the other strand and wherein the part is revealed for hybridisation as the two strands separate as the preceding target polynucleotide moves through the pore.

6. The method according to claim 1 , wherein the preceding target polynucleotide is double stranded and wherein both strands of the double stranded preceding target polynucleotide are linked at one end by a hairpin loop, optionally wherein the other end of the preceding target polynucleotide comprises a leader sequence which preferentially threads into the pore.

7. The method according to claim 1 , wherein the subsequent target polynucleotide is double stranded and the two strands are linked at one end by a hairpin loop.

8. The method according to claim 1 , wherein the one or more subsequent target polynucleotides are selectively attached to the first target polynucleotide by (i) covalent attachment; (ii) a ligase; (iii) a topoisomerase; or (iv) click chemistry.

9. The method according to claim 1 , wherein the movement of the concatenated polynucleotide through the pore is controlled by a molecular brake.

10. The method according to claim 1 , wherein the transmembrane pore is a protein pore or a solid state pore.

11. A method of sequentially passing polynucleotides through a transmembrane pore, the method comprising contacting a first target polynucleotide with the pore under conditions in which the first target polynucleotide enters the pore, wherein, following its entry, an attachment site is revealed on the first target polynucleotide, such that the first target polynucleotide attaches to a second target polynucleotide at the attachment site, thereby guiding sequential entry of the second target polynucleotide into the pore following passage of the first target polynucleotide through the pore.

Assignees

• Oxford Nanopore Tech Ltd

Inventors

• Heron Andrew John
• Garalde Daniel Ryan
• White James

Classifications

• C40B40/06

  Libraries containing nucleotides or polynucleotides, or derivatives thereof · CPC title

• C12N15/1093

  General methods of preparing gene libraries, not provided for in other subgroups · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q1/6806 Primary

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title