High throughput nucleic acid sequencing by expansion

Patent metadata

Field	Value
Publication number	US-2025109449-A1
Application number	US-202418665321-A
Country	US
Kind code	A1
Filing date	May 15, 2024
Priority date	Jun 19, 2007
Publication date	Apr 3, 2025
Grant date	—

Abstract

Nucleic acid sequencing methods and related products are disclosed. Methods for sequencing a target nucleic acid comprise providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond. The selectively cleavable bond(s) is/are cleaved to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid. Reporter elements of the Xpandomer are then detected. Corresponding products, including Xpandomers are also disclosed.

First claim

1 . A method for sequencing a target nucleic acid, comprising:
a) providing a daughter strand produced by a template-directed synthesis, the daughter strand comprising a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond; b) cleaving the at least one selectively cleavable bond to yield an Xpandomer of a length longer than the plurality of the subunits of the daughter strand, the Xpandomer comprising the tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid; and c) detecting the reporter elements of the Xpandomer.

2 . The method of claim 1 , wherein the reporter elements for parsing the genetic information are associated with the tethers of the Xpandomer.

3 . The method of claim 1 , wherein the reporter elements for parsing genetic information are associated with the daughter strand prior to cleavage of the at least one selectively cleavable bond.

4 . The method of claim 1 , wherein the reporter elements for parsing genetic information are associated with the Xpandomer after cleavage of the at least one selectively cleavable bond.

5 . The method of claim 1 , wherein the Xpandomer further comprises all or a portion of the at least one probe or nucleobase residue.

6 . The method of claim 5 , wherein the reporter elements for parsing the genetic information are or are associated with the at least one probe or nucleobase residue.

7 . The method of claim 1 , wherein the at least one selectively cleavable bond is a covalent bond.

8 . The method of claim 1 , wherein the at least one selectively cleavable bond is an intra-tether bond.

9 . The method of claim 1 , wherein the at least one selectively cleavable bond is a bond between or within probes or nucleobase residues of the daughter strand.

10 . The method of claim 1 , wherein the at least one selectively cleavable bond is a bond between the probes or nucleobase residues of the daughter strand and a target template.

11 . An oligomer substrate construct for use in a template directed synthesis for sequencing a target nucleic acid, comprising a first probe moiety joined to a second probe moiety, each of the first and second probe moieties having an end group suitable for the template directed synthesis, and a tether having a first end and a second end with at least the first end of the tether joined to at least one of the first and second probe moieties, wherein the oligomer substrate construct when used in the template directed synthesis is capable of forming a daughter strand comprising a constrained Xpandomer, the constrained Xpandomer having a plurality of subunits coupled in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, the first and second probe moieties and at least one selectively cleavable bond.

12 . An monomer substrate construct for use in a template directed synthesis for sequencing a target nucleic acid, comprising a nucleobase residue with end groups suitable for the template directed synthesis, and a tether having a first end and a second end with at least the first end of the tether joined to the nucleobase residue, wherein the monomer substrate construct when used in the template directed synthesis is capable of forming a daughter strand comprising a constrained Xpandomer, the constrained Xpandomer having a plurality of subunits coupled in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, the nucleobase residue and at least one selectively cleavable bond.

13 . A duplex daughter strand for use in a template directed synthesis for sequencing a target nucleic acid, comprising a daughter strand duplexed with a template strand, the daughter strand comprising a constrained Xpandomer and having a plurality of subunits coupled in a sequence corresponding to a contiguous nucleotide sequence of all or a portion of the target nucleic acid, wherein the individual subunits comprise a tether, at least one probe or nucleobase residue, and at least one selectively cleavable bond.

14 . An Xpandomer for use in a template directed synthesis for sequencing a target nucleic acid, comprising a plurality of tethers and reporter elements for parsing genetic information in a sequence corresponding to the contiguous nucleotide sequence of all or a portion of the target nucleic acid.

Assignees

• Roche Sequencing Solutions Inc

Inventors

• Kokoris Mark Stamatios
• Mcruer Robert N

Classifications

• C12Q1/6876

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• C07H21/00

  Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids · CPC title

• C12Q1/68

  involving nucleic acids · CPC title

• C12Q1/6897 Primary

  involving reporter genes operably linked to promoters · CPC title