Multivalent binding composition for nucleic acid analysis

Patent metadata

Field	Value
Publication number	US-2024230631-A1
Application number	US-202418431748-A
Country	US
Kind code	A1
Filing date	Feb 2, 2024
Priority date	May 1, 2019
Publication date	Jul 11, 2024
Grant date	—

Abstract

Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

First claim

What is claimed:

1 . A method of determining the identity of a nucleotide in a target nucleic acid comprising:
a. providing a composition comprising:
i. a target nucleic acid;
ii. a primer nucleic acid complementary to one or more regions of said target nucleic acid; and
iii. a polymerase molecule;
b. contacting said composition with a binding composition comprising a polymer-nucleotide conjugate under conditions sufficient to allow a binding complex to be formed between said polymer-nucleotide conjugate and the composition of step (a), wherein the polymer-nucleotide conjugate comprises a nucleotide and optionally one or more detectable labels; and c. detecting said binding complex, thereby establishing the identity of said nucleotide in the target nucleic acid.

2 . The method of claim 1 , wherein the target nucleic acid is DNA.

3 . The method of claim 1 wherein the detection of the binding complex is performed in the absence of unbound or solution-borne polymer nucleotide conjugates.

4 . The method of claim 1 wherein the target nucleic acid has been replicated or amplified or has been produced by replication or amplification.

5 . The method of claim 1 wherein the detectable label is a fluorescent label.

6 . The method of claim 1 wherein detecting the complex comprises a fluorescence measurement.

7 . The method of claim 1 wherein the multivalent binding composition comprises one type of polymer-nucleotide conjugate.

8 . The method of claim 1 wherein the multivalent binding composition comprises two or more types of polymer-nucleotide conjugates.

9 . The method of claim 8 , wherein each type of the two or more types of polymer-nucleotide conjugates comprises a different type of nucleotide.

10 . The method of claim 9 wherein the binding composition consists of three types of polymer-nucleotide conjugates and wherein each type of the three types of polymer-nucleotide conjugates comprises a different type of nucleotide.

11 . A system for determining the identity of a nucleotide in a target nucleic acid, the system comprising:
(a) a solid support having coupled thereto a primed target nucleic acid molecule; (b) a polymerase; and (c) a polymer-nucleotide conjugate, wherein the polymer-nucleotide conjugate comprises (i) a nucleotide and (ii) a detectable label.

12 . The system of claim 11 , wherein the detectable label is a fluorescent label.

13 . The system of claim 11 , wherein the polymer-nucleotide conjugate comprises two or more detectable labels.

14 . The system of claim 11 , wherein the target nucleic acid is DNA.

15 . The system of claim 11 , wherein the binding composition comprises one type of polymer-nucleotide conjugate.

16 . The system of claim 11 , wherein the binding composition comprises two or more types of polymer-nucleotide conjugates.

17 . The system of claim 16 , wherein each type of the two or more types of polymer-nucleotide conjugates comprises a different type of nucleotide.

18 . The system of claim 17 , wherein the binding composition consists of three types of polymer-nucleotide conjugates and wherein each type of the three types of polymer-nucleotide conjugates comprises a different type of nucleotide.

19 . The system of claim 11 , wherein the primed target nucleic acid has been replicated or amplified or has been produced by replication or amplification.

20 . The system of claim 11 , wherein the polymer-nucleotide conjugate is contacted with the target nucleic acid and polymerase under conditions sufficient to form a binding complex.

Assignees

• Element Biosciences Inc

Inventors

• Arslan Sinan
• He Molly
• Kellinger Matthew
• Levieux Jake
• Previte Michael
• Zhao Junhua
• Zhang Su

Classifications

• G01N33/5308 Primary

  for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites · CPC title

• G01N33/582

  with fluorescent label · CPC title

• C12Q1/6874

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

• C12Q1/6869 Primary

  Methods for sequencing · CPC title