Multivalent binding composition for nucleic acid analysis

Patent metadata

Field	Value
Publication number	US-2025172547-A1
Application number	US-202519041497-A
Country	US
Kind code	A1
Filing date	Jan 30, 2025
Priority date	Sep 23, 2019
Publication date	May 29, 2025
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 for identifying at least a portion of a cellular component within a sample in situ, the method comprising:
(a) detecting a signal from a binding complex between said cellular component and a nucleotide conjugate within said sample, wherein said nucleotide conjugate comprises at least one nucleotides that are transiently interacting with at least one of said cellular components; and (b) processing at least said signal detected in (a) to identify said at least said portion of said cellular component.

2 . The method of claim 1 , wherein said cellular component is a protein.

3 . The method of claim 1 , further comprising: (c) immobilizing said sample on a surface of a substrate.

4 . The method of claim 3 , further comprising: (d) coupling at least a portion of said cellular component to a capture molecule coupled to said surface.

5 . The method of claim 1 , further comprising permeabilizing said tissue or lysing said cell prior to said detecting in (a).

6 . The method of claim 3 , wherein said surface has a water contact angle of less than or equal to 45 degrees.

7 . The method of claim 4 , wherein said coupling in (d) comprises hybridizing said capture molecule with said at least said portion of said cellular component in a presence of a hybridization buffer comprising:
(a) a first polar aprotic solvent having a dielectric constant that is no greater than 40 and having a polarity index of 4-9; and (b) a second polar aprotic solvent having a dielectric constant that is less than or equal to 115.

8 . The method of claim 3 , wherein an image of said surface exhibits a contrast-to-noise ratio of greater than or equal to 5 as measured by:
(a) contacting said surface with a fluorescently labeled nucleotide molecule comprising a nucleic acid sequence that is complementary to at least a portion of a capture oligonucleotide immobilized to said surface; and (b) following (a), imaging said surface with an inverted microscope and a camera under non-signal saturating conditions while said surface is immersed in a buffer.

9 . The method of claim 1 , wherein detecting said signal from said binding complex in (a) comprises: performing a nucleotide binding reaction between a nucleotide moiety coupled to said nucleotide conjugate and said cellular component, wherein said nucleotide conjugate comprises one or more detectable moieties.

10 . The method of claim 1 , wherein said nucleotide conjugate comprises: two or more nucleotide moieties attached to a polymer core, wherein said nucleotide conjugate is configured to form said binding complex between said two or more nucleotide moieties and said cellular component.

11 . The method of claim 3 , further comprising: (d) determining an origin of said at least said portion of said cellular component in said cell or said tissue, wherein said origin comprises a cell type or a tissue type.

12 . The method of claim 1 , wherein (a) and (b) are performed with accuracy of base-calling that is characterized by a Q-score of greater than 25 for at least 80% of nucleotides identified.

13 . The method of claim 1 , wherein said cellular component is a nucleic acid sequence.

14 . The method of claim 13 , wherein said nucleic acid sequence is a deoxyribonucleic acid (DNA) sequence.

15 . The method of claim 13 , wherein said signal detected in (a) is from a detectable moiety coupled to said binding complex, and wherein said signal is indicative of an identity of a nucleotide in said nucleic acid sequence.

16 . The method of claim 11 , wherein said determining in (d) is performed, at least in part, by analyzing a relative three-dimensional relationship between said cellular component and a point of reference of said cell or said tissue.

17 . The method of claim 16 , wherein said immobilizing in (c) comprises immobilizing said sample on said surface in a manner that is sufficient to fix said relative three-dimensional relationship.

18 . The method of claim 4 , wherein said cellular component is a nucleic acid sequence.

19 . The method of claim 18 , further comprising amplifying said nucleic acid sequence on said surface of said substrate, wherein said amplifying comprises performing a rolling circle amplification reaction.

20 . The method of claim 19 , wherein said signal detected in (a) is from a detectable moiety coupled to said binding complex, and wherein said signal is indicative of an identity of a nucleotide in said nucleic acid sequence.

Assignees

• Element Biosciences Inc

Inventors

• Previte Michael
• He Molly
• Zhao Junhua
• Mah Hui Zhen
• Zhou Chunhong
• Arslan Sinan
• Kellinger Matthew
• Berti Lorenzo
• Chen Steve Xiangling

Classifications

• G01N33/582

  with fluorescent label · CPC title

• C12Q1/6874 Primary

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

• G01N33/5308 Primary

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