Systems and methods for biomolecule retention

Patent metadata

Field	Value
Publication number	US-12305167-B2
Application number	US-202418770462-A
Country	US
Kind code	B2
Filing date	Jul 11, 2024
Priority date	Mar 11, 2021
Publication date	May 20, 2025
Grant date	May 20, 2025

Abstract

Compositions, systems, and methods for the display of analytes such as biomolecules are described. Display of analytes is achieved by coupling of the analytes to displaying molecules that are configured to associate with surfaces or interfaces. Arrays of analytes may be formed from the described systems for utilization in assays and other methods.

First claim

What is claimed is:

1. A method, comprising:
a) forming a first plurality of nucleic acid nanoparticles, wherein the first plurality of nucleic acid nanoparticles is attached to a first plurality of polypeptides of interest, wherein each nucleic acid nanoparticle of the first plurality of nucleic acid nanoparticles is attached to only one polypeptide of the first plurality of polypeptides of interest, wherein a first unique identifier is attached to each nucleic acid nanoparticle of the first plurality of nucleic acid nanoparticles, and wherein the first plurality of polypeptides of interest comprises at least 10 3 different native-length protein primary sequences;
b) forming a second plurality of nucleic acid nanoparticles, wherein the second plurality of nucleic acid nanoparticles is attached to a second plurality of polypeptides of interest, wherein each nucleic acid nanoparticle of the second plurality of nucleic acid nanoparticles is attached to only one polypeptide of the second plurality of polypeptides of interest, wherein a second unique identifier is attached to each nucleic acid nanoparticle of the second plurality of nucleic acid nanoparticles, wherein the first unique identifier and the second unique identifier are different, and wherein the second plurality of polypeptides of interest comprises at least 10 3 different native-length protein primary sequences;
c) attaching to each site of a plurality of sites of a solid support only one nucleic acid nanoparticle of the first plurality of nucleic acid nanoparticles or the second plurality of nucleic acid nanoparticles, wherein each site of the plurality of sites is optically resolvable from any other site of the plurality of sites; and
d) detecting signals from the first unique identifiers at a first set of sites of the plurality of sites, detecting signals from the second unique identifiers at a second set of sites of the plurality of sites.

2. The method of claim 1 , further comprising obtaining the first plurality of polypeptides of interest from a first sample.

3. The method of claim 2 , further comprising obtaining the second plurality of polypeptides of interest from a second sample.

4. The method of claim 2 , further comprising obtaining the second plurality of polypeptides of interest from the first sample.

5. The method of claim 1 , wherein attaching to the plurality of sites of the solid support the first plurality of nucleic acid nanoparticles and the second plurality of nucleic acid nanoparticles comprises attaching at a site of the first set of sites a pendant oligonucleotide of a nucleic acid nanoparticle of the first plurality of nanoparticles to a surface-coupled oligonucleotide of the site.

6. The method of claim 1 , wherein attaching to the plurality of sites of the solid support the first plurality of nucleic acid nanoparticles and the second plurality of nucleic acid nanoparticles comprises attaching at a site of the second set of sites a pendant oligonucleotide of a nucleic acid nanoparticle of the second plurality of nanoparticles to a surface-coupled oligonucleotide of the site.

7. The method of claim 1 , wherein each site of the plurality of sites comprises one or more surface-coupled oligonucleotides, wherein each oligonucleotide of the one or more surface-coupled oligonucleotides comprises an identical nucleotide sequence.

8. The method of claim 7 , wherein each nucleic acid nanoparticle of the first plurality of nucleic acid nanoparticles comprises a pendant oligonucleotide, wherein the pendant oligonucleotide comprises a complementary nucleotide sequence to the identical nucleotide sequence.

9. The method of claim 8 , wherein each nucleic acid nanoparticle of the second plurality of nucleic acid nanoparticles comprises a pendant oligonucleotide, wherein the pendant oligonucleotide comprises the complementary nucleotide sequence to the identical nucleotide sequence.

10. The method of claim 9 , further comprising hybridizing the complementary nucleotide sequence of the pendant oligonucleotide of a nucleic acid nanoparticle of the first plurality of nucleic acid nanoparticles to the identical nucleotide sequence of a site of the first set of sites of the plurality of sites.

11. The method of claim 10 , further comprising hybridizing the complementary nucleotide sequence of the pendant oligonucleotide of a nucleic acid nanoparticle of the second plurality of nucleic acid nanoparticles to the identical nucleotide sequence of a site of the second set of sites of the plurality of sites.

12. The method of claim 1 , wherein attaching to the plurality of sites of the solid support the first plurality of nucleic acid nanoparticles and the second plurality of nucleic acid nanoparticles comprises:
i) attaching the first plurality of nucleic acid nanoparticles to the first set of sites; and
ii) after attaching the first plurality of nucleic acid nanoparticles to the first set of sites, attaching the second plurality of nucleic acid nanoparticles to the second set of sites.

13. The method of claim 12 , further comprising, before attaching the second plurality of nucleic acid nanoparticles to the second set of sites, determining the first set of sites containing the first plurality of nucleic acid nanoparticles.

14. The method of claim 13 , wherein determining the first set of sites containing the first plurality of nucleic acid nanoparticles comprises detecting signals from nucleic acid nanoparticles at addresses of the first set of sites.

15. The method of claim 12 , further comprising, after attaching the second plurality of nucleic acid nanoparticles to the second set of sites, determining the second set of sites containing the second plurality of nucleic acid nanoparticles.

16. The method of claim 15 , wherein determining the second set of sites containing the second plurality of nucleic acid nanoparticles comprises detecting signals from nucleic acid nanoparticles at addresses of the second set of sites.

17. The method of claim 1 , wherein the first unique identifier comprises a first detectable label and the second unique identifier comprises a second detectable label, wherein the first detectable label differs from the second detectable label.

18. The method of claim 17 , wherein the first detectable label and the second detectable label comprise differing fluorophores.

19. The method of claim 17 , wherein the first detectable label and the second detectable label comprises differing nucleic acid tags or peptide tags.

20. The method of claim 1 , wherein the first set of sites and the second set of sites have random spatial distributions.

21. The method of claim 1 , wherein the attaching occurs in the presence of a fluidic medium containing a denaturing species.

22. The method of claim 1 , wherein the first plurality of polypeptides of interest or the second plurality of polypeptides of interest comprises at least 10 6 polypeptide molecules.

23. The method of claim 22 , wherein the first plurality of polypeptides of interest comprises at least 10 6 polypeptide molecules and the second plurality of polypeptides of interest comprises at least 10 6 polypeptide molecules.

24. The method of claim 22 , wherein the first plurality of polypeptides of interest or the second plurality of polypeptides of interest comprises at least 10 8 polypeptide molecules.

25. The method of claim 1 , wherein the plurality of sites comprises at least 10 8 sites.

Assignees

• Nautilus Subsidiary Inc

Inventors

• Hao Pengyu
• Ikwa Elvis
• Indermuhle Pierre
• Inman Christina
• Mallick Parag
• Rinker Torri Elise
• Tan Steven
• Aksel Tural
• Hendricks Stephen
• Ingle Sadie

Classifications

• C12Q1/6837

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title

• B82Y5/00

  Nanobiotechnology or nanomedicine, e.g. protein engineering or drug delivery · CPC title

• B01J2219/0061

  The surface being organic · CPC title

• B01J19/0046

  Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays (synthesis methods per se C40B50/00) · CPC title

• C12Q1/6804

  Nucleic acid analysis using immunogens (immunoassay G01N33/53) · CPC title