Amplification oligonucleotides

Patent metadata

Field	Value
Publication number	US-11932905-B2
Application number	US-202318185785-A
Country	US
Kind code	B2
Filing date	Mar 17, 2023
Priority date	Sep 3, 2021
Publication date	Mar 19, 2024
Grant date	Mar 19, 2024

Abstract

Disclosed herein, inter alia, are polynucleotides, supports, kits, and methods of use thereof for amplifying, immobilizing, and sequencing polynucleotides.

First claim

What is claimed is:

1. A plurality of nucleic acid molecules, wherein each nucleic acid molecule comprises a first end, a target sequence, and a second end, wherein the first end comprises SEQ ID NO:92, and wherein each target sequence of said plurality of nucleic acid molecules is different from each other.

2. The plurality of claim 1 , wherein the second end comprises a sequence comprising SEQ ID NO:104, SEQ ID NO:4, SEQ ID NO:102, SEQ ID NO:106, SEQ ID NO:108, SEQ ID NO:134, SEQ ID NO:136, SEQ ID NO:138, or SEQ ID NO:140.

3. The plurality of claim 2 , wherein the second end comprises SEQ ID NO:4.

4. The plurality of claim 2 , wherein the second end comprises SEQ ID NO:136.

5. The plurality of claim 1 , wherein the target sequence comprises genomic DNA.

6. The plurality of claim 1 , wherein the target sequence comprises a cancer associated gene, or fragment thereof.

7. The plurality of claim 1 , wherein each nucleic acid molecule comprises 50 to 1000 nucleotides.

8. The plurality of claim 1 , wherein each nucleic acid molecule comprises 100 to 500 nucleotides.

9. The plurality of claim 1 , wherein each nucleic acid molecule consists of 50 to 1000 nucleotides.

10. The plurality of claim 1 , wherein one of said first end or said second end comprise a hairpin adapter.

11. The plurality of claim 1 , wherein said first end and said second end each comprise a hairpin adapter.

12. The plurality of claim 1 , wherein one of said first end or said second end comprise a Y polynucleotide adapter.

13. The plurality of claim 1 , wherein both said first end and said second end comprise a Y polynucleotide adapter.

14. The plurality of claim 1 , wherein said plurality of nucleic acid molecules comprises single-stranded DNA or double-stranded DNA.

15. The plurality of claim 1 , wherein each nucleic acid molecule comprises, from 5′ to 3′, said first end, said target sequence, and said second end.

16. The plurality of claim 1 , wherein the second end comprises SEQ ID NO:104.

17. The plurality of claim 1 , wherein one or more of the nucleic acid molecules are immobilized to a solid support.

18. The plurality of claim 17 , wherein said solid support further comprises one or more complements of said nucleic acid molecules.

19. The plurality of claim 17 , wherein said solid support further comprises a polymer, resist, and/or hydrogel.

20. The plurality of claim 17 , wherein said nucleic acid molecules are covalently attached to a polymer on the solid support via a linker.

21. The plurality of claim 20 , wherein the linker comprises 8 to 16 thymine nucleotides, and wherein the linker is at a 5′ end of the immobilized nucleic acid molecules.

22. The plurality of claim 20 , wherein the linker comprises a cleavable site.

23. The plurality of claim 22 , wherein the cleavable site comprises a deoxyuracil triphosphate (dUTP), diol linker, disulfide linker, photocleavable linker, abasic site, deoxy-8-Oxo-guanine triphosphate (d-8-oxoG), methylated nucleotide, ribonucleotide, or a sequence containing a modified or unmodified nucleotide that is specifically recognized by a cleaving agent.

24. The plurality of claim 17 , wherein said one or more nucleic acid molecules further comprise a first oligonucleotide hybridized to the first end, and wherein said first oligonucleotide is attached to said solid support.

25. The plurality of claim 17 , wherein said one or more nucleic acid molecules further comprise a second oligonucleotide hybridized to the second end, and wherein said second oligonucleotide is attached to said solid support.

26. The plurality of claim 17 , further comprising one or more complements of said nucleic acid molecules immobilized to said solid support.

27. The plurality of claim 26 , wherein said one or more immobilized complements of said nucleic acid molecules are hybridized to said immobilized nucleic acid molecules.

28. The plurality of claim 17 , wherein said one or more immobilized nucleic acid molecules is hybridized to a sequencing primer, and wherein said sequencing primer comprises a labeled nucleotide at a 3′ end.

Assignees

• Singular Genomics Systems Inc

Inventors

• Shultzaberger Ryan
• Lipson Allen
• Witters Daan

Classifications

• C12Q1/6855 Primary

  Ligating adaptors · CPC title

• C12Q1/6874

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

• C12Q1/6876

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

• C12Q1/6837

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

• B01L3/502707

  characterised by the manufacture of the container or its components · CPC title