High intensity labeled reactant compositions and methods for sequencing

Patent metadata

Field	Value
Publication number	US-11655504-B2
Application number	US-201816043547-A
Country	US
Kind code	B2
Filing date	Jul 24, 2018
Priority date	Jul 24, 2017
Publication date	May 23, 2023
Grant date	May 23, 2023

Abstract

Compositions useful for the detection of single molecules in a sample are provided. In some aspects, the disclosure provides a nucleic acid connected to a nucleotide and two or more luminescent labels. In some embodiments, the nucleic acids described herein comprise one or more structural features that provide enhanced fluorescence intensity. In some aspects, methods of sequencing using the labeled nucleotides of the disclosure are provided.

First claim

The invention claimed is:

1. A labeled molecule comprising a reactant connected to two or more luminescent labels via a nucleic acid linker, wherein each luminescent label is at least 5 angstroms separated from any other luminescent label, wherein
(i) at least one luminescent label is integrated within the nucleic acid linker, and wherein the at least one luminescent label that is integrated within the nucleic acid linker is a cyanine-based fluorophore; and/or
(ii) wherein at least one luminescent label is attached to the nucleic acid linker via a glycolamine spacer molecule, and wherein the labeled nucleotide comprises the structure:

where is the at least one luminescent label that is attached to the nucleic acid linker via the glycolamine spacer molecule.

2. The labeled molecule of claim 1 , wherein the cyanine-based fluorophore has the chemical structure:

3. The labeled molecule of claim 1 , wherein the at least one luminescent label attached to the nucleic acid linker via a glycolamine spacer molecule comprises a rhodamine dye, a BODIPY dye, or a cyanine dye.

4. A labeled nucleotide comprising a nucleoside polyphosphate connected to two or more luminescent labels via a nucleic acid linker, wherein the nucleic acid linker is connected to the terminal phosphate of the nucleoside polyphosphate, wherein each luminescent label is at least 5 angstroms separated from any other luminescent label, wherein
(i) at least one luminescent label is integrated into the nucleic acid linker, and wherein the at least one luminescent label that is integrated within the nucleic acid linker is a cyanine-based fluorophore; and/or
(ii) wherein at least one luminescent label is attached to the nucleic acid linker via a glycolamine spacer molecule, and wherein the labeled nucleotide comprises the structure:

where is the at least one luminescent label that is attached to the nucleic acid linker via the glycolamine spacer molecule.

5. The labeled nucleotide of claim 4 , wherein each luminescent label comprises a center of mass that is at least 5 angstroms separated from the center of mass of any other luminescent label.

6. The labeled nucleotide of claim 4 , wherein the cyanine-based fluorophore has the chemical structure:

7. The labeled nucleotide of claim 4 , wherein the at least one luminescent label attached to the nucleic acid linker via a glycolamine spacer molecule comprises a rhodamine dye, a BODIPY dye, or a cyanine dye.

8. The labeled nucleotide of claim 4 , wherein the nucleic acid linker is an oligomer that comprises at least 10 monomeric units.

9. The labeled nucleotide of claim 8 , wherein the oligomer comprises fewer than 150, fewer than 100, or fewer than 50 monomeric units.

10. The labeled nucleotide of claim 8 , wherein at least one luminescent label is attached to the nucleic acid linker at an attachment site that is at least 5 monomeric units separated from any other attachment site.

11. The labeled nucleotide of claim 4 , wherein the nucleic acid linker comprises a first oligonucleotide strand attached to the two or more luminescent labels at two or more attachment sites on the first oligonucleotide strand, and wherein each luminescent label comprises a steric volume having a center point that is at least 5 angstroms separated from that of any other luminescent label.

12. The labeled nucleotide of claim 11 , further comprising a second oligonucleotide strand hybridized with the first oligonucleotide strand, wherein the first oligonucleotide strand is attached to the nucleoside polyphosphate.

13. The labeled nucleotide of claim 11 , further comprising a second oligonucleotide strand hybridized with the first oligonucleotide strand, wherein the second oligonucleotide strand is attached to the nucleoside polyphosphate.

14. The labeled nucleotide of claim 11 , wherein the two or more attachment sites are separated from one another by at least 5 and fewer than 50 bases on the first oligonucleotide strand.

15. The labeled nucleotide of claim 11 , wherein each attachment site is at least 2 bases separated from a guanine or a cytosine on the first oligonucleotide strand.

16. The labeled nucleotide of claim 11 , wherein at least one attachment site occurs at an abasic site on the first oligonucleotide strand.

17. The labeled nucleotide of claim 11 , wherein the first oligonucleotide strand forms one or more stem-loops.

18. The labeled nucleotide of claim 17 , wherein a loop region of each stem-loop comprises an attachment site of the two or more attachment sites.

Assignees

• Quantum Si Inc

Inventors

• Rothberg Jonathan M
• Lackey Jeremy
• Reed Brian
• Shi Xinghua
• Huang Haidong
• Dodd David

Classifications

• C12Q1/6876 Primary

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

• C12Q1/6869

  Methods for sequencing · CPC title

• C07H19/073 Primary

  with 2-deoxyribosyl as the saccharide radical · CPC title

• C07H21/04

  with deoxyribosyl as saccharide radical · CPC title

• C12Q2600/16

  Primer sets for multiplex assays · CPC title