IP Library › Granted Patent US 12,378,600
Granted Patent B2
US 12,378,600 · App. 18/410,793 · Granted Aug 5, 2025

Linkers and methods for optical detection and sequencing

Inventors: Linda G. Lee (Palo Alto, CA); Gilad Almogy (Palo Alto, CA); Steven Menchen (Fremont, CA)
Assignee: Ultima Genomics, Inc.
C12Q1/6823C12Q1/6869C12Q1/6876
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Quick Facts
Patent No.
US 12,378,600
App. No.
18/410,793
Granted
Aug 5, 2025
Kind
B2
Abstract

The present disclosure provides labeling reagents for labeling substrates such as nucleotides, proteins, antibodies, lipids, and cells. The labeling reagents provided herein may comprise fluorescent labels and semi-rigid linkers. Methods for nucleic acid sequencing using materials comprising such labeling reagents are also provided here.

Claims (23)

1. A composition comprising a solution comprising a fluorescently labeled nucleotide of a plurality of fluorescently labeled nucleotides, wherein said fluorescently labeled nucleotide comprises a fluorescent dye that is connected to a nucleotide via a linker, wherein said linker comprises (i) one or more water soluble groups and (ii) two or more ring systems, wherein said linker is coupled to a nucleobase of said nucleotide, wherein at least two of said two or more ring systems are connected to each other by no more than two atoms, wherein said linker comprises a non-proteinogenic amino acid comprising a ring system of said two or more ring systems; and wherein said solution further comprises a plurality of unlabeled nucleotides.

2. The composition of claim 1 , wherein each fluorescently labeled nucleotide of said plurality of said fluorescently labeled nucleotides comprises said fluorescent dye that is connected to said nucleotide via said linker.

3. The composition of claim 2 , wherein each nucleotide of said plurality of unlabeled nucleotides is of a same base type as each nucleotide of said plurality of fluorescently labeled nucleotides.

4. The composition of claim 3 , wherein the ratio of said plurality of fluorescently labeled nucleotides to said plurality of unlabeled nucleotides in said solution is at least about 1:4.

5. The composition of claim 4 , wherein said ratio is at least about 1:1.

6. An oligonucleotide molecule comprising a first fluorescent labeling reagent and a second fluorescent labeling reagent, each comprising:

(a) a fluorescent dye; and

(b) a linker that is connected to said fluorescent dye and is coupled to a nucleotide of said oligonucleotide molecule,

wherein said linker comprises (i) one or more water soluble groups and (ii) two or more ring systems, wherein said linker is coupled to a nucleobase of said nucleotide, wherein at least two of said two or more ring systems are connected to each other by no more than two atoms, and wherein said linker comprises a non-proteinogenic amino acid comprising a ring system of said two or more ring systems.

7. The oligonucleotide molecule of claim 6 , wherein said first and second fluorescent labeling reagents comprise linkers having the same chemical structure.

8. The oligonucleotide molecule of claim 6 , wherein said first and second fluorescent labeling reagents comprise fluorescent dyes having the same chemical structure.

9. The oligonucleotide molecule of claim 6 , wherein said first and second fluorescent labeling reagents are connected to adjacent nucleotides of said oligonucleotide molecule.

10. The oligonucleotide molecule of claim 6 , wherein said first and second fluorescent labeling reagents are connected to nucleotides of said oligonucleotide molecule that are separated by one or more nucleotides that are not connected to fluorescent labeling reagents.

11. The oligonucleotide molecule of claim 6 , wherein said linker of said first and second fluorescent labeling reagents comprises a cleavable group that is configured to be cleaved to separate said fluorescent dye from said nucleotide with which it is associated.

12. The oligonucleotide molecule of claim 6 , wherein said linker comprises a plurality of amino acids.

13. The oligonucleotide molecule of claim 12 , wherein said linker comprises three or more hydroxyprolines.

14. The oligonucleotide molecule of claim 6 , wherein said first fluorescent labeling reagent or said second fluorescent labeling reagent further comprises a cleavable group that is configured to be cleaved to separate said first fluorescent labeling reagent or portion thereof or said second fluorescent labeling reagent or portion thereof from said nucleotide coupled to said first fluorescent labeling reagent or said nucleotide coupled to said second fluorescent labeling reagent, respectively, and wherein said cleavable group is cleavable by application of one or more members of the group consisting of tris(2-carboxyethyl) phosphine (TCEP), dithiothreitol (DTT), tetrahydropyranyl (THP), ultraviolet (UV) light, and a combination thereof.

15. The oligonucleotide molecule of claim 14 , wherein said cleavable group is selected from the group consisting of an azidomethyl group, a disulfide bond, a hydrocarbyldithiomethyl group, and a 2-nitrobenzyloxy group.

16. The composition of claim 1 , wherein said linker comprises a plurality of amino acids.

17. The composition of claim 16 , wherein said linker comprises three or more hydroxyprolines.

18. The composition of claim 1 , wherein said fluorescently labeled nucleotide further comprises a cleavable group that is configured to be cleaved to separate said fluorescent dye or portion thereof from said nucleotide, and wherein said cleavable group is cleavable by application of one or more members of the group consisting of tris(2-carboxyethyl) phosphine (TCEP), dithiothreitol (DTT), tetrahydropyranyl (THP), ultraviolet (UV) light, and a combination thereof.

19. The composition of claim 18 , wherein said cleavable group is selected from the group consisting of an azidomethyl group, a disulfide bond, a hydrocarbyldithiomethyl group, and a 2-nitrobenzyloxy group.

20. The composition of claim 1 , wherein said linker comprises a moiety selected from the group consisting of

Assignments (2)
SECURITY INTEREST Recorded Apr 3, 2026
From: ULTIMA GENOMICS, INC.
To: JPMORGAN CHASE BANK, N.A.
Reel/Frame 075435/0595 →
ASSIGNMENT OF ASSIGNOR'S INTEREST Recorded Feb 13, 2024
From: LEE, LINDA G.; ALMOGY, GILAD; MENCHEN, STEVEN
To: ULTIMA GENOMICS, INC.
Reel/Frame 066453/0876 →
Continuity (5)
Continuation 17697636 · Mar 17, 2022
Continuation 17395382 · Aug 5, 2021
Continuation PCTUS2020018699 · Feb 18, 2020
Provisional Application 62807550 · Feb 19, 2019
Related Publication 20240263216A1 · Aug 8, 2024
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