Granted Patent B2

US 12,234,507 · App. 18/366,621 · Granted Feb 25, 2025

Inventors: Hong Chen (Dublin, CA); Joshua Delaney (Northcote, AU); Yi Luo (Dublin, CA); Meiliana Tjandra (Dublin, CA)

Assignee: 10X GENOMICS, INC.

C12Q1/6841C12Q1/6806C12Q1/6876G01N1/30G01N21/64G01N2021/6432G01N2021/6439

Abstract

Claims (65)

1. A method, comprising:

(a) contacting a biological sample with a quencher comprising a quencher dye and a targeting moiety, wherein the targeting moiety covalently binds with a biological moiety endogenous to the biological sample, thereby targeting the quencher to the biological moiety;

(b) contacting the biological sample with a detectable probe that binds to a molecule of interest in the biological sample; and

(c) detecting a signal associated with the detectable probe bound to the molecule of interest in the biological sample,

thereby detecting the molecule of interest in the biological sample.

2. The method of claim 1 , wherein autofluorescence in the biological sample is reduced by at least 50% as compared to an unquenched biological sample.

3. The method of claim 1 , wherein the signal associated with the detectable probe is detected at a location in the biological sample, and the detected signal has a signal-to-noise ratio that is increased as compared to an unquenched biological sample.

4. The method of claim 1 , wherein the biological sample is contacted with the detectable probe in the contacting step (b) prior to being contacted with the quencher in the contacting step (a).

5. The method of claim 1 , wherein the biological sample is contacted with the detectable probe in the contacting step (b) after being contacted with the quencher in the contacting step (a).

6. The method of claim 1 , further comprising bleaching the biological sample with a chemical reagent, an enzyme, light, heat, or any combination thereof, prior to, simultaneously, or after the contacting in step (a).

7. The method of claim 1 , further comprising removing the detectable probe or a portion thereof from the biological sample, wherein the quencher remains in the biological sample.

8. The method of claim 7 , wherein the removing step comprises treating the biological sample with a denaturing agent comprising dimethyl sulfoxide (DMSO), formamide, and/or an alkaline solution.

9. The method of claim 1 , wherein the quencher dye comprises:

(a) at least three aromatic residues, wherein each aromatic residue is independently an unsubstituted aryl, a substituted aryl, an unsubstituted heteroaryl, or a substituted heteroaryl, wherein at least one of said aromatic residues is covalently linked to two other aromatic residues via two exocyclic azo bonds; or

(b) at least two aromatic residues, wherein each aromatic residue is independently an unsubstituted aryl, a substituted aryl, an unsubstituted heteroaryl, or a substituted heteroaryl, wherein at least two of said aromatic residues are covalently linked via an exocyclic azo bond, and wherein at least one said aromatic residue is an unsubstituted polycyclic aryl, a substituted polycyclic aryl, an unsubstituted polycyclic heteroaryl group, or a substituted polycyclic heteroaryl group.

10. The method of claim 1 , wherein the quencher dye comprises an optionally substituted 1,4-bis ((E)-phenyldiazenyl) benzene moiety

an optionally substituted (E)-5-phenyl-3-(phenyldiazenyl) phenazin-5-ium moiety

or a salt thereof.

11. The method of claim 10 , wherein the quencher has a UV-visible absorption profile with at least one absorption peak with an absorption maximum between 400 nm and 700 nm and a full-width half-maximum of at least 100 nm.

12. The method of claim 1 , wherein the quencher is a compound of formula (I)

or a salt thereof, wherein

each

 is independently selected from the group consisting of a substituted or unsubstituted aryl, and a substituted or unsubstituted heteroaryl;

X a is H, halo, —OH, C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, C 1 -C 6 alkoxy, C 1 -C 6 haloalkoxy, hydroxyl-C 1 -C 6 alkylene, —NR 1 R 2 , —NO 2 , —SO 3 H, —SO 3 − , —OSO 2 —C 1 -C 6 alkyl, —OSO 2 —C 1 -C 6 haloalkyl, —CN, —SCN, —NCO, or -L-(R target ) w , wherein w is 1 or 2;

X c is H, halo, —OH, C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, C 1 -C 6 alkoxy, C 1 -C 6 haloalkoxy, hydroxyl-C 1 -C 6 alkylene, —NR 1 R 2 , —NO 2 , —SO 3 H, —SO 3 − , —OSO 2 —C 1 -C 6 alkyl, —OSO 2 —C 1 -C 6 haloalkyl, —CN, —SCN, —NCO, or -L-(R target ) w , wherein w is 1 or 2;

wherein R 1 and R 2 are independently H, C 1 -C 6 alkyl or substituted C 1 -C 6 alkyl; and

each R a and R c is independently H, halo, —OH, C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, C 1 -C 6 alkoxy, C 1 -C 6 haloalkoxy, hydroxyl-C 1 -C 6 alkylene, —NR 1 R 2 , —NO 2 , —SO 3 H, —SO 3 − , —OSO 2 —C 1 -C 6 alkyl, —OSO 2 —C 1 -C 6 haloalkyl, —CN, —SCN, or —NCO;

each R b is independently H, halo, —OH, C 1 -C 6 alkyl, C 1 -C 6 haloalkyl, C 1 -C 6 alkoxy, C 1 -C 6 haloalkoxy, hydroxyl-C 1 -C 6 alkylene, —NR 1 R 2 , —NO 2 , —SO 3 H, —SO 3 − , —OSO 2 —C 1 -C 6 alkyl, —OSO 2 —C 1 -C 6 haloalkyl, —CN, —SCN, —NCO, R b1 , or -L-(R target ) w , wherein w is 1 or 2;

R b1 is a substituted or unsubstituted alkyl, a substituted or unsubstituted aryl, or a substituted or unsubstituted heteroaryl;

L is a bond or a linker moiety;

R target is a targeting moiety;

m is an integer from 0 to 6;

n is an integer from 0 to 6; and

each of x, y, and z is independently an integer from 0 to 5;

provided that at least one of m and n is nonzero; and provided that at least one of X a , X c , or R b is -L-(R target ) w , wherein w is 1 or 2.

13. The method of claim 12 , wherein each of at least one, at least two, or at least three instances of

is a substituted phenyl or an unsubstituted phenyl.

14. The method of claim 12 , wherein the quencher has the following structure:

or a salt thereof,

provided that at least one of X a and X c is -L-(R target ) w , wherein w is 1 or 2, and wherein L is a bond or a linker moiety; and R target is a targeting moiety.

15. The method of claim 12 , wherein

is:

wherein R b1 is a substituted or unsubstituted alkyl, a substituted or unsubstituted aryl, or a substituted or unsubstituted heteroaryl.

16. The method of claim 15 , wherein

is

wherein R d is H, C 1 -C 6 alkyl, or halo; and s is an integer from 0 to 5.

17. The method of claim 12 , wherein the quencher has the following structure:

or a salt thereof, wherein R d is H, C 1 -C 6 alkyl, or halo; and s is an integer from 0 to 5.

18. The method of claim 1 , wherein the molecule of interest is a nucleic acid of interest or a protein of interest.

19. The method of claim 1 , wherein the targeting moiety comprises a first functional group, and the endogenous biological moiety comprises a second functional group capable of reacting with the first functional group to form a covalent bond.

20. The method of claim 19 , wherein the first functional group is a carboxylic acid moiety or derivative thereof, an aldehyde or ketone moiety, a sulfonyl halide moiety, a hydroxyl moiety, a thiol moiety, an amino moiety, an alkenyl or dienyl moiety, an epoxide moiety, or a haloalkyl moiety.

21. The method of claim 20 , wherein the first functional group is a maleimido moiety, an azido moiety, an alkynyl moiety, an N-hydroxysuccinimidyl ester moiety, or a carbonylimidazolyl moiety.

22. The method of claim 21 , wherein the first functional group is a maleimido moiety.

23. The method of claim 1 , wherein the quencher is selected from the group consisting of:

and any salt thereof.

24. The method of claim 1 , wherein the quencher is a compound selected from the group consisting of:

and any salt thereof.

25. The method of claim 19 , further comprising a step of treating the biological sample to enrich, create, and/or introduce the second functional group in the endogenous biological moiety.

26. The method of claim 25 , wherein the second functional group is thiol, and the biological sample is treated with a reducing agent to convert disulfide groups to thiol groups.

27. The method of claim 25 , wherein the endogenous biological moiety comprises a third functional group, which is different from the second functional group, and wherein the biological sample is treated with a heterobifunctional crosslinker comprising the second functional group and a fourth functional group capable of reacting with the third functional group to form a covalent bond, thereby introducing the second functional group in the endogenous biological moiety.

28. The method of claim 1 , further comprising removing the detectable probe by treating the biological sample with a denaturing agent and/or heating, wherein the quencher remains in the biological sample, and contacting the biological sample with one or more additional detectable probes after treating the biological sample with the denaturing agent and/or heating.

29. The method of claim 1 , wherein the biological moiety endogenous to the biological sample is a polypeptide or a lipid.

30. The method of claim 12 , wherein the biological sample is a tissue sample and the method further comprises, prior to (a):

(a′) contacting the tissue sample with a nucleic acid probe that binds to an analyte in the tissue sample,

wherein the detectable probe in (b) is a fluorescently labeled detectable probe and the molecule of interest is the nucleic acid probe or an amplification product of the nucleic acid probe, and wherein the quencher dye reduces autofluorescence in the tissue sample.

Assignments (1)

Continuity (3)

References Cited (334)