Charged triplet-state quenchers for mitigation of photo-induced damage

Patent metadata

Field	Value
Publication number	US-9637782-B2
Application number	US-201314039397-A
Country	US
Kind code	B2
Filing date	Sep 27, 2013
Priority date	Sep 28, 2012
Publication date	May 2, 2017
Grant date	May 2, 2017

Abstract

Mitigation of photo-induced damage in excitation illuminated reactions and analyses utilizing such reactions results in an enhanced performance for the reactions and the analyses. There is provided a novel class of triplet-state quenchers for mitigating photo-induced damage which are both simple in structure and effective at preventing and/or reducing photo-induced damage to reaction components of excitation illuminated reaction mixtures. Also provided are methods of using the compounds of the invention, devices and kits incorporating the compounds of the invention.

First claim

What is claimed is:

1. A reaction mixture comprising a first reactant, a second reactant comprising a fluorescent or fluorogenic label, and an additive, the additive comprising:
a first photoprotective moiety linked to a polyanion moiety through a first linker, the first linker comprising at least one methylene group; and
a second photoprotective moiety linked to the polyanion moiety;
wherein the additive reduces an amount of photo-induced damage to the first reactant caused by interaction of the first and second reactants under excitation illumination.

2. The reaction mixture of claim 1 , wherein the first reactant is an enzyme selected from the group consisting of a polymerase, ribosome, helicase, nuclease, and ligase enzyme.

3. The reaction mixture of claim 1 , further comprising a template nucleic acid molecule.

4. The reaction mixture of claim 1 , wherein the second reactant comprises a nucleoside polyphosphate, tRNA, or analog thereof.

5. The reaction mixture of claim 1 , wherein at least one component of the reaction mixture is confined within a zero-mode waveguide.

6. The reaction mixture of claim 1 , wherein the additive is present at a concentration between 0.5 and 10 μM.

7. The reaction mixture of claim 1 , wherein the first photoprotective moiety comprises a nitrobenzene derivative.

8. The reaction mixture of claim 1 , wherein the polyanion moiety comprises at least three to six phosphate groups, sulfonate groups, phosphonate groups, arsonate groups, and carboxy groups.

9. The reaction mixture of claim 1 , wherein the additive has the formula:

wherein
R is the first photoprotective moiety;
L is the first linker;
n is selected from 1, 2, 3, 4, 5 and 6; and
X is L′-R′, wherein
L′ is a second linker; and
R′ is the second photoprotective moiety.

10. The reaction mixture of claim 9 , wherein R′ is a substituted or unsubstituted aryl moiety.

11. The reaction mixture of claim 1 , wherein the first and second photoprotective moiety are members independently selected from:

wherein
R 1 , R 2 , R 3 , R 4 , and R 5 are independently members selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, halogen, CN, CF 3 , acyl, —SO 2 NR 6 R 7 , —NR 6 R 7 , —OR 6 , —S(O) 2 R 6 , —C(O)R 6 , —COOR 6 , —CONR 6 R 7 , —S(O) 2 OR 6 , —OC(O)R 6 , —C(O)NR 6 R 7 , —NR 6 C(O)R 7 , —NR 6 SO 2 R 7 and —NO 2 , wherein two or more of R 1 , R 2 , R 3 , R 4 and R 5 , together with the atoms to which they are bonded, are optionally joined to form a ring system which is a member selected from substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl

wherein
R 6 and R 7 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl and substituted or unsubstituted heterocycloalkyl, and R 6 and R 7 , together with the atoms to which they are bonded, are optionally joined to form a 5-to 7-membered ring which is a member selected from substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl.

12. The reaction mixture of claim 11 , wherein at least one of R 1 , R 2 , R 3 , R 4 , and R 5 is NO 2 .

13. A method for protecting an enzyme from photo-induced damage in an illuminated reaction, the method comprising:
providing a reaction mixture comprising the enzyme, and a fluorescent or fluorogenic substrate for the enzyme, wherein interaction of the enzyme and the fluorescent or fluorogenic substrate under excitation illumination results in altered activity of the enzyme;
adding an additive to the reaction mixture, the additive comprising;
a first photoprotective moiety linked to a polyanion moiety through a first linker, the first linker comprising at least one methylene group; and
a second photoprotective moiety linked to the polyanion moiety; and

illuminating the reaction mixture with an excitation illumination, wherein the additive reduces an amount of photo-induced damage to the enzyme resulting from interaction of the enzyme with the fluorescent or fluorogenic substrate under the excitation illumination to an amount that is less than that which would occur in the absence of the additive.

14. The method of claim 13 , wherein the enzyme is a polymerase or a ligase.

15. The method of claim 13 , wherein the reaction mixture further comprises a template nucleic acid molecule, and further wherein the fluorescent or fluorogenic substrate comprises a nucleoside polyphosphate or analog thereof.

16. The method of claim 13 , wherein at least one component of the reaction mixture is confined within a zero-mode waveguide.

17. The method of claim 13 , wherein the first photoprotective moiety comprises a nitrobenzene derivative.

18. The method of claim 13 , wherein the additive is present at a concentration between 0.5 and 10 μM.

19. The method of claim 13 , wherein the polyanion_ moiety comprises at least three to six anion moieties selected from the group consisting of phosphate groups, sulfonate groups, phosphonate groups, arsonate groups, and carboxy groups.

20. The method of claim 13 , wherein the additive has the formula:

wherein
R is the first photoprotective moiety;
L is the first linker;
n is selected from 1, 2, 3, 4, 5 and 6; and
X is L′-R′, wherein
L′ is a second linker; and
R′ is the second photoprotective moiety.

21. A compound having the formula:

in which
R and R′ are independently selected photoprotective moieties;
L and L′ are linkers independently selected alkyl linkers;
n is selected from 1, 2, 3, 4, 5 and 6; and
m is 1.

22. The compound of claim 21 , wherein R and R′ are members independently selected from:

wherein
R 1 , R 2 , R 3 , R 4 , and R 5 are independently members selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted aryl, substituted or unsubstituted heteroaryl, halogen, CN, CF 3 , acyl, —SO 2 NR 6 R 7 , —NR 6 R 7 , —OR 6 , —S(O) 2 R 6 , —C(O)R 6 , —COOR 6 , —CONR 6 R 7 , —S(O) 2 OR 6 , —OC(O)R 6 , —C(O)NR 6 R 7 , —NR 6 C(O)R 7 , —NR 6 SO 2 R 7 and —NO 2 , wherein two or more of R 1 , R 2 , R 3 , R 4 and R 5 , together with the atoms to which they are bonded, are optionally joined to form a ring system which is a member selected from substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl and substituted or unsubstituted heteroaryl

wherein
R 6 and R 7 are members independently selected from H, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or

Assignees

• Pacific Biosciences California Inc

Inventors

• Shen Gene
• Fedorov Andrei
• Sun Wei-Chuan
• Yue Stephen

Classifications

• C12N9/96 Primary

  Stabilising an enzyme by forming an adduct or a composition; Forming enzyme conjugates · CPC title

• C12Q2527/127

  the enzyme inhibitor or activator used · CPC title

• C12Q1/6869 Primary

  Methods for sequencing · CPC title