Biotin containing C-glycoside nucleic acid labeling compounds

• US 6,864,059 B2
• Filed: 12/05/2002
• Issued: 03/08/2005
• Est. Priority Date: 01/23/1996
• Status: Expired due to Term

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Barone, Anthony D., McGall, Glenn
• Primary Examiner(s): MCKENZIE, THOMAS C
• Application Number:
  US10/314,012
• Publication Number:
  US 20030180757A1
• Time in Patent Office: 824 Days
• Field of Search: 435/6, 536/23.1, 536/25.1
• US Class Current: 435/6.14
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• CPC Class Codes: C07H 19/052 Imidazole radicals
• CPC Class Codes: C07H 19/06 Pyrimidine radicals
• CPC Class Codes: C07H 19/12 Triazine radicals
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C07H 7/00 Compounds containing non-saccharide radicals linked to saccharide radicals by a carbon-to-carbon bond
• CPC Class Codes: C07H 7/06 Heterocyclic radicals
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures

Abstract

Nucleic acid labeling compounds including the following structure are disclosed:
wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH₄+; X is O; Y is OH; Z is OH; L is selected from the group consisting of —CH═CH—C(O)—NH—CH₂—CH₂—NH—C(O)— and —CH₂—CH₂—C(O)—NH—CH₂—CH₂—NH—C(O); M is —(CH₂)₄₅—NH—, n is 1 and Q is biotin having the structure:
The labeling compounds are suitable for enzymatic attachment to a nucleic acid, either terminally or internally, to provide a mechanism of nucleic acid detection.

Claims

1. A nucleic acid labeling compound of the following structure:

wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH₄+;

X is O;

Y is OH;

Z is OH;

L is selected from the group consisting of —

CH═

CH—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O)— and

—

CH₂—

CH₂—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O);

M is —

(CH₂)₄₅—

NH—

, n is 1 and Q is biotin having the structure;

2. A nucleic acid labeling compound according to claim 1 wherein L is —

CH═

CH—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O)—

.

3. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 1 with a nucleic acid.

4. A hybridization product, wherein the hybridization product comprises the nucleic acid derivative according to claim 3 bound to a complementary probe.

5. The hybridization product according to claim 4, wherein the probe is attached to a glass chip.

6. A method of synthesizing a labeled nucleic acid comprising attaching a nucleic acid labeling compound according to claim 1 to a nucleic acid.

7. A method of detecting a nucleic acid comprising incubating a nucleic acid derivative according to claim 3 with a probe.

8. A method according to claim 7, wherein the probe is attached to a glass chip.

9. A nucleic acid labeling compound of the following structure:

wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH₄+;

X is O;

Y is OH;

Z is OH;

L is selected from the group consisting of —

CH═

CH—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O)— and

—

CH₂—

CH₂—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O);

M is —

(CH₂)₄₅—

NH—

, n is 1 and Q is biotin having the structure;

10. A nucleic acid labeling compound according to claim 9 wherein L is —

CH═

CH—

C(O)—

NH—

CH₂—

CH₂—

NH—

C(O)—

.

11. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 9 with a nucleic acid.

12. A hybridization product, wherein the hybridization product comprises the nucleic acid derivative according to claim 11 bound to a complementary probe.

13. The hybridization product according to claim 12, wherein the probe is attached to a glass chip.

14. A method of synthesizing a labeled nucleic acid comprising attaching a nucleic acid labeling compound according to claim 9 to a nucleic acid.

15. A method of detecting a nucleic acid comprising incubating a nucleic acid derivative according to claim 11 with a probe.

16. A method according to claim 15, wherein the probe is attached to a glass chip.

17. A nucleic acid labeling compound having the structure

wherein A is a triphosphate group with apporpriate counterions, said counterions selected from the group consisting of H+, Na+, Li+, K+, and NH₄+, Y is OH;

Z is OH;

L is —

C(O)NH(CH₂)₂NH—

, M is selected from the group consisting of —

C(O)(CH2)₅NH— and

—

C(O)((CH₂)₂O)₄(CH₂)₂NH—

, n is 1 and Q is biotin, having the structure;

18. A nucleic acid labeling compound according to claim 17 wherein M is —

C(O)(CH2)₅NH—

.

19. A nucleic acid derivative produced by coupling a nucleic acid labeling compound according to claim 17 with a nucleic acid.

20. A hybridization product, wherein the hybridization product comprises the nucleic acid derivative according to claim 19 bound to a complementary probe.

21. The hybridization product according to claim 20, wherein the probe is attached to a glass chip.

22. A hybridization product, wherein the hybridization product comprises the nucleic acid derivative according to claim 18 bound to a complementary probe.

23. The hybridization product according to claim 22, wherein the probe is attached to a glass chip.

24. A method of synthesizing a labeled nucleic acid comprising attaching a nucleic acid labeling compound according to claim 17 to a nucleic acid.

25. A method of detecting a nucleic acid comprising incubating a nucleic acid derivative according to claim 19 with a probe.

26. A method according to claim 25, wherein the probe is attached to a glass chip.