Compounds and methods for labeling oligonucleotides

• US 8,030,460 B2
• Filed: 08/10/2010
• Issued: 10/04/2011
• Est. Priority Date: 05/20/2005
• Status: Active Grant

• Current Assignee: Integrated DNA Technologies (Danaher Corporation)
• Original Assignee: Integrated DNA Technologies (Danaher Corporation)
• Inventors: Yong, Yawfui, Behlke, Mark, Podyminogin, Mikhail, Laikhter, Andrei, Walder, Joseph A.
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US12/853,741
• Publication Number:
  US 20100298554A1
• Time in Patent Office: 420 Days
• Field of Search: 435/6, 536/23.1, 536/24.2, 536/25.32, 536/26.6, 534/558, 530/391.3
• US Class Current: 534/558
• CPC Class Codes: C07C 245/10 with nitrogen atoms of azo groups bound to carbon atoms of six-membered aromatic rings being part of condensed ring systems
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C12Q 1/6818 involving interaction of two or more labels, e.g. resonant energy transfer

Abstract

A compound having the general formula shown below:

where R_1-6 are independently selected from the group consisting of an electron withdrawing group, an alkyl group, an aryl group, hydrogen, a heteroaryl group, and a five or six member ring structure formed from the R₁ and R₂ pair, the R₃ and R₄ pair, the R₄ and R₅ pair, or the R₅ and R₆ pair; R₇ is a substituted or unsubstituted aryl group; and Y is a nucleophile.

Claims

1. A compound comprising Formula (I):

2. The compound of claim 1, wherein the oxime forming nucleophile is aminooxy.

3. The compound of claim 1, wherein the oxime forming nucleophile is hydrazine.

4. The compound of claim 1, wherein the electron withdrawing group is independently selected from the group consisting of halogen, NO₂, SO₃R_S, SO₂N(R_N)₂, CN, CNS, keto, and alkoxy groups;

wherein R_N and R_S are independently selected from the group consisting of C₁-C₁₀ alkyl groups, which are branched or unbranched, saturated or unsaturated, and substituted or unsubstituted, and aryl groups, which are substituted or unsubstituted.

5. The compound of claim 1, wherein at least one of R_1-6 is an electron withdrawing group.

6. The compound of claim 1, wherein at least one of R_1-6 is an alkyl group.

7. The compound of claim 6, wherein the alkyl group has from one to ten carbon atoms.

8. The compound of claim 1, wherein at least one of R_1-6 is an aryl group.

9. The compound of claim 1, wherein at least one of R_1-6 is a heteroaryl group.

10. The compound of claim 1, wherein at least one of R_1-6 is a hydrogen.

11. The compound of claim 1, wherein at least one of the R₁ and R₂ pair, the R₃ and R₄ pair, the R₄ and R₅ pair, or the R₅ and R₆ pair are combined to form a ring having five or six ring members.

12. The compound of claim 11, wherein the ring has six ring members.

13. The compound of claim 1, wherein R₇ is an aryl group.

14. The compound of claim 13, wherein the aryl group is selected from the group consisting of phenyl, naphthyl, xylyl, tolyl, pyridyl, and anilinyl.

15. The compound of claim 14, wherein the aryl group is an anilinyl group.

16. The compound of claim 15, wherein the anilinyl group comprises:

17. A compound comprising:

18. A compound comprising:

19. The composition of claim 18, wherein the nucleobase is selected from the group consisting of adenine, guanine, cytosine, uracil and thymine.

20. The composition of claim 19, wherein the nucleobase is uracil.

21. A compound comprising Formula (I):

22. A compound comprising Formula (I):

23. The compound of claim 22, wherein the ring has six ring members.

24. A compound comprising Formula (I):

25. The compound of claim 24, wherein the anilinyl group comprises: