Compounds and methods for labeling oligonucleotides
View Patent ↗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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair; R 7 is a substituted or unsubstituted aryl group; and Y is a nucleophile.
1. A compound comprising Formula (I):
wherein 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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair;
R 7 is a substituted or unsubstituted aryl group; and
Y is an oxime forming nucleophile.
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, NO 2 , SO 3 R S , SO 2 N(R N ) 2 , CN, CNS, keto, and alkoxy groups; wherein R N and R S are independently selected from the group consisting of C 1 -C 10 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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 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 R 7 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:
wherein L and L′ are independently selected from the group consisting of substituted or unsubstituted C 1-10 alkyl, wherein the C 1-10 alkyl groups are saturated or unsaturated; and wherein one of L or L′ is substituted with an oxime forming nucleophile substituent.
17. A compound comprising:
18. A compound comprising:
wherein R is an alkyl group, B is a nucleobase, and W is selected from the group consisting of a protecting group, an oligonucleotide, a nucleotide or a nucleoside.
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):
wherein 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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair, and wherein at least one of R 1-6 is an alkyl group, an aryl group or a heteroaryl group;
R 7 is a substituted or unsubstituted aryl group; and
Y is a nucleophile.
22. A compound comprising Formula (I):
wherein 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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair, and wherein at least one of the R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair are combined to form a ring having five or six ring members;
R 7 is a substituted or unsubstituted aryl group; and
Y is a nucleophile.
23. The compound of claim 22 , wherein the ring has six ring members.
24. A compound comprising Formula (I):
wherein 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 R 1 and R 2 pair, the R 3 and R 4 pair, the R 4 and R 5 pair, or the R 5 and R 6 pair;
R 7 is an anilinyl group; and
Y is a nucleophile.
25. The compound of claim 24 , wherein the anilinyl group comprises:
wherein L and L′ are independently selected from the group consisting of substituted or unsubstituted C 1-10 alkyl, wherein the C 1-10 alkyl groups are saturated or unsaturated; and wherein one of L or L′ is substituted with an oxime forming nucleophile substituent.