Synthesis of 3′-, or 5′-, or internal methacrylamido-modified oligonucleotides
View Patent ↗New modifiers were synthesized for incorporation of a methacrylic function in 3′-, 5′- and internal positions of oligonucleotides during solid phase synthesis. A modifier was used for synthesis of 5′-methacrylated oligonucleotides for preparation of microarrays by a co-polymerization method.
1. A compound of the formula
wherein
R 1 , R 2 , and R 3 are each independently selected from the group consisting of hydrogen, alkyl;
L 1 , L 2 , and L 3 are each independently selected from the group consisting of a single bond, and a linker; and
Q 1 and Q 2 are each independently selected from the group consisting of hydrogen, a hydroxyl protecting group, a phosphoramidite group, an oligonucleotide, a solid support, and combinations thereof.
2. The compound of claim 1 wherein R 1 is hydrogen or alkyl; and R 2 and R 3 are each hydrogen.
3. The compound of claim 1 wherein L 3 is a linker selected from the group consisting of ω-amino acid fragments of the formula
—NH—(CH 2 ) n —CO—
wherein n is an integer from 2 to about 12.
4. The compound of claim 1 wherein Q 1 is an oligonucleotide attached at the 5′-end.
5. The compound of claim 1 wherein Q 2 is an oligonucleotide attached at the 3′-end.
6. The compound of claim 1 wherein Q 1 and Q 2 are each an independently selected oligonucleotide.
7. The compound of claim 1 wherein Q 1 is an oligonucleotide attached at the 5′-end and Q 2 is an oligonucleotide attached at the 3′-end.
8. The compound of claim 1 wherein L 2 is a single bond; and Q 2 is a hydroxyl protecting group.
9. The compound of claim 1 wherein the hydroxyl protecting group is an optionally substituted trityl group.
10. The compound of claim 1 wherein L 1 is a linker formed from a dicarbonic acid fragment.
11. The compound of claim 1 wherein the dicarbonic acid fragment is a fragment of aliphatic dicarbonic acid of the formula:
—CO—(CH 2 ) m —CO—
wherein m is an integer from 0 to about 8.
12. The compound of claim 1 wherein L 1 is a tinker formed from a dicarbonic acid fragment; and Q 1 is a solid support.
13. A reagent for forming a compound of any one of claims 1 to 12 , said reagent of the formula
wherein
R 1 , R 2 , and R 3 are each independently selected from the group consisting of hydrogen, alkyl;
L 1 , L 2 , and L 3 are each independently selected from the group consisting of a single bond, and a linker; and
P 1 and P 2 are each independently selected from the group consisting of hydrogen, a hydroxyl protecting group, a phosphoramidite group, a solid support, and combinations thereof.
14. The compound of claim 13 wherein P 1 is a cyanoethylphosphoramidite coupling group.
15. The compound of claim 13 wherein P 1 is a solid support.
16. The compound of claim 13 wherein L 1 is a linker; and P 1 is a solid support.
17. The compound of claim 13 wherein the linker is a fragment of aliphatic dicarbonic acid of the formula:
—CO—(CH 2 ) m —CO—
wherein
m is an integer from 0 to about 8; and
the linker is covalently attached to the solid support by nitrogen of amino group.
18. A method for preparing a biochip, the method comprising the steps of:
(a) placing a mixture comprising (i) a compound of claim 1 and (ii) gel forming monomers, or analogs or derivatives thereof on a solid support; and
(b) polymerizing the mixture.
19. The method of claim 18 , wherein the gel forming monomers are acrylamide or/and methacrylamide.
20. The method of claim 18 , wherein the placing step includes placing the mixture on the solid support in the form of a drop.