Compounds and methods for the characterization of oligonucleotides

1. A compound of Formula I, II or III:

wherein each R 1 , R 2 , R 3 and R 4 is independently a 2′-O—, 3′-O—, or 5′-O— linked nucleoside optionally attached to solid support, a 2′-O—, 3′-O—, or 5′-O— linked oligonucleotide optionally attached to solid support, —N i Pr 2 , —O(CH 2 ) 2 CN, —OH or —SH, and

each G us independently O or S.

2. A compound of Formula IV:

wherein each R 4 , R 5 and R 6 is independently a 2′-O—, 3′-O—, or 5′-O— linked nucleoside optionally attached to solid support, or a 2′-O—, 3′-O—, or 5′-O— linked oligonucleotide optionally attached to solid support,

G is O or S; and

wherein at least one of said 2′-O—, 3′-O—, and 5′-O— linked nucleoside further comprises a phosphorus group.

3. A compound of Formula V:

wherein R 7 and R 8 are independently a 2′-O—, 3′-O—, or 5′-O— linked nucleoside optionally attached to solid support, or a 2′-O—, 3′-O—, or 5′-O— linked oligonucleotide optionally attached to solid support, —SH or —OH,

Each G is independently O or S, and

R 2 is H, OH, O-rg wherein rg is a removable protection group, or a 2′ substituent.

4. The compound of claim 1 , wherein R 1 , R 2 , R 3 and R 4 are —N i Pr 2 , or —O(CH 2 ) 2 CN.

5. The compound of claim 1 , wherein at least one of R 1 , R 2 , R 3 or R 4 is a 2′-O—, 3′-O—, or 5′-O— linked nucleoside optionally attached to solid support or a 2′-O—, 3′-O—, or 5′-O— linked oligonucleotide optionally attached to solid support.

6. The compound of claim 1 , wherein at least two of R 1 , R 2 , R 3 or R 4 are 2′-O—, 3′-O—, or 5′-O— linked nucleosides optionally attached to solid support or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides optionally attached to solid support.

7. The compound of claim 1 , wherein at least three of R 1 , R 2 , R 3 or R 4 are 2′-O—, 3′-O—, or 5′-O— linked nucleosides optionally attached to solid support or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides optionally attached to solid support.

8. The compound of claim 1 , wherein R 1 , R 2 , R 3 and R 4 are 2′-O—, 3′-O—, or 5′-O— linked nucleosides optionally attached to solid support or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides optionally attached to solid support.

9. The compound of claim 1 , wherein said 2′-O—, 3′-O—, or 5′-O— linked nucleosides or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides are not attached to solid support.

10. The compound of claim 2 , wherein said 2′-O—, 3′-O—, or 5′-O— linked nucleosides or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides are not attached to solid support.

11. The compound of claim 3 , wherein said 2′-O—, 3′-O—, or 5′-O— linked nucleosides or 2′-O—, 3′-O—, or 5′-O— linked oligonucleotides are not attached to solid support.

12. The compound of claim 1 , wherein the purity of said compound is greater than about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 percent.

13. The compound of claim 1 , wherein the purity of said compound is greater than 10 percent.

14. The compound of claim 2 , wherein the purity of said compound is greater than about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 percent.

15. The compound of claim 2 , wherein the purity of said compound is greater than 10 percent.

16. The compound of claim 3 , wherein the purity of said compound is greater than about 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 percent.

17. The compound of claim 3 , wherein the purity of said compound is greater than 10 percent.

18. A compound of Formula VII:

wherein:

each G 1 is, independently, O or S;

each G 2 is, independently, OH or SH;

each G 3 is, independently, O, S, CH 2 , or NH;

each G 5 is, independently, O, S, CH 2 , CFH, CF 2 , or —CH═CH—;

each R 2 ′ is, independently, H, OH, O-Pg, a 2′-substituent, or together with R 4 ′ forms a bridge;

each R 3 ′ is, independently, H, a substituent, or together with R 4 ′ forms a bridge;

each R 4 ′ is, independently, H, a substituent, or together with R 2 ′ forms a bridge, together with R 3′ forms a bridge, or together with R 5 ′ forms a bridge;

each q is, independently, 0 or 1;

each R 5 ′ is, independently, H, a substituent, or together with R 4 ′ forms a bridge;

each G 6 is, independently, O, S, CH 2 or NH;

G 8 is H or a protecting group;

each G 10 is, independently, OH, O-Pg, a nucleoside, a nucleotide, or a nucleoside linked to a solid support or a nucleoside linked to a conjugate group;

Pg is a protecting group;

m is an integer from 1 to about 100;

n and o are each identical integers from 0 to about 100, provided that when n and o are 0, then each G 10 is an independently selected nucleoside linked to a solid support; and

each Bx is a naturally occurring or modified nucleobase.

19. The compound of claim 18 wherein each G 3 is O or S.

20. The compound of claim 18 wherein each G 1 is S.