Functional biopolymer modification reagents and uses thereof

Abstract

Hydrazino, oxyamino and carbonyl-based reagents and methods for incorporation into oligonucleotides during their solid phase synthesis are provided. Modified oligonucleotides are provided that incorporate the reagents provided herein. Immobilized oligonucleotides and oligonucleotide conjugates that contain covalent hydrazone or oxime linkages are provided. Methods for preparation of surface bound oligonucleotides are provided. Methods for the preparation of oligonucleotide conjugates are also provided.

What is claimed is: 
     
       1. A compound that has formula (I):
   P 1 -M-X   
       wherein:
 P 1  is a phosphorous based coupling group selected from the group consisting of phosphoramidite, H-phosphonate and phosphotriester; 
 X is selected from the group consisting of: 
 
       —NHNH—R 4 , —NHN═C(CH 3 ) 2 , —(C═O)CH 3 , —(C═O)H and —ONHR 4    
       wherein R 4  is a protecting group; and
 M is a divalent group of the formula —(CH 2 ) n —NH—(C═R 1 )—R 2 — wherein R 1  is S or O; R 2  is pyrimidinyl group, a quinolinyl group or a pyrrolyl group; and n is 2, 3, 4, 5, 6, 7, 8, 9, or 10. 
 
     
     
       2. The compound of  claim 1 , wherein R 4  is a protecting group selected from the group consisting of monomethoxytrityl (MMT), dimethoxytrityl (DMT), 9-fluorenylmethoxycarbonyl (FMOC) and trifluoroacetyl (TEA). 
     
     
       3. The compound of  claim 1  wherein X is —NHNH—R 4 . 
     
     
       4. The compound of  claim 1  wherein X is —NHN═C(CH 3 ) 2 . 
     
     
       5. The compound of  claim 1  wherein X is —(C═O)CH 3 . 
     
     
       6. The compound of  claim 1  wherein X is —(C═O)H. 
     
     
       7. The compound of  claim 1  wherein X is —ONR 4 . 
     
     
       8. The compound of  claim 1  wherein R 4  is MMT. 
     
     
       9. The compound of  claim 1  wherein R 4  DMT. 
     
     
       10. The compound of  claim 1  wherein R 4  FMOC. 
     
     
       11. The compound of  claim 1  wherein R 4  is TFA. 
     
     
       12. A compound that has formula (I):
   P 1 -M-X   wherein:   P 1  is a phosphorous based coupling group selected from the group consisting of phosphoramidite, H-phosphonate and phosphotriester;   X is selected from the group consisting of:   —NHNH—R 4 , —NHN═C(CH 3 ) 2 , —(C═O)CH 3 , —(C═O)H and —ONHR 4  wherein R 4  is a protecting group; and   M is a divalent group of the formula —(CH 2 ) n —NH—(C═R 1 )—R 2 — wherein R 1  is S or O; R 2  is pyrimidinyl group, a quinolinyl group or a pyrrolyl group; and n is 2, 3, 4, 5, 6, 7, 8, 9, or 10.   
     
     
       13. The compound of claim 12, wherein R 4  is a protecting group selected from the group consisting of monomethoxytrityl (MMT), dimethoxytrityl (DMT), 9-fluorenylmethoxycarbonyl (FMOC) and trifluoroacetyl (TEA). 
     
     
       14. The compound of claim 12 wherein X is —NHNH—R 4 . 
     
     
       15. The compound of claim 12 wherein X is —NHN═C(CH 3 ) 2 . 
     
     
       16. The compound of claim 12 wherein X is —(C═O)CH 3 . 
     
     
       17. The compound of claim 12 wherein X is —(C═O)H. 
     
     
       18. The compound of claim 12 wherein X is —ONR 4 . 
     
     
       19. The compound of claim 12 wherein R 4  is MMT. 
     
     
       20. The compound of claim 12 wherein R 4  is DMT. 
     
     
       21. The compound of claim 12 wherein R 4  is FMOC. 
     
     
       22. The compound of claim 12 wherein R 4  is TFA. 
     
     
       23. A compound that has formula (I):
   P 1 -M-X   wherein:   P 1  is a phosphoramidite;   X is selected from the group consisting of:   —NHNH—R 4 , —NHN═C(CH 3 ) 2 , —(C═O)CH 3 , —(C═O)H and —ONHR 4  wherein R 4  is a protecting group; and   M is selected from a pyrimidinyl group, a quinolinyl group or a pyrrolyl group.