Efficient conjugation and preferential DNA binding of oligonucleotides containing 2′-O-(2-oxoethyl)arabinouridine

Oligodeoxyribonucleotides were synthesized that contain a novel nucleoside, 2′-O-(2-oxoethyl)arabinouridine. Whereas such oligonucleotides showed only a slight reduction in the T M values of their complexes with complementary DNA, a significant destabilization was observed in the case of duplexes formed with RNA. This may be explained by the C 2′-endo conformation of 2′-O-(2,3-dihydroxypropyl)arabinouridine as demonstrated by NMR experiments in D 2O. The modified oligonucleotides were used to synthesize a number of conjugates with dyes, biotin and a N-modified laminin peptide, by hydrazone and oxime formation. We suggest that the 2′-arabinoaldehyde-containing DNA duplexes may be valuable tools for affinity modification of DNA-binding proteins. © 2004 Published by Elsevier Ltd.