Dodecanucleotides Containing (E)-5-(2-Bromovinyl)-2′-Deoxyuridine: Influence of a Bulky Major Groove Substituent on Duplex Stability and Endodeoxyribonuclease Eco Ri Recognition

Self-complementary dodecanucleotides containing BVDU ( 1 ) have been prepared by solid-phase synthesis employing the phosphoramidite technique. The phosphoramidite of BVDU was obtained after 4, 4′-dimethoxytritylation and subsequent phosphitylation of the nucleoside 1 . Melting experiments of the dodecamers containing one BVDU residue showed that the stability of such duplexes is only slightly affected by the bulky bromovinyl residue. The dodecamers d(GTAGAAbv 5 UTCTAC) ( 9 ) and d(GTAGAATbv 5 UCTAC) ( 10 ) were subject to hydrolysis experiments with the endodeoxyribonuclease Eco RI under star activity conditions. Whereas regioselective hydrolysis was decreased in case of the oligomer 10 , compared to the non-modified oligomer 8 , the oligomer 9 -was not hydrolyzed at all under these conditions. This can be explained by a steric interference of the bulky bromovinyl substituent with the nitrogen-7 of the adjacent adenine moiety being a proton acceptor site during endonuclease binding. A complete assignment of 1 H and 13 C NMR spectra of BVDU ( 1 ) is also reported.