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

Abstract 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(GTAGAAbv5UTCTAC) (9) and d(GTAGAATbv5UCTAC) (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 1H and 13C NMR spectra of BVDU (1) is also reported.