Development of the strategy for chemical modifications to nucleic acids

The site-directed reaction with high efficiency and specificity to nucleic acids has become of the great interests, as such modification may be possible to induce point mutation of a genetic code and to apply the labeling for a target nucleic acid. In this study, we have developed the new reactive probes for the selective reactions to duplex DNA containing an abasic site. We designed three kinds of probes, which consist of 2-amino-6-vinylpurine (AVP) as a reactive moiety and peptides, acridine, and Hoechst as a binding moiety with high affinity to duplex DNA. We expected that AVP derivatives might form hydrogen bonds with target nucleobases at the opposite an abasic site in DNA. In the three kinds of probes Hoechst-AVP probe exhibited high selectivity and efficient reactivity to thymine at the site opposite an abasic site in DNA. These studies provide the proof-of concept that AVP derivatives conjugated with binding molecules to nucleic acids might form hydrogen bonds with target bases in the hydrophobic pocket and lead to the selective alkylation. Now we are going to investigate the new reactive probes for the other hydrophobic pockets.