Molecular probes for DNA bulges: Viologen linked acridine DNA bulge photocleavers

ORGN 296

Thabisile S. Ndlebe1, Danaboyina Ramaiah2, and Gary B. Schuster1. (1) Department of Chemistry and Biochemistry, Georgia Institute of Technology, 770 State Street, Boggs Room 1-44, Atlanta, GA 30332, (2) Photophysics and Photonics Division, Regional Research Laboratory (CSIR), Trivandrum, Trivandrum, 695 019, India
Viologen linked acridine derivatives were analyzed to determine their potential as specific probes for DNA bulges. Such molecular probes that can photocleave DNA under physiological conditions have potential applications in nucleic acid sequencing, or as antitumor or antiviral drugs. The derivatives were designed to optimize their DNA binding and electron transfer capabilities. The acridine moiety, a well known DNA intercalator, served as the electron donor. The viologen moiety, a DNA groove binder, served as the electron acceptor. The alkyl linker length between these moieties was varied to optimize electron transfer. In addition, some bis-acridine viologen linked derivatives were analyzed to determine if they could induce double stranded cleavage in DNA. The results of these experiments will be presented in the presentation.