A new fluorescent ribonucleotide reporter: Synthesis, enzymatic incorporation and utilization

BIOL 88

Srivatsan G Seergazhi, Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, 0358, La Jolla, CA 92093-0358 and Yitzhak Tor, ytor@ucsd.edu, Department of Chemistry and Biochemistry, University of California, San Diego, MC 0358, 9500 Gilman Drive, La Jolla, CA 92093.
Small molecules that target viral-specific RNA sites and prevent the formation of key RNA-protein and RNA-RNA complexes are promising candidates for anti-viral drug discovery. It is therefore desirable to develop a rapid and quantitative real-time assay to identify small molecules that target protein-RNA interactions with high affinity and selectivity. Environmentally sensitive fluorescent nucleoside analogues allow real-time analysis of nucleic acid structure and dynamics as well as nucleic acid-protein interactions. Several fluorescent nucleosides have been developed to probe the dynamics of melting, abasic sites, mismatched base pairs, metal ion binding and the thermodynamics and kinetics of protein-nucleic acid complexes. Here, we describe the synthesis and enzymatic incorporation of a fluorescent ribonucleoside triphosphate. To substantiate the efficacy of the fluorescent ribonucleoside analogue, an assay was developed to study the specificity and affinity of aminoglycosides for HIV-1 transactivating response element (TAR).
 

Chemistry and Metabolism
4:30 PM-6:30 PM, Tuesday, 12 September 2006 Moscone Center -- Hall D, Poster

Division of Biological Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006