Pii: S1386-1425(02)00004-5

The fluorescence spectroscopy of 7-azaindole (In) incorporated in DNA oligonucleotides is investigated. Incorporation of In into DNA oligonucleotides is accomplished through standard solid-phase phosphoramidite chemistry. Fluorescence emission of the In chromophore shifts slightly to the red (from 386 nm to 388 nm) upon glycosylation at the N−1 position, but its relative fluorescence quantum yield increases 23 times, from 0.023 to 0.53. Upon incorporation into DNA, the fluorescence emission of In is greatly quenched with fluorescence quantum yields of 0.020 and 0.016 in single and double strand DNA, respectively. The fluorescence emission for In in DNA oligonucleotides shifts to the blue with an emission maximum at 379 nm. Both the strong fluorescence quenching and the blue shift of the emission spectrum signify that In is stacked with neighboring DNA bases in both single and double strand DNA. As the duplex DNA melts due to temperature increase, the fluorescence of the In chromophore increases, indicating the transition from the less fluorescent duplex DNA to the more fluorescent single strand DNA. Since this fluorescent In is a structural analog of purine, its fluorescence property may be utilized as a probe for studying nucleic acid structure and dynamics. © 2002 Elsevier Science B.V. All rights reserved.