✦ LIBER ✦

Intrinsic Bending in GGCC Tracts as Probed by Fluorescence Resonance Energy Transfer

✍ Scribed by Jessi Wildeson; Catherine J. Murphy

Publisher: Elsevier Science
Year: 2000
Tongue: English
Weight: 136 KB
Volume: 284
Category: Article
ISSN: 0003-2697
DOI: 10.1006/abio.2000.4677

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✦ Synopsis

Double-stranded oligonucleotides containing the sequence 5-GGCC-3 can be intrinsically bent, according to X-ray crystallography and gel electrophoresis mobility studies. We have performed fluorescence resonance energy transfer (FRET) experiments with dyelabeled oligonucleotides to further investigate the solution structure of this sequence. We find that 5-GGCC-3-containing oligonucleotides bring 5-attached donor and acceptor dyes much closer together than a comparable "straight" sequence that contains 5-GCGC-3. The bend angle for the 5-GGCC-3 sequence is estimated to be ϳ70°, much larger than the crystallographically observed 23°kink but in agreement with other FRET work. In contrast to gel electrophoresis studies, divalent metal ions do not promote increased kinking in 5-GGCC-3 above background as judged by FRET. Thus, sequence-dependent structural effects in DNA may be a complicating feature of FRET experiments.

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