Intrinsic bending in GGCC tracts as probed by fluorescence resonance energy transfer

Jessi Wildeson, Catherine J. Murphy

Research output: Contribution to journalArticle

Abstract

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 dye-labeled 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 -70°, 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. (C) 2000 Academic Press.

Original languageEnglish (US)
Pages (from-to)99-106
Number of pages8
JournalAnalytical Biochemistry
Volume284
Issue number1
DOIs
StatePublished - Aug 15 2000

ASJC Scopus subject areas

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

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