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

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.