TY - JOUR
T1 - Intrinsic bending in GGCC tracts as probed by fluorescence resonance energy transfer
AU - Wildeson, Jessi
AU - Murphy, Catherine J.
N1 - Funding Information:
We thank the National Institutes of Health for funding. This work was also supported in part by the National Science Foundation, the Research Corporation, the Alfred P. Sloan Foundation, and the Dreyfus Foundation.
PY - 2000/8/15
Y1 - 2000/8/15
N2 - 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.
AB - 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.
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U2 - 10.1006/abio.2000.4677
DO - 10.1006/abio.2000.4677
M3 - Article
C2 - 10933862
AN - SCOPUS:0034663655
SN - 0003-2697
VL - 284
SP - 99
EP - 106
JO - Analytical Biochemistry
JF - Analytical Biochemistry
IS - 1
ER -