Kinetics of the Triplex-Duplex Transition in DNA

The kinetics of triplex folding/unfolding is investigated by the single-molecule fluorescence resonance energy transfer (FRET) technique. In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally...

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Bibliographic Details
Published in:Biophysical journal 2012-12, Vol.103 (12), p.2492-2501
Main Authors: Lee, Il-Buem, Hong, Seok-Cheol, Lee, Nam-Kyung, Johner, Albert
Format: Article
Language:English
Subjects:
Base Sequence
Biophysics
Deoxyribonucleic acid
DNA
DNA - chemistry
DNA - genetics
DNA - metabolism
DNA-Directed RNA Polymerases - metabolism
energy transfer
Fluorescence
Fluorescence Resonance Energy Transfer
Hydrogen-Ion Concentration
Kinetics
Molecular physics
Nucleic Acid Conformation
Proteins and Nucleic Acids
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Summary:The kinetics of triplex folding/unfolding is investigated by the single-molecule fluorescence resonance energy transfer (FRET) technique. In neutral pH conditions, the average dwell times in both high-FRET (folded) and low-FRET (unfolded) states are comparable, meaning that the triplex is marginally stable. The dwell-time distributions are qualitatively different: while the dwell-time distribution of the high-FRET state should be fit with at least a double-exponential function, the dwell-time distribution of the low-FRET state can be fit with a single-exponential function. We propose a model where the folding can be trapped in metastable states, which is consistent with the FRET data. Our model also accounts for the fact that the relevant timescales of triplex folding/unfolding are macroscopic.
ISSN:0006-3495
1542-0086
DOI:10.1016/j.bpj.2012.10.029