Bubble Dynamics in Double-Stranded DNA

2003/04/01 by Grégoire Altan‐Bonnet, Albert Libchaber, Oleg Krichevsky · 8 citations
Biochemistry, Genetics and Molecular Biology · Environmental Science · Engineering · #DNA and Nucleic Acid Chemistry #Bacteriophages and microbial interactions #Nanopore and Nanochannel Transport Studies

paper · doi:10.1103/physrevlett.90.138101

openalex publication_date 2003/04/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30

Abstract

We report the first measurement of the dynamics of bubble formation in double-stranded DNA. Fluctuations of fluorescence of a synthetic DNA construct, internally tagged with a fluorophore and a quencher, are monitored by fluorescence correlation spectroscopy. The relaxation dynamics follow a multistate relaxation kinetics, with a characteristic time scale of 50 microseconds. A simple model of bubble dynamics based on constant zipping-unzipping rates is proposed to account for our experimental data. The role of different secondary structures stabilizing the open bubble is tested.

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• Distribution Functions, Loop Formation Probabilities, and Force-Extension Relations in a Model for Short Double-Stranded DNA Molecules
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• Thermal Denaturation of Fluctuating DNA Driven by Bending Entropy
• DNA Flexibility on Short Length Scales Probed by Atomic Force Microscopy
• Stretching chimeric DNA: A test for the putative S-form
• How nanochannel confinement affects the DNA melting transition within the Poland-Scheraga model
• Denaturation (biochemistry) [wikipedia]