Single molecule study of the DNA denaturation phase transition in the force-torsion space

We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the formation of so-called denaturation bubbles, which...

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Bibliographic Details
Published in:arXiv.org 2012-03
Main Authors: Salerno, D, Tempestini, A, Mai, I, Brogioli, D, Ziano, R, Cassina, V, Mantegazza, F
Format: Article
Language:English
Subjects:
Boundaries
Bubbles
Denaturation
Deoxyribonucleic acid
DNA
Phase transitions
Position measurement
Torsion
Variations
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Summary:We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the formation of so-called denaturation bubbles, which have an essential role in the replication and transcription of DNA. We experimentally map the region of the force-torsion space where the denaturation takes place. We observe that large fluctuations in DNA extension occur at one of the boundaries of this region, i.e., when the formation of denaturation bubbles and of plectonemes are competing. To describe the experiments, we introduce a suitable extension of the classical model. The model correctly describes the position of the denaturation regions, the transition boundaries, and the measured values of the DNA extension fluctuations.
ISSN:2331-8422
DOI:10.48550/arxiv.1203.6251