Issue 33, 2012
From the journal:

Soft Matter

Quantifying supercoiling-induced denaturation bubbles in DNA

Jozef Adamcik,a   Jae-Hyung Jeon,b   Konrad J. Karczewski,a   Ralf Metzler*bc  and  Giovanni Dietlera  

* Corresponding authors

a Laboratoire de Physique de la Matière Vivante, Institute of Physics of Biological Systems (IPSB), Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland

b Physics Department, Tampere University of Technology, FI-33101 Tampere, Finland

c Institute for Physics & Astronomy, Potsdam University, 14476 Potsdam-Golm, Germany
E-mail: rmetzler@uni-potsdam.de

Abstract

In both eukaryotic and prokaryotic DNA sequences of 30–100 base-pairs rich in AT base-pairs have been identified at which the double helix preferentially unwinds. Such DNA unwinding elements are commonly associated with origins for DNA replication and transcription, and with chromosomal matrix attachment regions. Here we present a quantitative study of local DNA unwinding based on extensive single DNA plasmid imaging. We demonstrate that long-lived single-stranded denaturation bubbles exist in negatively supercoiled DNA, at the expense of partial twist release. Remarkably, we observe a linear relation between the degree of supercoiling and the bubble size, in excellent agreement with statistical modelling. Furthermore, we obtain the full distribution of bubble sizes and the opening probabilities at varying salt and temperature conditions. The results presented herein underline the important role of denaturation bubbles in negatively supercoiled DNA for biological processes such as transcription and replication initiation in vivo.

Graphical abstract: Quantifying supercoiling-induced denaturation bubbles in DNA

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Article information

DOI
https://doi.org/10.1039/C2SM26089A
Article type
Paper
Submitted
09 May 2012
Accepted
20 Jun 2012
First published
09 Jul 2012

Soft Matter, 2012,8, 8651-8658

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Quantifying supercoiling-induced denaturation bubbles in DNA

J. Adamcik, J. Jeon, K. J. Karczewski, R. Metzler and G. Dietler, Soft Matter, 2012, 8, 8651 DOI: 10.1039/C2SM26089A

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