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research article

Quantifying supercoiling-induced denaturation bubbles in DNA

Adamcik, Jozef  
•
Jeon, Jae-Hyung
•
Karczewski, Konrad J.
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2012
Soft Matter

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.

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Type
research article
DOI
10.1039/c2sm26089a
Web of Science ID

WOS:000307021300014

Author(s)
Adamcik, Jozef  
Jeon, Jae-Hyung
Karczewski, Konrad J.
Metzler, Ralf
Dietler, Giovanni  
Date Issued

2012

Publisher

Royal Society of Chemistry

Published in
Soft Matter
Volume

8

Issue

33

Start page

8651

End page

8658

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LPMV  
Available on Infoscience
February 27, 2013
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/89974
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