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Issue 33, 2012
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Quantifying supercoiling-induced denaturation bubbles in DNA

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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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Publication details

The article was received on 09 May 2012, accepted on 20 Jun 2012 and first published on 09 Jul 2012

Article type: Paper
DOI: 10.1039/C2SM26089A
Citation: 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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