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Quantifying supercoiling-induced denaturation bubbles in DNA

  • 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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Author:Jozef Adamcik, Jae-Hyung Jeon, Konrad J. Karczewski, Ralf MetzlerORCiDGND, Giovanni Dietler
ISSN:1744-683X (print)
Parent Title (English):Soft matter
Publisher:Royal Society of Chemistry
Place of publication:Cambridge
Document Type:Article
Year of first Publication:2012
Year of Completion:2012
Release Date:2017/03/26
First Page:8651
Last Page:8658
Funder:Deutsche Forschungsgemeinschaft; Academy of Finland
Organizational units:Mathematisch-Naturwissenschaftliche Fakultät / Institut für Physik und Astronomie
Peer Review:Referiert