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Single DNA conformations and biological function

Metzler, Ralf ; Ambjörnsson, Tobias LU ; Hanke, Andreas ; Zhang, Yongli and Levene, Stephen (2007) In Journal of Computational and Theoretical Nanoscience 4(1). p.1-49
Abstract

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on... (More)

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.

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author
; ; ; and
publishing date
type
Contribution to journal
publication status
published
subject
keywords
DNA, DNA denaturation, DNA looping, Gene regulation, Knots, Single molecules
in
Journal of Computational and Theoretical Nanoscience
volume
4
issue
1
pages
49 pages
publisher
American Scientific Publishers
external identifiers
  • scopus:34247495997
ISSN
1546-1955
language
English
LU publication?
no
id
8f2244fb-177f-44e8-aae2-66f048dfdf74
date added to LUP
2019-05-03 11:40:14
date last changed
2022-03-31 17:17:12
@article{8f2244fb-177f-44e8-aae2-66f048dfdf74,
  abstract     = {{<p>From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.</p>}},
  author       = {{Metzler, Ralf and Ambjörnsson, Tobias and Hanke, Andreas and Zhang, Yongli and Levene, Stephen}},
  issn         = {{1546-1955}},
  keywords     = {{DNA; DNA denaturation; DNA looping; Gene regulation; Knots; Single molecules}},
  language     = {{eng}},
  month        = {{01}},
  number       = {{1}},
  pages        = {{1--49}},
  publisher    = {{American Scientific Publishers}},
  series       = {{Journal of Computational and Theoretical Nanoscience}},
  title        = {{Single DNA conformations and biological function}},
  volume       = {{4}},
  year         = {{2007}},
}