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Design and Construction of a One- Dimensional DNA Track for an Artificial Molecular Motor

Kovacic, Suzana; Samii, Laleh; Woolfson, Derek N.; Curmi, Paul M. G.; Linke, Heiner LU ; Forde, Nancy R. and Blab, Gerhard A. (2012) In Journal of Nanomaterials
Abstract
DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences... (More)
DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences from which the ideal sequence must be chosen. In order to find a suitable DNA sequence, we have adapted a genetic algorithm which is well suited for a large but sparse search space. This algorithm readily identifies long DNA sequences that include all the necessary elements to both facilitate DNA track construction and to present appropriate binding sites for the molecular motor. We have successfully experimentally incorporated the sequence identified by the algorithm into a long DNA track meeting the criteria for observation of the molecular motor's activity. (Less)
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Contribution to journal
publication status
published
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in
Journal of Nanomaterials
publisher
Hindawi Publishing Corporation
external identifiers
  • wos:000301455800001
  • scopus:84858147189
ISSN
1687-4129
DOI
10.1155/2012/109238
language
English
LU publication?
yes
id
e078a694-870c-445c-bd07-4a01c76f071d (old id 2516909)
date added to LUP
2012-05-09 13:27:59
date last changed
2017-07-02 03:03:23
@article{e078a694-870c-445c-bd07-4a01c76f071d,
  abstract     = {DNA is a versatile heteropolymer that shows great potential as a building block for a diverse array of nanostructures. We present here a solution to the problem of designing and synthesizing a DNA-based nanostructure that will serve as the track along which an artificial molecular motor processes. This one-dimensional DNA track exhibits periodically repeating elements that provide specific binding sites for the molecular motor. Besides these binding elements, additional sequences are necessary to label specific regions within the DNA track and to facilitate track construction. Designing an ideal DNA track sequence presents a particular challenge because of the many variable elements that greatly expand the number of potential sequences from which the ideal sequence must be chosen. In order to find a suitable DNA sequence, we have adapted a genetic algorithm which is well suited for a large but sparse search space. This algorithm readily identifies long DNA sequences that include all the necessary elements to both facilitate DNA track construction and to present appropriate binding sites for the molecular motor. We have successfully experimentally incorporated the sequence identified by the algorithm into a long DNA track meeting the criteria for observation of the molecular motor's activity.},
  articleno    = {109238},
  author       = {Kovacic, Suzana and Samii, Laleh and Woolfson, Derek N. and Curmi, Paul M. G. and Linke, Heiner and Forde, Nancy R. and Blab, Gerhard A.},
  issn         = {1687-4129},
  language     = {eng},
  publisher    = {Hindawi Publishing Corporation},
  series       = {Journal of Nanomaterials},
  title        = {Design and Construction of a One- Dimensional DNA Track for an Artificial Molecular Motor},
  url          = {http://dx.doi.org/10.1155/2012/109238},
  year         = {2012},
}