Design and construction of a one-dimensional DNA track for an artificial molecular motor

  • Authors:

  • Suzana Kovacic;Laleh Samii;Derek N. Woolfson;Paul M. G. Curmi;Heiner Linke;Nancy R. Forde;Gerhard A. Blab

  • Affiliations:

  • Department of Physics, Simon Fraser University, Burnaby, BC, Canada;Department of Physics, Simon Fraser University, Burnaby, BC, Canada;School of Chemistry, University of Bristol, Bristol, UK and School of Biochemistry, University of Bristol, Bristol, UK;School of Physics, University of New South Wales, Sydney, NSW, Australia and Centre for Applied Medical Research, St. Vincent’s Hospital, Sydney, NSW, Australia;The Nanometer Structure Consortium, and Division of Solid State Physics, Lund University, Lund, Sweden;Department of Physics, Simon Fraser University, Burnaby, BC, Canada;Molecular Biophysics, Utrecht University, Utrecht, The Netherlands

  • Venue:
  • Journal of Nanomaterials - Special issue on 1D Nanomaterials 2011
  • Year:
  • 2012

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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.