NP-completeness of the energy barrier problem without pseudoknots and temporary arcs

  • Authors:

  • Ján Maňuch;Chris Thachuk;Ladislav Stacho;Anne Condon

  • Affiliations:

  • Department of Mathematics, Simon Fraser University, Burnaby, Canada and Department of Computer Science, University of British Columbia, Vancouver, Canada;Department of Computer Science, University of British Columbia, Vancouver, Canada;Department of Mathematics, Simon Fraser University, Burnaby, Canada;Department of Computer Science, University of British Columbia, Vancouver, Canada

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2011

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Abstract

Knowledge of energy barriers between pairs of secondary structures for a given DNA or RNA molecule is useful, both in understanding RNA function in biological settings and in design of programmed molecular systems. Current heuristics are not guaranteed to find the exact energy barrier, raising the question whether the energy barrier can be calculated efficiently. In this paper, we study the computational complexity of a simple formulation of the energy barrier problem, in which each base pair contributes an energy of 驴1 and only base pairs in the initial and final structures may be used on a folding pathway from initial to final structure. We show that this problem is NP-complete.