title: Energy landscape of k-point mutants of an RNA molecule.
abstract: BACKGROUND
  A k-point mutant of a given RNA sequence s = s(1), ..., s(n) is an RNA sequence s' = s'(1),..., s'(n) obtained by mutating exactly k-positions in s; i.e. Hamming distance between s and s' equals k. To understand the effect of pointwise mutation in RNA, we consider the distribution of energies of all secondary structures of k-point mutants of a given RNA sequence.
  
  
  RESULTS
  Here we describe a novel algorithm to compute the mean and standard deviation of energies of all secondary structures of k-point mutants of a given RNA sequence. We then focus on the tail of the energy distribution and compute, using the algorithm AMSAG, the k-superoptimal structure; i.e. the secondary structure of a < or =k-point mutant having least free energy over all secondary structures of all k'-point mutants of a given RNA sequence, for k' < or = k. Evidence is presented that the k-superoptimal secondary structure is often closer, as measured by base pair distance and two additional distance measures, to the secondary structure derived by comparative sequence analysis than that derived by the Zuker minimum free energy structure of the original (wild type or unmutated) RNA.
authors.affiliation: Department of Biology, Boston College, Chestnut Hill, MA 02467, USA. clote@bc.edu
authors.forename: P
authors.initials: P
authors.lastname: Clote
authors.forename: J
authors.initials: J
authors.lastname: Waldispühl
authors.forename: B
authors.initials: B
authors.lastname: Behzadi
authors.forename: J-M
authors.initials: JM
authors.lastname: Steyaert
mesh_terms: D000465:Algorithms; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D005798:Genes, Bacterial; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D009154:Mutation; D009690:Nucleic Acid Conformation; D017354:Point Mutation; D012313:RNA / Q000737:chemistry*; D012984:Software; D013816:Thermodynamics
chemical_list: D012313:RNA