RNA denaturation: excluded volume, pseudoknots, and transition scenarios

Phys Rev Lett. 2003 Nov 7;91(19):198102. doi: 10.1103/PhysRevLett.91.198102. Epub 2003 Nov 6.

Abstract

A lattice model of RNA denaturation which fully accounts for the excluded volume effects among nucleotides is proposed. A numerical study shows that interactions forming pseudoknots must be included in order to get a sharp continuous transition. Otherwise a smooth crossover occurs from the swollen linear polymer behavior to highly ramified, almost compact conformations with secondary structures. In the latter scenario, which is appropriate when these structures are much more stable than pseudoknot links, probability distributions for the lengths of both loops and main branches obey scaling with nonclassical exponents.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Models, Chemical*
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Nucleotides / chemistry
  • RNA / chemistry*
  • RNA / metabolism

Substances

  • Nucleotides
  • RNA