Experimentally derived nearest-neighbor parameters for the stability of RNA three- and four-way multibranch loops

Biochemistry. 2002 Jan 22;41(3):869-80. doi: 10.1021/bi011441d.

Abstract

Algorithms for predicting RNA secondary structure require approximations for the free energies of multibranch loops, also called junctions. The stabilities of 62 RNA duplexes with three- and four-way multibranch loops were determined by optical melting. To account for the observed sequence dependence, a revised loop free-energy approximation is proposed that accounts for the strain in three-way junctions with fewer than two unpaired nucleotides, penalizes asymmetry in the distribution of unpaired nucleotides, and gives a bonus for four-way loops relative to three-way loops. Parameters for this equation were determined by linear regression.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Base Sequence
  • Drug Stability
  • Indicators and Reagents
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • Nucleic Acid Denaturation
  • Nucleic Acid Heteroduplexes / chemical synthesis
  • RNA / chemical synthesis
  • RNA / chemistry*
  • Thermodynamics

Substances

  • Indicators and Reagents
  • Nucleic Acid Heteroduplexes
  • RNA