title: Base pairing at the stem-loop junction in the SL1 kissing complex of HIV-1 RNA: a thermodynamic study probed by molecular dynamics simulation.
abstract: The thermodynamics of the opening/closure process of a GC base pair located at the stem-loop junction of the SL1 sequence from HIV-1(Lai) genomic RNA was investigated in the context of a loop-loop homodimer (or kissing complex) using molecular dynamics simulation. The free energy, enthalpy and entropy changes for the closing reaction are 0 kcal x mol(-1), -11 kcal x mol(-1) and -0.037 kcal x mol(-1) x K(-1) at 300 degrees K respectively. Furthermore it is found that the free energy change is the same for the formation of a 11 nucleotide loop closed with UG and for the formation of a 9 nucleotide loop closed with GC. Our study evidences the high flexibility of the nucleotides at the stem-loop junction explaining the weak stability of this structure.
authors.affiliation: Centre de Biophysique Moleculaire, CNRS - Affiliated to the University of Orleans, Rue Charles Sadron, 45071 Orleans cedex 02, France.
authors.forename: S
authors.initials: S
authors.lastname: Aci
authors.forename: J
authors.initials: J
authors.lastname: Ramstein
authors.forename: D
authors.initials: D
authors.lastname: Genest
mesh_terms: D020029:Base Pairing; D003198:Computer Simulation; D019281:Dimerization; D015497:HIV-1 / Q000235:genetics*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D012367:RNA, Viral