Base pairing at the stem-loop junction in the SL1 kissing complex of HIV-1 RNA: A thermodynamic study probed by molecular dynamics simulation

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(.)mol(-1), -11 kcal(.)mol(-1) and -0.037 kcal(.)mol(-1.)K(-1) at 300degrees K respectively. Furthermore it is found that the free energy change is the same for the formation of a I I 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.