Monte Carlo (MC) structural simulation of short RNA sequences has been carried out by random variations of the nucleotide conformational angles (i.e., phosphodiester chain torsional angles and sugar pucker pseudorotational angles). All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker ring. In this article we present the simulated structures of RNA trimers-r(AAA) and r(AAG)-obtained at 11 o C and 70 o C. The influence of various initial conformations (selected as starting points in the MC simulations) on the equilibrium conformations has been discussed. The simulated conformational angles have been compared with those estimated by nuclear magnetic resonance (NMR) spectroscopy
['Mahmoud Ghomi', 'Jean-Marc Victor', 'Charles Henriet']
Monte Carlo simulations on short single-stranded oligonucleotides. I.: application to RNA trimers