{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2023,10,25]],"date-time":"2023-10-25T17:11:00Z","timestamp":1698253860564},"reference-count":31,"publisher":"Wiley","issue":"4","license":[{"start":{"date-parts":[[2004,9,7]],"date-time":"2004-09-07T00:00:00Z","timestamp":1094515200000},"content-version":"vor","delay-in-days":3812,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J Comput Chem"],"published-print":{"date-parts":[[1994,4]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>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\u2014r(AAA) and r(AAG)\u2014obtained at 11\u00b0C and 70\u00b0C. 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. For both of the oligonucleotides studied here, the most stable structures are helical conformations with stacked bases, at 11\u00b0C and 70\u00b0C. However, when the starting point is a stretched chain, it is found that r(AAA) adopts a reverse\u2010stacked structure at low temperature (11\u00b0C), in which the A3 base is located between the A1 and A2 bases. Although the energies of these conformations (helical and reverse stacked) are very close to each other, the potential barrier between them is extremely high (close to 30 kcal\/mol). This hinders the conformational transition from one structure to the other at a given temperature (and in the course of a same MC simulation). However, it is possible to simulate this structural transition by heating the reverse\u2010stacked structure up to 500\u00b0C and cooling down progressively to 70\u00b0C and 11\u00b0C: Canonical helical structures have been obtained by this procedure. \u00a9 1994 by john Wiley &amp; Sons, Inc.<\/jats:p>","DOI":"10.1002\/jcc.540150407","type":"journal-article","created":{"date-parts":[[2005,1,2]],"date-time":"2005-01-02T01:03:30Z","timestamp":1104627810000},"page":"433-445","source":"Crossref","is-referenced-by-count":9,"title":["Monte Carlo simulations on short single\u2010stranded oligonucleotides. I. 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