Computer simulation of secondary structure folding of random and ‘‘edited’’ RNA chains

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Abstract
Computer simulation of secondary structure folding of RNA chains demonstrates that these chains under some temperature and solvent conditions find their native conformations much faster than by exhaustive sorting of all the possible chain conformations. This is true both for the random and the edited chains. However, for a random chain the native structure is thermodynamically stable in one region of temperature and solvent quality, while fast folding (and even faster unfolding) of the random chain occurs in another region. Some editing of a chain is necessary to make its native structure thermodynamically stable at the optimal for a fast folding range of conditions. Only for the edited chains can the thermodynamically stable native secondary structures fold fast. The dependence of folding time on the chain length is not an exponential one but much less steep.