COMPUTER-SIMULATION OF SECONDARY STRUCTURE FOLDING OF RANDOM AND EDITED RNA CHAINS

Computer simulation of secondary structure folding of RNA chains demon strates that these chains under some temperature and solvent condition s find their native conformations much faster than by exhaustive sorti ng of all the possible chain conformations. This is true both for the random and the edited chains. However, for a random chain the native s tructure 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 nec essary to make its native structure thermodynamically stable at the op timal for a fast folding range of conditions. Only for the edited chai ns can the thermodynamically stable native secondary structures fold f ast. The dependence of folding time on the chain length is not an expo nential one but much less steep. (C) 1996 American Institute of Physic s.