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Vol 46(2012) N 1 p. 34-46; E.I. Leonova1,2, M.V. Baranov1,3, O.V. Galzitskaya1* Formation of RNA Spatial Structures 1Institute of Protein Reseach, Russian Academy of Sciences, Pouschino, 142290 Russia2Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Pushchino Branch, Russian Academy of Sciences, Pushchino, Moscow Region, 142290 Russia 3Biological Faculty, Moscow State University, Moscow, 119992 Russia *ogalzit@vega.protres.ru Received - 2011-03-03; Accepted - 2011-06-21 The review considers different experimental and theoretical approaches to the investigation of RNA folding and identification of nucleotides that critically affect the folding of molecules, such as tRNA, and several classes of ribozymes. For instance, it has been shown that nucleotides of the D- and T-loop regions are the last to be involved in the tRNA structure, or, rather, they are not included in the tRNA folding nucleus. A specially developed SHAPE method was used to show that the long-recognized hierarchical folding model does not hold true for tRNA folding. In the second part of the review, algorithms and programs used for the prediction of RNA secondary structures, as well as for modeling RNA folding, are considered. RNA folding, folding nucleus, H-bonds, base stacking, hydrophobic interactions, nonhierarchical model of folding |
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