Nucleic Acids Research, 2003, Vol. 31, No. 7 2006-2013
© 2003 Oxford University Press
Analysis of the conformational energy landscape of human snRNA with a metric based on tree representation of RNA structures
1 Information Science Seminar, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan, 2 Department of Medical Ecology and Informatics, Research Institute, International Medical Center of Japan, 1-21-1 Toyama, Shinjuku-ku, Tokyo 162-8655, Japan and 3 Department of Chemical System Engineering, School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
*To whom correspondence should be addressed at Department of Medical Ecology and Informatics, Research Institute, International Medical Center of Japan, 1-21-1 Toyama, Shinjuka-Ku, Tokyo 162 8655, Japan. Tel: +81 3 3202 7181; Fax: +81 3 3202 7364; Email: kitagawa{at}miv.t.u-tokyo.ac.jp
It is an outstanding problem to clarify how the RNA sequence is related to its structure and biological functions. We developed a simplified definition of a metric for tree representation of RNA secondary structures and analyzed the conformational energy landscapes of human spliceosomal snRNAs. We discuss the structural properties of the biological sequence by calculating the conformational energy landscapes based on the structural distance between each of the pairs in the set of suboptimal structures. The new index value is introduced for estimating the shapes of distribution patterns in conformational energy landscapes. We apply our method to the five human snRNAs and show that U1 snRNA has a multi-valley profile of the landscape, whereas the landscapes of the other four snRNAs have one steep valley. This result reflects different biological functions of these snRNAs in the pre-mRNA splicing process. The results of analyzing tRNAs and rRNAs show that the conformational energy landscapes of these sequences have multi-valley profiles.
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