© 2005 The Japanese Biochemical Society
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Single-Strand Conformation Polymorphism (SSCP) of Oligodeoxyribonucleotides: An Insight into Solution Structural Dynamics of DNAs Provided by Gel Electrophoresis and Molecular Dynamics Simulations
1 Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama 338-8570 and 2 Rational Evolutionary Design of Advanced Biomolecules, Saitama Small Enterprise Promotion Corporation, SKIP City, 3-12-18 Kamiaoki, Kawaguchi, Saitama 333-0844
* To whom correspondence should be addressed at: Department of Functional Materials Science, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama-shi, Saitama 338-8570. Tel/Fax: +81-48-858-3533, E-mail: koichi{at}fms.saitama-u.ac.jp
Studies on the solution structure dynamics of RNA/DNA are becoming crucially important. The phenomena of SSCP (single-strand conformation polymorphism), small RNA dynamics in a cell, and others can be related to the conformational changes of single-stranded (ss) RNAs/DNAs in solution. However, little is known about those dynamics. Only the intra-structural transition of ssDNAs in solution has been reported based on Watson-Crick (W-C) base-pairing. Here, we found a general feature of the SSCP phenomenon by studying the simpler molecules of ss-oligodeoxyribonucleotides. A single base substitution or a positional exchange of nucleotide in a highly homologous series of ss-dodecanucleotides led to a change in the mobility-in-gel. This was unexpected, since most of these nucleotides [such as d(A11G) or d(A11C)] have no possibility of forming W-C base-pairing. MD (molecular dynamics) experiments revealed differences in shape and size between the dynamic structures of these molecules which could affect their mobility-in-gel. In addition, a high correlation was observed between the electrophoretic mobility and the size-related parameters such as end-to-end distance obtained from MD simulations. Because the simulation was considerably shorter (nanosecond) than the experimental time-scale (second), the result must be considered conservatively; but it is nevertheless encouraging for utilizing MD simulation for structural analysis of oligonucleotides.
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