2005 Fiscal Year Final Research Report Summary
Analysis of stability and dynamics of tertiary structure of nucleic acid molecules by using computer simulation
| Project/Area Number |
16570132
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| Research Category |
Grant-in-Aid for Scientific Research (C)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
Biophysics
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| Research Institution | The University of Tokyo |
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Principal Investigator |
NAKAMURA Shugo The University of Tokyo, Graduate School of Agricultural and Life Sciences, Associate Professor, 大学院・農学生命科学研究科, 助教授 (90272442)
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| Project Period (FY) |
2004 – 2005
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| Keywords | nucleic acids / mini hairpin molecule / generalized ensemble method / folding |
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| Research Abstract |
This research is about the analysis of the stability of nucleic acids hairpin structures by large scale structure sampling using multicanonical molecular dynamics simulation and local enhanced sampling (LES). Target molecules are dGC(GAA)GC and its mutants at tri-loop region. Starting from unfold structure, folding event was found in the trajectories of a multicanonical molecular dynamics simulation, and this folding/unfolding pathway was analyzed in detail. Sorin et al. proposed two folding pathways, zipping and compaction, for RNA tetra-loop hairpins. According to the analysis in this research, the folding pathway for dGC(GAA)GC was compaction-type. Structure sampling using LES was also applied to stable dGC(GNA)GC (N=A,G,T,C) and unstable dGC(GAG)GC and dGC(GAC)GC. Similar folding pathways were observed in dGC(GNA)GC trajectories : first, A5 stacks on the stem (G6), then G3 stacks on the stem (C2), and finally, N4 stacks on G3. For dGC(GNA)GC, structures were converged to near-native hairpin in 10 ns simulation. For dGC(GAG)GC and dGC(GAC)GC, structures were not converged, that corresponds to the fact that these molecules cannot form stable hairpin structures. These analysis may be able to extend to the stability analysis of other nucleic acid molecules.
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