Minimum basin algorithm: an effective analysis technique for DNA energy landscapes

Authors:
Mitsuhiro Kubota;Masami Hagiya
Affiliations:
Japan Science and Technology Agency (JST-CREST), Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Bunkyo-ku, Tokyo, Japan;Japan Science and Technology Agency (JST-CREST), Department of Computer Science, Graduate School of Information Science and Technology, University of Tokyo, Bunkyo-ku, Tokyo, Japan
Venue:
DNA'04 Proceedings of the 10th international conference on DNA computing
Year:
2004

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Abstract

To design DNA nano-machines or analyze DNA molecular reactions, it is important to be able to predict the energy landscape of molecular structures and the energy barrier of a transition between structures on the landscape. Unfortunately, this is difficult for DNA molecules longer than 100 bases. In this paper, we propose an effective new technique for analyzing a structural transition over a DNA energy landscape. Imagine a very undulating landscape. Suddenly, water starts to gush out from one site and keeps flowing. How will the water surface expand over the landscape? Using a variant of Dijkstra's and Jarník-Prim's algorithms, we generate the shape of the basin from its formation process. The resulting basin contains the true energy barrier. Furthermore, a comparison between the basin feature and the corresponding actual chemical reaction shows that the basin can be used as a criterion to explain the reaction.