Minimum Basin Algorithm: An Effective Analysis Technique for DNA Energy Landscapes

• Published in: DNA Computing pp. 202 - 214
• Main Authors: Kubota, Mitsuhiro, Hagiya, Masami
• Format: Book Chapter Conference Proceeding
• Language: English; Japanese
• Published: Berlin, Heidelberg Springer Berlin Heidelberg 2005; Springer
• Series: Lecture Notes in Computer Science
• Subjects: Algorithmics. Computability. Computer arithmetics; Applied sciences; Computer science; control theory; systems; Energy Landscape; Exact sciences and technology; Lower Energy Barrier; Minimum Span Tree; Neighboring Structure; Theoretical computing; Transition Path; Energy analysis; Nanometer scale; Machine design; DNA computation; Landscape; Chemical reaction; Molecular structure; DNA; Algorithm analysis; Molecular computation
• ISBN: 9783540261742; 3540261745
• ISSN: 0302-9743; 1611-3349
• DOI: 10.1007/11493785_18

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.