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

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 Jarn

• Type: Conference
• Year: 2004
• Where: DNA
• Authors: Mitsuhiro Kubota, Masami Hagiya
• Keywords: Bioinformatics, DNA 2004, DNA Energy Landscape, Energy Barrier, Energy Landscape