Dynamics of the DNA open state based on ab initio method
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概要
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Several modeled theoretical works have been carried out for the open states caused by local deformations in DNA. These models are based on the Dynamic Plane Base Rotator (DPBR) approach, but simplify the potentials of the base-stacking as well as the interbase H bondings. In the present work, we exactly introduce the realistic potentials of the above interactions by ab initio calculations, and investigate the generation and propagation of the open states in DNA double helices. The actual potentials reveal that the open states do not propagate as a sine-Gordon type solitary wave but rather play a stationary wave. This is because the actual potential strongly differs from the conventional cosine potential which produces the sine-Gordon solitons. An inclusion of the sugar phosphate backbone strengthens the stacking potential and causes a possibility of another type of the DNA open states.
- 日本コンピュータ化学会の論文
日本コンピュータ化学会 | 論文
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