期刊
NUCLEIC ACIDS RESEARCH
卷 40, 期 21, 页码 10668-10678出版社
OXFORD UNIV PRESS
DOI: 10.1093/nar/gks884
关键词
-
资金
- Spanish Ministry of Science and Innovation [BIO2009-10964]
- European Research Council
- Fundacion Marcelino Botin
- PEDECIBA-Uruguay
- SNI (ANII)
- EMBO [ALTF 1107]
- CNRS
- Spanish Ministry of Science and Innovation [Consolider E-Science]
The traditional mesoscopic paradigm represents DNA as a series of base-pair steps whose energy response to equilibrium perturbations is elastic, with harmonic oscillations (defining local stiffness) around a single equilibrium conformation. In addition, base sequence effects are often analysed as a succession of independent XpY base-pair steps (i.e. a nearest-neighbour (NN) model with only 10 unique cases). Unfortunately, recent massive simulations carried out by the ABC consortium suggest that the real picture of DNA flexibility may be much more complex. The paradigm of DNA flexibility therefore needs to be revisited. In this article, we explore in detail one of the most obvious violations of the elastic NN model of flexibility: the bimodal distributions of some helical parameters. We perform here an in-depth statistical analysis of a very large set of MD trajectories and also of experimental structures, which lead to very solid evidence of bimodality. We then suggest ways to improve mesoscopic models to account for this deviation from the elastic regime.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据