DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
DNA Nanotweezers Studied with a Coarse-Grained Model of DNA
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DOI：
10.1103/physrevlett.104.178101
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发表时间：
2010-04-30
影响因子：
8.6
通讯作者：
Doye, Jonathan P. K.
中科院分区：
文献类型：
--
作者：
Ouldridge, Thomas E.;Louis, Ard A.;Doye, Jonathan P. K.
我们介绍了一个粗粒度的刚性核苷酸模型的DNA，重现短链，双链杂交，单链堆叠，发夹形成的基本热力学，并捕捉到DNA的基本结构特性：螺旋间距，持久性长度和扭转刚度的双链分子，以及比较灵活的非堆叠单链。我们应用这个模型来计算一个完整的DNA“镊子”循环的详细自由能景观，“镊子”是一种由杂交和链置换驱动的简单机器。
We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands, duplex hybridization, single-stranded stacking, and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length, and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA "tweezers,'' a simple machine driven by hybridization and strand displacement.