4.7 Article

Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation

期刊

PHYSICAL REVIEW E
卷 77, 期 1, 页码 -

出版社

AMER PHYSICAL SOC
DOI: 10.1103/PhysRevE.77.011913

关键词

-

向作者/读者索取更多资源

Statistical DNA models available in the literature are often effective models where the base-pair state only (unbroken or broken) is considered. Because of a decrease by a factor of 30 of the effective bending rigidity of a sequence of broken bonds, or bubble, compared to the double stranded state, the inclusion of the molecular conformational degrees of freedom in a more general mesoscopic model is needed. In this paper we do so by presenting a one-dimensional Ising model, which describes the internal base-pair states, coupled to a discrete wormlike chain model describing the chain configurations [J. Palmeri, M. Manghi, and N. Destainville, Phys. Rev. Lett. 99, 088103 (2007)]. This coupled model is exactly solved using a transfer matrix technique that presents an analogy with the path integral treatment of a quantum two-state diatomic molecule. When the chain fluctuations are integrated out, the denaturation transition temperature and width emerge naturally as an explicit function of the model parameters of a well defined Hamiltonian, revealing that the transition is driven by the difference in bending (entropy dominated) free energy between bubble and double-stranded segments. The calculated melting curve (fraction of open base pairs) is in good agreement with the experimental melting profile of poly(dA)-poly(dT) and, by inserting the experimentally known bending rigidities, leads to physically reasonable values for the bare Ising model parameters. Among the thermodynamical quantities explicitly calculated within this model are the internal, structural, and mechanical features of the DNA molecule, such as bubble correlation length and two distinct chain persistence lengths. The predicted variation of the mean-square radius as a function of temperature leads to a coherent explanation for the experimentally observed thermal viscosity transition. Finally, the influence of the DNA strand length is studied in detail, underlining the importance of finite size effects, even for DNA made of several thousand base pairs. Simple limiting formulas, useful for analyzing experiments, are given for the fraction of broken base pairs, Ising and chain correlation functions, effective persistence lengths, and chain mean-square radius, all as a function of temperature and DNA length.

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。

评论

主要评分

4.7
评分不足

次要评分

新颖性
-
重要性
-
科学严谨性
-
评价这篇论文

推荐

暂无数据
暂无数据