Presentation of large DNA molecules for analysis as nanoconfined dumbbells.
Presentation of large DNA molecules for analysis as nanoconfined dumbbells.
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DOI：
10.1021/ma400926h
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发表时间：
2013-10-22
期刊：
影响因子：
5.5
通讯作者：
Schwartz DC
中科院分区：
文献类型：
--
作者：
Kounovsky-Shafer KL;Hernández-Ortiz JP;Jo K;Odijk T;de Pablo JJ;Schwartz DC
对非常大的DNA分子的分析本质上支持远程，相序列信息，但需要新的方法来有效地作为任何基因组分析平台的一部分。采用多管齐下的方法，将分子约束、离子环境和DNA弹性特性组合在一起，但通过分子模拟强调，我们开发了一种高效且可扩展的方法，用于在纳米级狭缝中呈现大的DNA分子。我们的方法依赖于DNA哑铃的形成，其中大部分分子留在用于限制它们的纳米缝之外。低离子环境，协同我们方法的其他特征，使DNA分子采用完全拉伸的构象，与轮廓长度相当，从而便于光学显微镜分析。因此，提出了一种分子模型来描述纳米缝内DNA分子的构象和动力学；聚合物动力学采用朗之万描述，其中流体动力学效应通过格林函数形式包含在内。我们的模拟表明，静电和水动力相互作用之间的微妙平衡是观察到的分子构象的原因。我们证明并进一步证实，当约束尺寸大小与分子的持续长度相同的数量级时，“Odijk制度”确实开始。我们还总结了目前有关哑铃动力学的理论。
The analysis of very large DNA molecules intrinsically supports long-range, phased sequence information, but requires new approaches for their effective presentation as part of any genome analysis platform. Using a multi-pronged approach that marshaled molecular confinement, ionic environment, and DNA elastic properties–but tressed by molecular simulations–we have developed an efficient and scalable approach for presentation of large DNA molecules within nanoscale slits. Our approach relies on the formation of DNA dumbbells, where large segments of the molecules remain outside the nanoslits used to confine them. The low ionic environment, synergizing other features of our approach, enables DNA molecules to adopt a fully stretched conformation, comparable to the contour length, thereby facilitating analysis by optical microscopy. Accordingly, a molecular model is proposed to describe the conformation and dynamics of the DNA molecules within the nanoslits; a Langevin description of the polymer dynamics is adopted in which hydrodynamic effects are included through a Green’s function formalism. Our simulations reveal that a delicate balance between electrostatic and hydrodynamic interactions is responsible for the observed molecular conformations. We demonstrate and further confirm that the “Odijk regime” does indeed start when the confinement dimensions size are of the same order of magnitude as the persistence length of the molecule. We also summarize current theories concerning dumbbell dynamics.
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DOI：
10.1137/s0895479895291765
发表时间：
1999-07-13
影响因子：
1.5
作者：
Demmel, JW;Eisenstat, SC;Liu, JWH
通讯作者：
Liu, JWH
影响因子：
4.4
作者：
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影响因子：
4.4
作者：
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通讯作者：
MCCRACKIN, FL
影响因子：
4.4
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DEGENNES, PG
影响因子：
4.4
作者：
ESSMANN, U;PERERA, L;PEDERSEN, LG
通讯作者：
PEDERSEN, LG