Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.
Characterization of the geometry and topology of DNA pictured as a discrete collection of atoms.
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DOI：
10.1021/ct200657e
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发表时间：
2012-03-13
影响因子：
5.5
通讯作者：
Tobias, Irwin
中科院分区：
文献类型：
--
作者：
Clauvelin, Nicolas;Olson, Wilma K.;Tobias, Irwin
DNA的结构和物理性质与其几何和拓扑结构密切相关。用理想的光滑空间曲线对DNA几何和拓扑进行经典的数学处理，并不是为了表征在高分辨率和模拟的双螺旋结构中发现的原子的空间排列。在这里，我们提出了新的和严格的数值方法的快速和准确的评估的几何形状和拓扑结构的双螺旋DNA结构的组成原子。这些方法被很好地设计用于在详细的数值模拟中获得的或在高分辨率下实验确定的大型DNA数据集。我们说明了我们的方法的有用性，通过将其应用到三个典型的双螺旋DNA链，在最近的分子动力学模拟中获得的65 bp的小环，和蛋白质结合的DNA双链体的晶体阵列的分析。虽然我们专注于完全碱基配对的DNA结构，我们的方法可以扩展到治疗的几何形状和拓扑结构的熔化的DNA结构，以及表征任意分子，如RNA和环肽的折叠。
The structural and physical properties of DNA are closely related to its geometry and topology. The classical mathematical treatment of DNA geometry and topology in terms of ideal smooth space curves was not designed to characterize the spatial arrangements of atoms found in high-resolution and simulated double-helical structures. We present here new and rigorous numerical methods for the rapid and accurate assessment of the geometry and topology of double-helical DNA structures in terms of the constituent atoms. These methods are well designed for large DNA datasets obtained in detailed numerical simulations or determined experimentally at high-resolution. We illustrate the usefulness of our methodology by applying it to the analysis of three canonical double-helical DNA chains, a 65-bp minicircle obtained in recent molecular dynamics simulations, and a crystallographic array of protein-bound DNA duplexes. Although we focus on fully base-paired DNA structures, our methods can be extended to treat the geometry and topology of melted DNA structures as well as to characterize the folding of arbitrary molecules such as RNA and cyclic peptides.
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影响因子：
4.4
作者：
Britton, Lauren A.;Olson, Wilma K.;Tobias, Irwin
通讯作者：
Tobias, Irwin
影响因子：
3.4
作者：
BERMAN, HM;OLSON, WK;SCHNEIDER, B
通讯作者：
SCHNEIDER, B
DOI：
10.1073/pnas.68.4.815
发表时间：
1971-01-01
影响因子：
11.1
作者：
FULLER, FB
通讯作者：
FULLER, FB
影响因子：
14.9
作者：
Harris, Sarah A.;Laughton, Charles A.;Liverpool, Tanniemola B.
通讯作者：
Liverpool, Tanniemola B.
影响因子：
2.9
作者：
Hud, NV;Plavec, J
通讯作者：
Plavec, J