Coarse-graining DNA for simulations of DNA nanotechnology

被引：159

作者：

Doye, Jonathan P. K. ^{[1
]}

Ouldridge, Thomas E. ^{[2
]}

Louis, Ard A. ^{[2
]}

Romano, Flavio ^{[1
]}

Sulc, Petr ^{[2
]}

Matek, Christian ^{[2
]}

Snodin, Benedict E. K. ^{[1
]}

Rovigatti, Lorenzo ^{[3
]}

Schreck, John S. ^{[1
]}

Harrison, Ryan M. ^{[1
]}

Smith, William P. J. ^{[1
]}

机构：

[1] Univ Oxford, Dept Chem, Phys & Theoret Chem Lab, Oxford OX1 3QZ, England

[2] Rudolf Peierls Ctr Theoret Phys, Oxford OX1 3NP, England

[3] Univ Roma La Sapienza, Dipartimento Fis, I-00185 Rome, Italy

来源：

PHYSICAL CHEMISTRY CHEMICAL PHYSICS | 2013年 / 15卷 / 47期

基金：

英国工程与自然科学研究理事会; 欧洲研究理事会; 美国国家科学基金会;

关键词：

MOLECULAR-DYNAMICS SIMULATIONS; PARANEMIC CROSSOVER; ENTROPIC ELASTICITY; NANOSCALE SHAPES; MELTING BUBBLES; STRANDED-DNA; PEELED SSDNA; BASE-PAIR; S-DNA; MODEL;

D O I：

10.1039/c3cp53545b

中图分类号：

O64 [物理化学（理论化学）、化学物理学];

学科分类号：

070304 ; 081704 ;

摘要：

To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.

引用

页码：20395 / 20414

页数：20

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