A coarse-grained model for DNA origami

被引：23

作者：

Reshetnikov, Roman V. ^{[1
,2
,3
]}

Stolyarova, Anastasia V. ^{[3
,4
]}

Zalevsky, Arthur O. ^{[3
]}

Panteleev, Dmitry Y. ^{[1
]}

Pavlova, Galina V. ^{[1
]}

Klinov, Dmitry V. ^{[5
,6
]}

Golovin, Andrey V. ^{[2
,3
,7
]}

Protopopova, Anna D. ^{[5
,8
]}

机构：

[1] Russian Acad Sci, Inst Gene Biol, Vavilova Str 34-5, Moscow 119334, Russia

[2] Lomonosov Moscow State Univ, AN Belozersky Inst Phys & Chem Biol, Leninskye Gory 1-40, Moscow 119992, Russia

[3] Lomonosov Moscow State Univ, Fac Bioengn & Bioinformat, GSP 1,Leninskiye Gory 1-73, Moscow 119234, Russia

[4] Skolkovo Inst Sci & Technol, Nobel St 3, Moscow 143026, Russia

[5] Fed Res & Clin Ctr Phys Chem Med, Malaya Pirogovskaya Str 1a, Moscow 119435, Russia

[6] State Univ, Moscow Inst Phys & Technol, 9 Inst Skiy Per, Dolgoprudnyi 141700, Moscow Region, Russia

[7] Sechenov First Moscow State Med Univ, Inst Mol Med, Trubetskaya Str 8-2, Moscow 119991, Russia

[8] Univ Penn, Dept Cell & Dev Biol, Perelman Sch Med, BRB II-III 421 Curie Blvd, Philadelphia, PA 19104 USA

来源：

NUCLEIC ACIDS RESEARCH | 2018年 / 46卷 / 03期

基金：

俄罗斯科学基金会; 俄罗斯基础研究基金会;

关键词：

FORCE-FIELD; DYNAMICS; SIMULATIONS; DESIGN; SHAPES; LONG;

D O I：

10.1093/nar/gkx1262

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Modeling tools provide a valuable support for DNA origami design. However, current solutions have limited application for conformational analysis of the designs. In this work we present a tool for a thorough study of DNA origami structure and dynamics. The tool is based on a novel coarse-grained model dedicated to geometry optimization and conformational analysis of DNA origami. We explored the ability of the model to predict dynamic behavior, global shapes, and fine details of two single-layer systems designed in hexagonal and square lattices using atomic force microscopy, Forster resonance energy transfer spectroscopy, and all-atom molecular dynamic simulations for validation of the results. We also examined the performance of the model for multilayer systems by simulation of DNA origami with published cryo-electron microscopy and atomic force microscopy structures. A good agreement between the simulated and experimental data makes the model suitable for conformational analysis of DNA origami objects. The tool is available at http://vsb.fbb.msu.ru/cosm as a web-service and as a standalone version.

引用

页码：1102 / 1112

页数：11

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