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Molecules 2017, 22(1), 145; doi:10.3390/molecules22010145

Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model

1
Center for Systems Biology, Soochow University, Suzhou 215006, China
2
Cambridge-Suda (CAM-SU) Genomic Resource Center, Soochow University, Suzhou 215123, China
3
Department of Biology, University of Rome “Tor Vergata”, Rome 00133, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Roberta Galeazzi
Received: 25 November 2016 / Revised: 9 January 2017 / Accepted: 10 January 2017 / Published: 16 January 2017
(This article belongs to the Special Issue Biomolecular Simulations)
View Full-Text   |   Download PDF [8659 KB, uploaded 16 January 2017]   |  

Abstract

DNA is a fundamental component of living systems where it plays a crucial role at both functional and structural level. The programmable properties of DNA make it an interesting building block for the construction of nanostructures. However, molecular mechanisms for the arrangement of these well-defined DNA assemblies are not fully understood. In this paper, the intrinsic dynamics of a DNA octahedron has been investigated by using two types of Elastic Network Models (ENMs). The application of ENMs to DNA nanocages include the analysis of the intrinsic flexibilities of DNA double-helices and hinge sites through the calculation of the square fluctuations, as well as the intrinsic collective dynamics in terms of cross-collective map calculation coupled with global motions analysis. The dynamics profiles derived from ENMs have then been evaluated and compared with previous classical molecular dynamics simulation trajectories. The results presented here revealed that ENMs can provide useful insights into the intrinsic dynamics of large DNA nanocages and represent a useful tool in the field of structural DNA nanotechnology. View Full-Text
Keywords: DNA nanotechnology; molecular dynamics; hinge regions; collective motions; Gaussian Network Model; Anisotropic Network Model DNA nanotechnology; molecular dynamics; hinge regions; collective motions; Gaussian Network Model; Anisotropic Network Model
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Hu, G.; He, L.; Iacovelli, F.; Falconi, M. Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model. Molecules 2017, 22, 145.

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