title: Intrinsic Dynamics Analysis of a DNA Octahedron by Elastic Network Model.
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.
authors.affiliation: Center for Systems Biology, Soochow University, Suzhou 215006, China. huguang@suda.edu.cn.
authors.forename: Guang
authors.initials: G
authors.lastname: Hu
authors.affiliation: Cambridge-Suda (CAM-SU) Genomic Resource Center, Soochow University, Suzhou 215123, China. lhe@suda.edu.cn.
authors.forename: Lei
authors.initials: L
authors.lastname: He
authors.affiliation: Department of Biology, University of Rome "Tor Vergata", Rome 00133, Italy. federico.iacovelli@uniroma2.it.
authors.forename: Federico
authors.initials: F
authors.lastname: Iacovelli
authors.affiliation: Department of Biology, University of Rome "Tor Vergata", Rome 00133, Italy. falconi@uniroma2.it.
authors.forename: Mattia
authors.initials: M
authors.lastname: Falconi
mesh_terms: D004247:DNA / Q000737:chemistry*; D004548:Elasticity / Q000502:physiology*; D056004:Molecular Dynamics Simulation; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*
chemical_list: D004247:DNA
keywords: Anisotropic Network Model; DNA nanotechnology; Gaussian Network Model; collective motions; hinge regions; molecular dynamics