scholarly journals Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

Methods ◽  
2012 ◽  
Vol 57 (1) ◽  
pp. 25-39 ◽  
Author(s):  
Jiří Šponer ◽  
Xiaohui Cang ◽  
Thomas E. Cheatham
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulations ◽  
Nucleic Acid Structures

scholarly journals Understanding nucleic acid structural changes by comparing wide-angle x-ray scattering (WAXS) experiments to molecular dynamics simulations

2016 ◽  
Vol 144 (20) ◽  
pp. 205102 ◽  
Author(s):  
Suzette A. Pabit ◽  
Andrea M. Katz ◽  
Igor S. Tolokh ◽  
Aleksander Drozdetski ◽  
Nathan Baker ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Structural Changes ◽  
Wide Angle ◽  
X Ray ◽  
X Ray Scattering ◽  
Dynamics Simulations ◽  
Ray Scattering

Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations

Nano Letters ◽  
2012 ◽  
Vol 12 (5) ◽  
pp. 2509-2514 ◽  
Author(s):  
Ting I.N.G. Li ◽  
Rastko Sknepnek ◽  
Robert J. Macfarlane ◽  
Chad A. Mirkin ◽  
Monica Olvera de la Cruz
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Spherical Nucleic Acid ◽  
Dynamics Simulations

scholarly journals Analyzing ion distributions around DNA

2014 ◽  
Vol 42 (12) ◽  
pp. 8138-8149 ◽  
Author(s):  
Richard Lavery ◽  
John H. Maddocks ◽  
Marco Pasi ◽  
Krystyna Zakrzewska
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Dna Conformation ◽  
Ion Binding ◽  
Dna Oligomers ◽  
Cartesian Space ◽  
Ion Distributions ◽  
Dynamics Simulations ◽  
Convergence Sequence

Abstract We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.

Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations*

2020 ◽  
pp. 555-569
Author(s):  
Ting I. N. G. Li ◽  
Rastko Sknepnek ◽  
Robert J. Macfarlane ◽  
Chad A. Mirkin ◽  
Monica Olvera de la Cruza
Keyword(s):  
Molecular Dynamics ◽  
Nucleic Acid ◽  
Molecular Dynamics Simulations ◽  
Spherical Nucleic Acid ◽  
Dynamics Simulations
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