Journal ArticleDOI
Coarse-Grained Molecular Dynamics Model of Double-Stranded DNA for DNA Nanostructure Design
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TLDR
From calculation results, it is confirmed that the dependency of the salt concentration on the persistence length of the nCG-dsDNA model at the 30% charge is in good agreement with the Poisson-Boltzmann theoretical model.Abstract:
A new coarse-grained molecular dynamics double-stranded DNA model (nCG-dsDNA model) using an improved beads–spring model was proposed. In this model, nucleotide comprising phosphate, sugar, and base group were replaced by a single bead. The double stranded model with 202 base pairs was created to tune the parameters of the bond, the nonbond, stack, angle bending, and electrostatic interaction. The average twisted angle and the persistence length of the model without electrostatic interaction were calculated at 35.3° and 120.3 bp, confirming that the proposed model successfully realized the experimentally observed double-stranded DNA structure. Moreover, the model with electrostatic interaction was discussed. From calculation results, we confirmed that the dependency of the salt concentration on the persistence length of the nCG-dsDNA model at the 30% charge is in good agreement with the Poisson–Boltzmann theoretical model.read more
Citations
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Journal ArticleDOI
The potential of DNA origami to build multifunctional materials
Kosti Tapio,Ilko Bald +1 more
Journal ArticleDOI
Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution.
Jae Young Lee,Jae Gyung Lee,Giseok Yun,Chanseok Lee,Young Joo Kim,Kyung Soo Kim,Tae Hwi Kim,Do-Nyun Kim +7 more
TL;DR: In this article, the sequence-dependent relative geometry and mechanical properties of DNA motifs are characterized by the all-atom molecular dynamics simulation and incorporated into the structural finite element model successfully without significant loss of atomic information.
Journal ArticleDOI
Uncertainty quantification of a DNA origami mechanism using a coarse-grained model and kinematic variance analysis.
TL;DR: A hybrid computational framework combining coarse-grained modeling with kinematic variance analysis to predict uncertainties in the motion pathway of a multi-component DNA origami mechanism and the ability to predict the probability density of DNA Origami mechanism conformations based on analysis of mechanical properties of individual joints is reported.
Journal ArticleDOI
Tuning Formation of Protein-DNA Coacervates by Sequence and Environment.
Kathryn M. Lebold,Robert West +1 more
TL;DR: Coacervates are readily formed at physiological ionic strengths, in agreement with experiment, with a progressive increase in local ordering at low ionic strength, and for more extreme blockiness (and consequently higher local charge density), a qualitative change in the condensed phase is seen.
Journal ArticleDOI
Dynamic DNA-based biomaterials interacting with external, macroscopic, and molecular stimuli
Shuaidong Huo,Shuaidong Huo,Minseok Kwak,Minseok Kwak,Jingbo Qin,Barbara Dittrichn,Andreas Herrmann,Andreas Herrmann +7 more
TL;DR: The molecular basis and resources of DNA-based biomaterials, notably benefited by programmability, biocompatibility, chemical synthesis/modification, and enzymatic manipulation of nucleic acids, are summarized.
References
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Journal ArticleDOI
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Kurt Kremer,Gary S. Grest +1 more
TL;DR: In this article, an extensive molecular-dynamics simulation for a bead spring model of a melt of linear polymers is presented, where the number of monomers N covers the range from N=5 to N=400.
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DNA in a material world
TL;DR: The specific bonding of DNA base pairs provides the chemical foundation for genetics and this powerful molecular recognition system can be used in nanotechnology to direct the assembly of highly structured materials with specific nanoscale features, as well as in DNA computation to process complex information.
Book ChapterDOI
A structure for deoxyribose nucleic acid
James D. Watson,Francis Crick +1 more
TL;DR: In this article, the authors summarize Watson and Crick's descrip2on of the DNA molecule and conclude that the purpose of this ar2cle was to find out why they wrote it.