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Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.


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Patent
19 Feb 2015
TL;DR: A dynamic DNA model and DNA model kit that is based on the atomic coordinates of double-stranded DNA can be easily untwisted to form a flattened 2-D ladder structure.
Abstract: A dynamic DNA model and DNA model kit that is based on the atomic coordinates of double-stranded DNA, but can be easily untwisted to form a flattened 2-D ladder structure. Once untwisted, the two strands of DNA can be easily “unzipped” to create single-stranded DNA templates that can be used to demonstrate the processes of DNA replication and transcription. The model and kit include two joints that allow the DNA model to be dynamically transformed from its helical arrangement into a straight ladder-like arrangement, with parallel base pairs and anti-parallel “backbones.” One joint is a pin joint, having rotation about one axis, and translation along that axis. The second joint can be a “compound” joint having multiple degrees of freedom at different points; or, it can be simplified to a single rotation axis with a separate translation axis.

9 citations

Proceedings ArticleDOI
01 Mar 2019
TL;DR: This paper defines this promising technique and the most important challenges, still open issues, and future trends of DNA-based cryptanalysis and reviews the most relevant results of this field of science at the level of attacking cryptosystems.
Abstract: Recently, a range of parallel computations have been suggested and implemented in the natural inspire techniques to attack and analyze cryptosystem as P and NP problems. DNA cryptanalysis or DNA-based cryptanalysis is an inventive computational mechanism. As a new paradigm for digital simulation of DNA cryptanalysis emerges, the development of model and tools for these paradigms will help to facilitate the design of biological or digital DNA model and its automatic computations to parallel search about nucleotide strands(solutions) for attacking and cryptanalysis the cryptosystem. DNA cryptanalysis pledges and keeps one's word of substantial links between bio-operations of DNA and search methods about keys and week points of encryption algorithms, in addition pledging massively parallel searches. Before the DNA-cryptanalysis pledges are carried out, many substantial challenges related to irregularity and pragmatism has to be descripted. On the other side, new trends toward exploitation of molecular progression and DNA models might concern the difficulties that have obstacle cryptanalysis efforts, until now. DNA-based cryptanalysis is a promising technique for solving complex problems facing analyzing and attacking cipher text wherefore; this paper defines this promising technique and the most important challenges, still open issues, and future trends of DNA-based cryptanalysis. This paper is a review of information related to the new scientific field and also reviews the most relevant results of this field of science at the level of attacking cryptosystems.

9 citations

Journal ArticleDOI
TL;DR: 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.

9 citations

Journal ArticleDOI
TL;DR: A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis and has been shown to rather well reproduce the DNA structure under low and room temperatures.
Abstract: A new coarse-grained model of the DNA molecule has been proposed, which was elaborated on the basis of its all-atomic model analysis. The model has been shown to rather well reproduce the DNA structure under low and room temperatures. The Young’s and torsion moduli calculated using the coarse-grained model are in close agreement with experimental data and the theoretical results of other authors. The model can be used for DNA fragments of several hundreds base pairs for rather long time scales (of the order of μs) and for simulating their interactions with other structures.

9 citations

Journal ArticleDOI
TL;DR: It is confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.
Abstract: Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model which prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.

9 citations

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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20216
20208
20194
201810
201712
201617