Topic
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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01 Jan 2006
TL;DR: The author reveals insights into a Biological Computer: Detangling Scrambled Genes of Ciliates and Modeling Simple Operations for Gene Assembly, and bottom-up approach to Complex Molecular Behaviors.
Abstract: Part 1 DNA Nanotechnology Algorithmic Self-assembly: Scaffolded DNA Origami: From Generalized Multi-crossovers to Polygonal Networks.- A Fresh Look at DNA Nanotechnology.- DNA Nanotechnology: An Evolving Field.- Self-healing Tile Sets.- Compact Error Resilient Computational DNA Tilings.- Forbidding-Enforcing Conditions in DNA Self-assembly of Graphs.- Part 2: Codes for DNA Nanotechnology: Finding MFE Structures Formed by Nucleic Acid Strands in a Combinatorial Set.- Selection of Large Independent Sets of DNA Oligonucleotides.- Involution Solid Codes.- Part III: DNA Nanodevices: DNA-Based Motor Work at Bell Laboratories.- Nanoscale Molecular Transport by Synthetic DNA Machines.- Part IV: Electronics, Nanowires and DNA: A Supramolecular Approach to Metal Array Programming Using Artificial DNA.- Multicomponent Assemblies Including Long DNA and Nanoparrticles An Answer for the Integration Problem? Molecular Electronics From Physics to Computing.- Part V: Other Bio-molecules in Self-assembly: Towards an Increase of the Hierarchy in the Construction of DNA-Based Nanostructures Through the Integration of Inorganic Materials.- Adding Functionality to DNA Arrays: The Developments of Semisynthetic DNA-Protein Conjugates.- Bacterial Surface Layer Proteins: A Simple but Versatile Biological Self-assembly System in Nature.- Part VI: Biomolecular Computational Models: Computing with Hairpins and Secondary Structures of DNA.- Bottom-up Approach to Complex Molecular Behaviors.- Aqueous Computing: Writing on Molecules Dissolved in Water.- Part VII: Computations Inspired by Cells: Turing Machines with Cells on the Tape.- Insights into a Biological Computer: Detangling Scrambled Genes of Ciliates.- Modeling Simple Operations for Gene Assembly.-
66 citations
TL;DR: A pseudo-atomic model of supercoiled DNA is described, which was found to behave very much like rubber-tubing and elastomechanical models and to examine the effects of super coiling pressure, base-sequence and mechanical properties on the conformations and energies of five sequences.
66 citations
TL;DR: The results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible are reported.
Abstract: Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible. Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA-DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. Analysis of the MD trajectories determined the DNA-DNA force in a DNA condensate to be pairwise, the DNA condensation to be driven by electrostatics of polycations and not hydration, and the concentration of bridging cations, not adsorbed cations, to determine the magnitude and the sign of the DNA-DNA force. Finally, our simulations quantitatively characterized the orientational correlations of DNA in DNA arrays as well as diffusive motion of DNA and cations.
66 citations
TL;DR: In this article, the authors present recent progress in development of low-energy electron tracks in condensed media and high-energy proton tracks and discuss progress in characterizing DNA damage in terms of types and complexity.
65 citations
TL;DR: An elastic DNA molecular mechanics model is used to compare DNA structures and packing thermodynamics in two bacteriophage systems, T7 and phi29, and two-dimensional projections of the packed structures from T7 simulations are consistent with cryo-electron micrographs of T7 phage DNA.
64 citations