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.

Innovations in Biomolecular Modeling and Simulations

Abstract: Volume 1 Beginnings Personal Perspective Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model Integral Equation Theory of Biomolecules and Electrolytes Molecular Simulation in the Energy Biosciences Sampling and rates Dynamics Simulations with Trajectory Fragments Computing Reaction Rates in Biomolecular Systems using discrete macrostates Challenges in applying Monte Carlo sampling to biomolecular systems Coarse graining and multiscale models Coarse Grained Protein Models Generalized Multi-Level Coarse-Grained Molecular Simulation and Its Applucation to Myosin-V Movement Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Trafficking Studying Proteins and Peptides at Material Surfaces Multiscale Design: From Theory to Practice. Volume 2 Atomistic simulations of nucleic acids and nucleic acid complexes Modeling nucleic acid structure and flexibility: from atomic to mesoscopic scale Molecular dynamics and force field based methods for studying quadruplex nucleic acids Opposites attract: Shape and Electrostatic Complementarity in Protein/DNA Complexes Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism Molecular Dynamics Structure Prediction of a Novel Protein/DNA Complex: Two HU Proteins with a DNA Four-way Junction Molecular Dynamics Simulations of RNA Molecules The Structure and Folding of Helical Junctions in RNA DNA folding, knotting, sliding and hopping Simulations of DNA Knots and Catenanes Monte Carlo Simulations of Nucleosome Chains to Idenitfy Factors that control DNA Compaction and Access Sliding Dynamics Along DNA: a Molecular Perspective Drug design Structure-based design technology: CONTOUR and its aplication to drug discovery Molecular simulation in computer-aided drug design: algorithms and applications Computer-aided drug discovery: two antiviral drugs for HIV AIDS

Biophysics of DNA

Abstract: Surveying the last sixty years of research, this book describes the physical properties of DNA in the context of its biological functioning. It is designed to enable both students and researchers of molecular biology, biochemistry and physics to better understand the biophysics of DNA, addressing key questions and facilitating further research. The chapters integrate theoretical and experimental approaches, emphasising throughout the importance of a quantitative knowledge of physical properties in building and analysing models of DNA functioning. For example, the book shows how the relationship between DNA mechanical properties and the sequence specificity of DNA-protein binding can be analyzed quantitatively by using our current knowledge of the physical and structural properties of DNA. Theoretical models and experimental methods in the field are critically considered to enable the reader to engage effectively with the current scientific literature on the physical properties of DNA.

DNA Liquid-Crystalline Dispersions and Nanoconstructions

Abstract: THE LIQUID-CRYSTALLINE STATE OF DNA The Condensed State of the High-Molecular-Mass Double-Stranded DNA The DNA Condensation and Aggregation Polyphosphates as a Simplified DNA Model Models of High-Molecular-Mass DNA Condensation in Water-Polymeric Solutions Grosberg Model of High-Molecular-Mass DNA Condensation Liquid-Crystalline Phases of the Low-Molecular-Mass Double-Stranded DNA Molecules Ordering of Low-Molecular-Mass Double-Stranded DNAs Brief Concept of Types of Liquid-Crystalline Phases Liquid-Crystalline Phases of Low-Molecular-Mass Double-Stranded DNA Molecules Dispersions of Low-Molecular-Mass Double-Stranded DNA Molecules Low-Molecular-Mass Double-Stranded DNA Dispersions in Water-Polymer Solutions Formation of DNA Dispersions in PEG-Containing Solutions Circular Dichroism of Nucleic Acid Dispersions Circular Dichroism as a Method of Proof of Cholesteric Packing of Nucleic Acid Molecules in Dispersion Particles and Analysis of Their Properties Effect of Different Factors on Formation and Properties of CLCD Particles Parameter of Nucleic Acid Molecule Order in CLCD Particles Polymorphism of Liquid-Crystalline Structures Formed by (DNA-Polycation) Complexes Some Peculiarities of Interaction of DNA Molecules with Polycations Specificity of Chitosan Binding to DNA Formation of Dispersions of (DNA-Chitosan) Complexes CD Spectra of Dispersions Formed by (DNA-Chitosan) Complexes X-Ray Parameters of Phases Formed by (DNA-Chitosan) Complexes Dependence of Efficiency of CLCD Formation by (DNA-Chitosan) Complexes on Various Factors Peculiarities of Interaction of Chitosan Molecules with Nucleic Acids Attempt at a Theoretical Description of Interactions Occurring in the (DNA-Chitosan) Complexes and Resulting in the Formation of Liquid-Crystalline Dispersions with Different Optical Properties Liquid-Crystalline State of DNA Circular Molecules Phase Exclusion of Circular Molecules of Nucleic Acids Formation of Dispersions From Circular Superhelical DNA CD Spectra of Circular Superhelical DNA Dispersions Under Conditions That Modify Parameters of Their Secondary Structure Packing Density and Rearrangement of the Spatial Structure of Superhelical DNA Molecules in LCD Particles Topological Forms and Rearrangement of the Spatial Organization of Superhelical DNA Molecules in LCD Particles DNA LIQUID-CRYSTALLINE FORMS AND THEIR BIOLOGICAL ACTIVITY Liquid-Crystalline State of DNA in Biological Objects DNA and Biological Objects DNA Reactions under Conditions Causing Liquid-Crystalline Dispersions Molecular Crowding Condensation of DNA under the Effect of Chitosan in Conditions Causing Molecular Crowding Activity of Nucleolytic Enzymes Under Conditions of Molecular Crowding Activity of Proteolytic Enzymes under Conditions of Molecular Crowding DNA LIQUID-CRYSTALLINE DISPERSIONS IN NANOTECHNOLOGY AND BIOSENSORICS Nanoconstructions Based on Nucleic Acid Molecules The General Concept of Nanotechnology Biological Molecules as a Background for Nanodesign Two Strategies of Nanodesign Based on NA Molecules Biosensors Based on Nucleic Acids General Concept of Construction and Operation of Biosensors Double-Stranded DNA Molecule as Polyfunctional Biosensing Unit Content and Principle of Operation of an Optical Biosensor Based on DNA Liquid-Crystalline Dispersions DNA CLCD Particles as Sensing Units Sandwich-Type Biosensing Units Based on (DNA-Polycation) Liquid-Crystalline Dispersions DNA Nanoconstruction as a Sensing Unit (New Type of Biodetectors) Hydrogels Containing DNA NaCs as New "Film-Type Biodetectors Index

DNA Enables Nanoscale Control of the Structure of Matter

Abstract: Structural DNA nanotechnology consists of constructing objects, lattices and devices from branched DNA molecules. Branched DNA molecules open the way for the construction of a variety of N-connected motifs. These motifs can be joined by cohesive interactions to produce larger constructs in a bottom-up approach to nanoconstruction. The first objects produced by this approach were stick polyhedra and topological targets, such as knots and Borromean rings. These were followed by periodic arrays with programmable patterns. It is possible to exploit DNA structural transitions and sequence-specific binding to produce a variety of DNA nanomechanical devices, which include a bipedal walker and a machine that emulates the translational capabilities of the ribosome. Much of the promise of this methodology involves the use of DNA to scaffold other materials, such as biological macromolecules, nanoelectronic components, and polymers. These systems are designed to lead to improvements in crystallography, computation and the production of diverse and exotic materials.