Coarse-graining dna for simulations of dna nanotechnology pdf

Selfassembly of twodimensional binary quasicrystals. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the selfassembly processes associated with dna nanotechnology to be studied. Coarsegraining rna nanostructures for molecular dynamics simulations. Selfassembly of knotted polymers without breaking or forming covalent bonds is challenging, as the chain needs to be threaded. The growing interest in the dnabased mesoscale systems of biological and. Selfassembly offers a route to arranging matter at the nanoscale with high accuracy and at low cost. Similar to the computeraided design cad of the realworld machines e. Hirerna, a recently proposed highresolution coarsegrained rna.

He is mainly interested in nucleic acids modeling dna and rna using coarse grained models, which allow for simulations of longer timescales and larger systems than if fullyatomistic representation is used. Pdf coarsegraining dna for simulations of dna nanotechnology. We have used fully atomistic molecular dynamics simulations to study the structure, stability. Pdf coarsegrained simulations of dna overstretching. Coarsegraining rna nanostructures for molecular dynamics. Coarsegrained models for dna molecules and cnts have both been developed in the last decade, whereas the coarsegraining schemes are markedly different. Molecular dynamics simulation of supercoiled dna rings arman fathizadeh, helmut schiessel, and mohammad reza ejtehadi. Multiscale coarsegrained modelling of chromatin components. A coarsegrained model of dna with explicit solvation by water and ions.

We present a bottom up approach for the construction and characterization of these structures. Dna nanotechnology is a rapidly expanding field that enables highthroughput construction of dna based submicronsize nanomachines with nanoscale accuracy. School of physics, institute for research in fundamental sciences ipm, tehran, iran institute for nanoscience and nanotechnology, sharif university of technology, tehran, iran. Louis1 1rudolf peierls centre for theoretical physics, university of oxford, 1 keble road, oxford, ox1 3np, united kingdom.

He is mainly interested in nucleic acids modeling dna and rna using coarsegrained models, which allow for simulations of longer timescales and larger systems than if fullyatomistic representation is used. We apply a recentlydeveloped coarsegrained model of dna, designed to capture the basic physics of nanotechnological dna systems, to the study of a burntbridges dna motor consisting of a singlestranded cargo that steps processively along a track of singlestranded stators. In this paper we focus on the computer simulation studies of dna. We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the. A series of coarse grained models have been developed for study of the molecular dynamics of rna nanostructures. Dna nanotechnology and its biological applications1 chapter of book. The models in the series have one to three beads per nucleotide and include. Physical chemistry chemical physics 20, 15 47, 20395. Coarsegraining dna for simulations of dna nanotechnology jonathan p. Coarsegrained molecular dynamics simulation of dna translocation in chemicallymodified nanopores. Stimulated by the dirth of reliable coarsegrained singlestranded dna models, a the aksimentiev and ha groups collaborated to create the first computational model of dna specifically optimized for singlestranded dna using. Design principles for rapid folding of knotted dna.

Coarsegraining dna for simulations of dna nanotechnology core. Smitha received xth xxxxxxxxxx 20xx, accepted xth xxxxxxxxx 20xx. Hirerna, a recently proposed highresolution coarse grained rna that captures many. Sequencedependent thermodynamics of a coarsegrained dna model petr sulc,1 flavio romano,2 thomas e. Overstretching at 23 c occurs at 74 pn in the model, about 67 pn higher than the experimental value. Comprehensive understanding of such bio nano system could help achieve the ultimate goal of highthroughput genome sequencing. First published on the web xth xxxxxxxxxx 200x doi. In paper iv we further explore the power of coarsegrained molecular dynamics simulation to predict the dynamics of dna nanostructures.

The cg dna surface potential was combined with the cg dna model explained in section 2. No matter the approach used to derive the forcefield, nor the final application of the model, one of the key difficulties specific to the dna coarse graining is the correct handling of longrange electrostatics, something that is crucial to correctly represent one of the most highly charged naturally occurring polyelectrolytes. We have recently proposed a coarse grained model of dna that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of dna nanotechnology, the formation of duplexes from single strands. To address this challenge, multiscale approaches, including coarsegraining methods, become necessary.

We demonstrate that the model is able to simulate such a system, and investigate the sensitivity of the stepping. Pdf we use a recently developed coarsegrained model to simulate the overstretching of duplex dna. Structure, stability and elasticity of dna nanotubes. Published 24 june 2010 2010 iop publishing ltd physical biology, volume 7, number 3. May 19, 2011 the lj potential parameters chosen for the cg model accurately reproduced the trajectory and energy data from allatom md simulations.

One successful application of the selfassembly principle is dna origami, a method of folding a long dna strand into a predetermined threedimensional 3d shape 2,3. The growing interest in the dna based mesoscale systems of biological and nonbiological nature has encouraged the computational molecular science com. Dna nanotubes are tubular structures composed of dna crossover molecules. By decreasing the degrees of freedom much longer simulation times can be studied at the expense of molecular detail.

Pdf coarse graining rna nanostructures for molecular. In particular, his group uses computational models to study problems in biology, and bioinspired nanotechnology systems. Cartoon of the coarse graining process proposed by bianca mladek and coworkers for modeling metal nanoparticles coated with dna strands. We use a recently developed coarsegrained model to simulate the overstretching of duplex dna. A practical guide to molecular dynamics simulations of dna. The field of dna nanotechnology was invented by american nanotechnologist and crystallographer nadrian c. The coarsegrained modeling originates from work by michael levitt and ariel warshel in.

Maxim paliy 1,2, roderick melnik 1,3 and bruce a shapiro 4. Dna nanotechnology is the design and manufacture of artificial nucleic acid structures for technological uses. Coarsegraining dna for simulations of dna nanotechnology jpk doye, te ouldridge, aa louis, f romano, p sulc, c matek. We present a multiresolution approach to modeling complexes between protein and dna that contain looped or coiled dna. Seeman realised that a threedimensional lattice could be created from dna, which could. The models in the series have one to three beads per nucleotide and include different amounts of detailed structural information. Elaine chan, sharon glotzer, peter cummings, clare mccabe and alberto striolo, effective interaction potentials for coarse grained simulations of polymertethered nanoparticle selfassembly in solution, coarse graining of condensed phase and biomolecular systems, 10. Knots are some of the most remarkable topological features in nature. All atom and coarse grained dna simulation studies julija zavadlav abstract the deoxyribonucleic acid is due to its biological importance, probably the most studied macromolecule. Dna nanomachines 86, 87 and with atomistic simulations to elucidate the. To simulate long time and length scale processes involving dna it is necessary to use a coarse grained description. The approach combines a coarse grained model of the dna loop, based on the classical theory of elasticity, with an atom level model of proteins and protein dna interfaces based on molecular dynamics. To simulate long time and length scale processes involving dna it is necessary to use a coarsegrained description. Jun 03, 20 although rnas play many cellular functions, little is known about the dynamics and thermodynamics of these molecules.

Hirerna, a recently proposed highresolution coarsegrained rna that captures many. Coarsegrained simulations of the selfassembly of dnalinked. A coarse grained model for atomicdetailed dna simulations. Mognettib and daan frenkelc by exploiting the exquisite selectivity of dna hybridization, dnacoated colloids dnaccs can be made to selfassemble in a wide variety of structures. Simulating a burntbridges dna motor with a coarsegrained. Coarsegraining dna for simulations of dna nanotechnology by jpk doye, te ouldridge, aa louis, f romano, p sulc, c matek, bek snodin, l rovigatti, js schreck, rm harrison and wpj smith no static citation data no static citation data cite. Dna and rna nanotechnology biophysics statistical physics and optimization smart. Quantitative prediction of the phase diagram of dna functionalized nanosized colloids bianca m. Martinezveracoechea,1 alexandre dawid,4 and daan frenkel1 1department of chemistry, university of cambridge, lens. Jul 26, 2006 we present a multiresolution approach to modeling complexes between protein and dna that contain looped or coiled dna. Here we provide an overview of different approaches to such coarsegraining, focussing on those at the nucleotide level that allow the selfassembly processes associated with dna nanotechnology to be studied. C coarsegrained single strand of dna and hairpin loop dna. The ones marked may be different from the article in the profile.

Aug 30, 20 we apply a recentlydeveloped coarsegrained model of dna, designed to capture the basic physics of nanotechnological dna systems, to the study of a burntbridges dna motor consisting of a singlestranded cargo that steps processively along a track of singlestranded stators. Coarsegrainedmoleculardynamicssimulationofdnatranslocation. One of the main unresolved problems in biological science is the timescale and lengthscale gap between computational and experimental methods of studying biological systems. Optimizing dna nanotechnology through coarsegrained. Coarsegrained molecular dynamics simulation of dna. Multiscale method for simulating proteindna complexes. As a test case, we focus on nano sized colloids carrying singlestranded dna strands of length comparable to the colloids size. Optimizing dna nanotechnology through coarsegrained modeling. This could be due to the different force field used in the allatom simulations of dna charmm27 in our case versus amber10 in the papoian group case and to the differences in the coarse graining of dna or may be related to different form of ionic potentials used. The coarsegrained models have mostly been used to simulate large biomolecules, such as proteins, lipids, dna and polymers.

For a fragment of any given length and sequence, cgdna calculates the configuration of the associated free energy minimizer, i. This cited by count includes citations to the following articles in scholar. The parameters of this model are transferable and are solely based on experimental data. Quantitative prediction of the phase diagram of dna. Compared to dna nanostructures, rna as a nano engineering material brings additional challenging features, such as much larger diversity. In order to provide a realistic simulation of large models, the multiscale methods such as coarsegraining, have therefore become very popular. Physical chemistry chemical physics 15 47, 2039520414, 20. Design, optimization, and analysis of large dna and rna.

Although rnas play many cellular functions, little is known about the dynamics and thermodynamics of these molecules. Coarse graining dna for simulations of dna nanotechnology. Coarsegrained simulations of rna and dna duplexes the. It ought to be borne in mind that this phase diagram relates to the twodimensional setup considered in the patchyparticle simulations. We draw on the oxdna2 model for coarsegrained simulation of dna 21. Molecular dynamics simulation of supercoiled dna rings. For more complex systems, however, rational design and optimization can become difficult. Dna nanotechnology is a rapidly growing field of science that holds great promise for creating nanodevices capable of programmable transport and delivery of molecular cargoes, highprecision molecular sensing, nanomanufacturing, molecular computing, and countless other applications. We present a quantitative, multiscale coarsegrained model of dna coated colloids. Here we provide an overview of different approaches to such coarsegraining, focussing on those at the nucleotide level that allow the selfassembly processes associated with dna nanotechnology to. Various possible topologies of nanotubes are constructed such as 6helix, 8helix and tritubes with different sequences and lengths. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that allow the selfassembly processes associated with dna nanotechnology to. Pdf to simulate long time and length scale processes involving dna it is necessary to use a coarsegrained description.

Connecting the molecular world to biology requires understanding how molecularscale dynamics propagate upward in scale to define the function of biological structures. Boolean threshold networks as models of genotypephenotype maps c. We have recently proposed a coarsegrained model of dna that captures the basic thermodynamic, structural, and mechanical changes associated with the fundamental process in much of dna nanotechnology, the formation of duplexes from single strands. Sequencedependent thermodynamics of a coarsegrained dna model. Coarsegraining methods for computational biology annual. Also, the model was used to simulate nanoassemblies which had not been produced. In this field, nucleic acids are used as nonbiological engineering materials for nanotechnology rather than as the carriers of genetic information in living cells. Jun 25, 2012 in the next coarse graining step bottom, the nonbinding part of all polymers is condensed into a single soft sphere pink, while each binding sequence is condensed into a separate soft particle green. We discuss here the theoretical underpinnings and history of coarsegraining and summarize the state of the field. Dec 15, 2015 the present work investigates the capability of bottomup coarse graining cg methods for accurately modeling both structural and thermodynamic properties of allatom aa models for molecular liq. First we present the two most widely used simulation methods. Bottomup coarsegrained models that accurately describe the.

Bioinspired and nano scale integrated computing edited by mary eshaghian publisher. Molecular dynamics simulations of selfassembled dna. Coarsegrained models have found practical applications in molecular dynamics simulations. The dna origami method exploits the selfassembly property of nucleic acids to build diverse nanoscale systems.