201
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Weik F, Kesselheim S, Holm C. A coarse-grained DNA model for the prediction of current signals in DNA translocation experiments. J Chem Phys 2017; 145:194106. [PMID: 27875892 DOI: 10.1063/1.4967458] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present an implicit solvent coarse-grained double-stranded DNA (dsDNA) model confined to an infinite cylindrical pore that reproduces the experimentally observed current modulations of a KaCl solution at various concentrations. Our model extends previous coarse-grained and mean-field approaches by incorporating a position dependent friction term on the ions, which Kesselheim et al. [Phys. Rev. Lett. 112, 018101 (2014)] identified as an essential ingredient to correctly reproduce the experimental data of Smeets et al. [Nano Lett. 6, 89 (2006)]. Our approach reduces the computational effort by orders of magnitude compared with all-atom simulations and serves as a promising starting point for modeling the entire translocation process of dsDNA. We achieve a consistent description of the system's electrokinetics by using explicitly parameterized ions, a friction term between the DNA beads and the ions, and a lattice-Boltzmann model for the solvent.
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Affiliation(s)
- Florian Weik
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Stefan Kesselheim
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
| | - Christian Holm
- Institut für Computerphysik, Universität Stuttgart, Allmandring 3, D-70569 Stuttgart, Germany
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202
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Fernandez-Castanon J, Bomboi F, Rovigatti L, Zanatta M, Paciaroni A, Comez L, Porcar L, Jafta CJ, Fadda GC, Bellini T, Sciortino F. Small-angle neutron scattering and molecular dynamics structural study of gelling DNA nanostars. J Chem Phys 2017; 145:084910. [PMID: 27586949 DOI: 10.1063/1.4961398] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed of 196 nucleotides) and to explore the structural signatures of their aggregation process. We report small-angle neutron scattering experiments focused on the evaluation of both the form factor and the temperature evolution of the scattered intensity at a nanostar concentration where the system forms a tetravalent equilibrium gel. We also perform molecular dynamics simulations of one isolated tetramer to evaluate the form factor numerically, without resorting to any approximate shape. The numerical form factor is found to be in very good agreement with the experimental one. Simulations predict an essentially temperature-independent form factor, offering the possibility to extract the effective structure factor and its evolution during the equilibrium gelation.
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Affiliation(s)
| | - F Bomboi
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
| | - L Rovigatti
- Rudolf Peierls C.T.P., University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - M Zanatta
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - A Paciaroni
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Comez
- Dipartimento di Fisica, Università di Perugia, Via Pascoli, 06123 Perugia, Italy
| | - L Porcar
- Institut Laue-Langevin, 71 Avenue des Martyrs, CS 20156, 38042 Grenoble Cedex 9, France
| | - C J Jafta
- Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, 14109 Berlin, Germany
| | - G C Fadda
- Laboratoire Léon Brillouin, LLB, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - T Bellini
- Department of Medical Biotechnology and Translational Medicine, Università di Milano, I-20133 Milano, Italy
| | - F Sciortino
- Sapienza-Università di Roma, P.le A. Moro 5, 00185 Roma, Italy
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203
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Reinhardt A, Schreck JS, Romano F, Doye JPK. Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:014006. [PMID: 27830657 DOI: 10.1088/0953-8984/29/1/014006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We use Monte Carlo simulations and free-energy techniques to show that binary solutions of penta- and hexavalent two-dimensional patchy particles can form thermodynamically stable quasicrystals even at very narrow patch widths, provided their patch interactions are chosen in an appropriate way. Such patchy particles can be thought of as a coarse-grained representation of DNA multi-arm 'star' motifs, which can be chosen to bond with one another very specifically by tuning the DNA sequences of the protruding arms. We explore several possible design strategies and conclude that DNA star tiles that are designed to interact with one another in a specific but not overly constrained way could potentially be used to construct soft quasicrystals in experiment. We verify that such star tiles can form stable dodecagonal motifs using oxDNA, a realistic coarse-grained model of DNA.
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Affiliation(s)
- Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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204
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Fosado YAG, Michieletto D, Allan J, Brackley CA, Henrich O, Marenduzzo D. A single nucleotide resolution model for large-scale simulations of double stranded DNA. SOFT MATTER 2016; 12:9458-9470. [PMID: 27845464 DOI: 10.1039/c6sm01859a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The computational modelling of DNA is becoming crucial in light of new advances in DNA nano-technology, single-molecule experiments and in vivo DNA tampering. Here we present a mesoscopic model for double stranded DNA (dsDNA) at the single nucleotide level which retains the characteristic helical structure, while being able to simulate large molecules - up to a million base pairs - for time-scales which are relevant to physiological processes. This is made possible by an efficient and highly-parallelised implementation of the model which we discuss here. The model captures the main characteristics of DNA, such as the different persistence lengths for double and single strands, pitch, torsional rigidity and the presence of major and minor grooves. The model constitutes a starting point for the future implementation of further features, such as sequence specificity and electrostatic repulsion. We show that the behaviour of the presented model compares favourably with single molecule experiments where dsDNA is manipulated by external forces or torques. We finally present some results on the kinetics of denaturation of linear DNA and supercoiling of closed dsDNA molecules.
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Affiliation(s)
- Y A G Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - D Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - J Allan
- Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - C A Brackley
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - O Henrich
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK and EPCC, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
| | - D Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, Scotland, UK
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205
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Matek C, Šulc P, Randisi F, Doye JPK, Louis AA. Coarse-grained modelling of supercoiled RNA. J Chem Phys 2016; 143:243122. [PMID: 26723607 DOI: 10.1063/1.4933066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.
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Affiliation(s)
- Christian Matek
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, United Kingdom
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206
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Reinhardt A, Frenkel D. DNA brick self-assembly with an off-lattice potential. SOFT MATTER 2016; 12:6253-60. [PMID: 27378398 DOI: 10.1039/c6sm01031h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report Monte Carlo simulations of a simple off-lattice patchy-particle model for DNA 'bricks'. We relate the parameters that characterise this model with the binding free energy of pairs of single-stranded DNA molecules. We verify that an off-lattice potential parameterised in this way reproduces much of the behaviour seen with a simpler lattice model we introduced previously, although the relaxation of the geometric constraints leads to a more error-prone self-assembly pathway. We investigate the self-assembly process as a function of the strength of the non-specific interactions. We show that our off-lattice model for DNA bricks results in robust self-assembly into a variety of target structures.
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Affiliation(s)
- Aleks Reinhardt
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
| | - Daan Frenkel
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK.
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207
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Multiscale coarse-grained modelling of chromatin components: DNA and the nucleosome. Adv Colloid Interface Sci 2016; 232:36-48. [PMID: 26956528 DOI: 10.1016/j.cis.2016.02.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/05/2016] [Accepted: 02/05/2016] [Indexed: 11/23/2022]
Abstract
To model large biomolecular systems, such as cell and organelles an atomistic description is not currently achievable and is not generally practical. Therefore, simplified coarse-grained (CG) modelling becomes a necessity. One of the most important cellular components is chromatin, a large DNA-protein complex where DNA is highly compacted. Recent progress in coarse graining modelling of the major chromatin components, double helical DNA and the nucleosome core particle (NCP) is presented. First, general principles and approaches allowing rigorous bottom-to-top generation of interaction potentials in the CG models are presented. Then, recent CG models of DNA are reviewed and their adequacy is benchmarked against experimental data on the salt dependence of DNA flexibility (persistence length). Furthermore, a few recent CG models of the NCP are described and their application for studying salt-dependent NCP-NCP interaction is discussed. An example of a multiscale approach to CG modelling of chromatin is presented where interactions and self-assembly of thousands of NCPs in solution are observed.
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208
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Dunn NJH, Noid WG. Bottom-up coarse-grained models with predictive accuracy and transferability for both structural and thermodynamic properties of heptane-toluene mixtures. J Chem Phys 2016; 144:204124. [DOI: 10.1063/1.4952422] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Nicholas J. H. Dunn
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - W. G. Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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209
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Schreck JS, Romano F, Zimmer MH, Louis AA, Doye JPK. Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model. ACS NANO 2016; 10:4236-47. [PMID: 27010928 DOI: 10.1021/acsnano.5b07664] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
We use oxDNA, a coarse-grained model of DNA at the nucleotide level, to simulate large nanoprisms that are composed of multi-arm star tiles, in which the size of bulge loops that have been incorporated into the tile design is used to control the flexibility of the tiles. The oxDNA model predicts equilibrium structures for several different nanoprism designs that are in excellent agreement with the experimental structures as measured by cryoTEM. In particular we reproduce the chiral twisting of the top and bottom faces of the nanoprisms, as the bulge sizes in these structures are varied due to the greater flexibility of larger bulges. We are also able to follow how the properties of the star tiles evolve as the prisms are assembled. Individual star tiles are very flexible, but their structures become increasingly well-defined and rigid as they are incorporated into larger assemblies. oxDNA also finds that the experimentally observed prisms are more stable than their inverted counterparts, but interestingly this preference for the arms of the tiles to bend in a given direction only emerges after they are part of larger assemblies. These results show the potential for oxDNA to provide detailed structural insight as well as to predict the properties of DNA nanostructures and hence to aid rational design in DNA nanotechnology.
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Affiliation(s)
- John S Schreck
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca' Foscari Venezia , I-30123 Venezia, Italy
| | - Matthew H Zimmer
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford OX1 3QZ, United Kingdom
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210
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Ghobadi AF, Jayaraman A. Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study. SOFT MATTER 2016; 12:2276-87. [PMID: 26777980 DOI: 10.1039/c5sm02868j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this paper we study how varying oligonucleic acid backbone chemistry affects the hybridization/melting thermodynamics of oligonucleic acids. We first describe the coarse-grained (CG) model with tunable parameters that we developed to enable the study of both naturally occurring oligonucleic acids, such as DNA, and their chemically-modified analogues, such as peptide nucleic acids (PNAs) and locked nucleic acids (LNAs). The DNA melting curves obtained using such a CG model and molecular dynamics simulations in an implicit solvent and with explicit ions match with the melting curves obtained using the empirical nearest-neighbor models. We use these CG simulations to then elucidate the effect of backbone flexibility, charge, and nucleobase spacing along the backbone on the melting curves, potential energy and conformational entropy change upon hybridization and base-pair hydrogen bond residence time. We find that increasing backbone flexibility decreases duplex thermal stability and melting temperature mainly due to increased conformational entropy loss upon hybridization. Removing charges from the backbone enhances duplex thermal stability due to the elimination of electrostatic repulsion and as a result a larger energetic gain upon hybridization. Lastly, increasing nucleobase spacing decreases duplex thermal stability due to decreasing stacking interactions that are important for duplex stability.
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Affiliation(s)
- Ahmadreza F Ghobadi
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA.
| | - Arthi Jayaraman
- Department of Chemical and Biomolecular Engineering, Colburn Laboratory, University of Delaware, 150 Academy Street, Newark, DE 19716, USA. and Department of Materials Science and Engineering, University of Delaware, Newark, DE 19716, USA
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211
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Snodin BEK, Romano F, Rovigatti L, Ouldridge TE, Louis AA, Doye JPK. Direct Simulation of the Self-Assembly of a Small DNA Origami. ACS NANO 2016; 10:1724-37. [PMID: 26766072 DOI: 10.1021/acsnano.5b05865] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
By using oxDNA, a coarse-grained nucleotide-level model of DNA, we are able to directly simulate the self-assembly of a small 384-base-pair origami from single-stranded scaffold and staple strands in solution. In general, we see attachment of new staple strands occurring in parallel, but with cooperativity evident for the binding of the second domain of a staple if the adjacent junction is already partially formed. For a system with exactly one copy of each staple strand, we observe a complete assembly pathway in an intermediate temperature window; at low temperatures successful assembly is prevented by misbonding while at higher temperature the free-energy barriers to assembly become too large for assembly on our simulation time scales. For high-concentration systems involving a large staple strand excess, we never see complete assembly because there are invariably instances where two copies of the same staple both bind to the scaffold, creating a kinetic trap that prevents the complete binding of either staple. This mutual staple blocking could also lead to aggregates of partially formed origamis in real systems, and helps to rationalize certain successful origami design strategies.
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Affiliation(s)
- Benedict E K Snodin
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lorenzo Rovigatti
- Faculty of Physics, University of Vienna , Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College , 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford , 1 Keble Road, Oxford, OX1 3NP, United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , South Parks Road, Oxford, OX1 3QZ, United Kingdom
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212
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Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M. Computing Nonequilibrium Conformational Dynamics of Structured Nucleic Acid Assemblies. J Chem Theory Comput 2015; 12:261-73. [PMID: 26636351 DOI: 10.1021/acs.jctc.5b00965] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Synthetic nucleic acids can be programmed to form precise three-dimensional structures on the nanometer-scale. These thermodynamically stable complexes can serve as structural scaffolds to spatially organize functional molecules including multiple enzymes, chromophores, and force-sensing elements with internal dynamics that include substrate reaction-diffusion, excitonic energy transfer, and force-displacement response that often depend critically on both the local and global conformational dynamics of the nucleic acid assembly. However, high molecular weight assemblies exhibit long time-scale and large length-scale motions that cannot easily be sampled using all-atom computational procedures such as molecular dynamics. As an alternative, here we present a computational framework to compute the overdamped conformational dynamics of structured nucleic acid assemblies and apply it to a DNA-based tweezer, a nine-layer DNA origami ring, and a pointer-shaped DNA origami object, which consist of 204, 3,600, and over 7,000 basepairs, respectively. The framework employs a mechanical finite element model for the DNA nanostructure combined with an implicit solvent model to either simulate the Brownian dynamics of the assembly or alternatively compute its Brownian modes. Computational results are compared with an all-atom molecular dynamics simulation of the DNA-based tweezer. Several hundred microseconds of Brownian dynamics are simulated for the nine-layer ring origami object to reveal its long time-scale conformational dynamics, and the first ten Brownian modes of the pointer-shaped structure are predicted.
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Affiliation(s)
| | | | | | - Oskar Hallatschek
- Department of Physics, University of California, Berkeley , Berkeley, California 94720, United States
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213
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Mak CH. Atomistic Free Energy Model for Nucleic Acids: Simulations of Single-Stranded DNA and the Entropy Landscape of RNA Stem-Loop Structures. J Phys Chem B 2015; 119:14840-56. [PMID: 26548372 DOI: 10.1021/acs.jpcb.5b08077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While single-stranded (ss) segments of DNAs and RNAs are ubiquitous in biology, details about their structures have only recently begun to emerge. To study ssDNA and RNAs, we have developed a new Monte Carlo (MC) simulation using a free energy model for nucleic acids that has the atomisitic accuracy to capture fine molecular details of the sugar-phosphate backbone. Formulated on the basis of a first-principle calculation of the conformational entropy of the nucleic acid chain, this free energy model correctly reproduced both the long and short length-scale structural properties of ssDNA and RNAs in a rigorous comparison against recent data from fluorescence resonance energy transfer, small-angle X-ray scattering, force spectroscopy and fluorescence correlation transport measurements on sequences up to ∼100 nucleotides long. With this new MC algorithm, we conducted a comprehensive investigation of the entropy landscape of small RNA stem-loop structures. From a simulated ensemble of ∼10(6) equilibrium conformations, the entropy for the initiation of different size RNA hairpin loops was computed and compared against thermodynamic measurements. Starting from seeded hairpin loops, constrained MC simulations were then used to estimate the entropic costs associated with propagation of the stem. The numerical results provide new direct molecular insights into thermodynaimc measurement from macroscopic calorimetry and melting experiments.
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Affiliation(s)
- Chi H Mak
- Department of Chemistry and Center of Applied Mathematical Sciences, University of Southern California , Los Angeles, California 90089, United States
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214
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Abstract
We present a general coarse-grained model of sodium, magnesium, spermidine, and chlorine in implicit solvent. The effective potentials between ions are systematically parametrized using a relative entropy coarse-graining approach [Carmichael, S. P. and M. S. Shell, J. Phys. Chem. B, 116, 8383-93 (2012)] that maximizes the information retained in a coarse-grained model. We describe the local distribution of ions in the vicinity of a recently published coarse-grained DNA model and demonstrate a dependence of persistence length on ionic strength that differs from that predicted by Odijk-Skolnick-Fixman theory. Consistent with experimental observations, we show that spermidine induces DNA condensation whereas magnesium and sodium do not. This model can be used alongside any coarse-grained DNA model that has explicit charges and an accurate reproduction of the excluded volume of dsDNA.
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Affiliation(s)
- Daniel M Hinckley
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Juan J de Pablo
- Institute for Molecular Engineering, University of Chicago , Chicago, Illinois 60637, United States.,Materials Science Division Argonne National Laboratory , Argonne, Illinois 60439, United States
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215
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Jabbari H, Aminpour M, Montemagno C. Computational Approaches to Nucleic Acid Origami. ACS COMBINATORIAL SCIENCE 2015; 17:535-47. [PMID: 26348196 DOI: 10.1021/acscombsci.5b00079] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Recent advances in experimental DNA origami have dramatically expanded the horizon of DNA nanotechnology. Complex 3D suprastructures have been designed and developed using DNA origami with applications in biomaterial science, nanomedicine, nanorobotics, and molecular computation. Ribonucleic acid (RNA) origami has recently been realized as a new approach. Similar to DNA, RNA molecules can be designed to form complex 3D structures through complementary base pairings. RNA origami structures are, however, more compact and more thermodynamically stable due to RNA's non-canonical base pairing and tertiary interactions. With all these advantages, the development of RNA origami lags behind DNA origami by a large gap. Furthermore, although computational methods have proven to be effective in designing DNA and RNA origami structures and in their evaluation, advances in computational nucleic acid origami is even more limited. In this paper, we review major milestones in experimental and computational DNA and RNA origami and present current challenges in these fields. We believe collaboration between experimental nanotechnologists and computer scientists are critical for advancing these new research paradigms.
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Affiliation(s)
- Hosna Jabbari
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Maral Aminpour
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
| | - Carlo Montemagno
- Ingenuity Lab, 11421 Saskatchewan
Drive, Edmonton, Alberta T6G 2M9, Canada
- Department
of Chemical and Materials Engineering, University of Alberta, Edmonton T6G 2V4, Canada
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216
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Zavadlav J, Podgornik R, Praprotnik M. Adaptive Resolution Simulation of a DNA Molecule in Salt Solution. J Chem Theory Comput 2015; 11:5035-44. [DOI: 10.1021/acs.jctc.5b00596] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julija Zavadlav
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Hajdrihova
19, SI-1001 Ljubljana, Slovenia
| | - Rudolf Podgornik
- Department
of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Jadranska 19, SI-1000 Ljubljana, Slovenia
- Theoretical
Physics Department, J. Stefan Institute, Jamova c. 39, SI-1000 Ljubljana, Slovenia
| | - Matej Praprotnik
- Laboratory
for Molecular Modeling, National Institute of Chemistry, Hajdrihova
19, SI-1001 Ljubljana, Slovenia
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217
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Yanao T, Sano S, Yoshikawa K. Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity. AIMS BIOPHYSICS 2015. [DOI: 10.3934/biophy.2015.4.666] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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