201
|
Rovigatti L, Šulc P, Reguly IZ, Romano F. A comparison between parallelization approaches in molecular dynamics simulations on GPUs. J Comput Chem 2014; 36:1-8. [DOI: 10.1002/jcc.23763] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 09/30/2014] [Accepted: 10/04/2014] [Indexed: 01/20/2023]
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica; Sapienza-Università di Roma; Piazzale A. Moro 5 00185 Roma Italy
- Faculty of Physics; University of Vienna; Boltzmanngasse 5 A-1090 Vienna Austria
| | - Petr Šulc
- Department of Physics, Rudolf Peierls Centre for Theoretical Physics; University of Oxford; 1 Keble Road Oxford OX1 3NP United Kingdom
| | - István Z. Reguly
- Mathematical, Physical and Life Sciences Division; Oxford e-Research Centre, University of Oxford; Oxford, 7 Keble Road Oxford OX1 3QG United Kingdom
| | - Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry; University of Oxford; South Parks Road Oxford OX1 3QZ United Kingdom
| |
Collapse
|
202
|
Freeman GS, Hinckley DM, Lequieu JP, Whitmer JK, de Pablo JJ. Coarse-grained modeling of DNA curvature. J Chem Phys 2014; 141:165103. [DOI: 10.1063/1.4897649] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Gordon S. Freeman
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Daniel M. Hinckley
- Department of Chemical and Biological Engineering, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
| | - Joshua P. Lequieu
- Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| | - Jonathan K. Whitmer
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA
| | - Juan J. de Pablo
- Materials Science Division, Argonne National Laboratory, Argonne, Illinois 60439, USA and Institute for Molecular Engineering, University of Chicago, Chicago, Illinois 60637, USA
| |
Collapse
|
203
|
Biophysically inspired rational design of structured chimeric substrates for DNAzyme cascade engineering. PLoS One 2014; 9:e110986. [PMID: 25347066 PMCID: PMC4210168 DOI: 10.1371/journal.pone.0110986] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 09/18/2014] [Indexed: 12/21/2022] Open
Abstract
The development of large-scale molecular computational networks is a promising approach to implementing logical decision making at the nanoscale, analogous to cellular signaling and regulatory cascades. DNA strands with catalytic activity (DNAzymes) are one means of systematically constructing molecular computation networks with inherent signal amplification. Linking multiple DNAzymes into a computational circuit requires the design of substrate molecules that allow a signal to be passed from one DNAzyme to another through programmed biochemical interactions. In this paper, we chronicle an iterative design process guided by biophysical and kinetic constraints on the desired reaction pathways and use the resulting substrate design to implement heterogeneous DNAzyme signaling cascades. A key aspect of our design process is the use of secondary structure in the substrate molecule to sequester a downstream effector sequence prior to cleavage by an upstream DNAzyme. Our goal was to develop a concrete substrate molecule design to achieve efficient signal propagation with maximal activation and minimal leakage. We have previously employed the resulting design to develop high-performance DNAzyme-based signaling systems with applications in pathogen detection and autonomous theranostics.
Collapse
|
204
|
Maffeo C, Yoo J, Comer J, Wells DB, Luan B, Aksimentiev A. Close encounters with DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:413101. [PMID: 25238560 PMCID: PMC4207370 DOI: 10.1088/0953-8984/26/41/413101] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.
Collapse
Affiliation(s)
- C Maffeo
- Department of Physics, University of Illinois, Urbana, IL, USA
| | | | | | | | | | | |
Collapse
|
205
|
Andrews CT, Elcock AH. COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids. J Chem Theory Comput 2014; 10:5178-5194. [PMID: 25400526 PMCID: PMC4230375 DOI: 10.1021/ct5006328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Indexed: 02/06/2023]
Abstract
![]()
We describe the derivation of a set
of bonded and nonbonded coarse-grained
(CG) potential functions for use in implicit-solvent Brownian dynamics
(BD) simulations of proteins derived from all-atom explicit-solvent
molecular dynamics (MD) simulations of amino acids. Bonded potential
functions were derived from 1 μs MD simulations of each of the
20 canonical amino acids, with histidine modeled in both its protonated
and neutral forms; nonbonded potential functions were derived from
1 μs MD simulations of every possible pairing of the amino acids
(231 different systems). The angle and dihedral probability distributions
and radial distribution functions sampled during MD were used to optimize
a set of CG potential functions through use of the iterative Boltzmann
inversion (IBI) method. The optimized set of potential functions—which
we term COFFDROP (COarse-grained Force Field for Dynamic Representation
Of Proteins)—quantitatively reproduced all of the “target”
MD distributions. In a first test of the force field, it was used
to predict the clustering behavior of concentrated amino acid solutions;
the predictions were directly compared with the results of corresponding
all-atom explicit-solvent MD simulations and found to be in excellent
agreement. In a second test, BD simulations of the small protein villin
headpiece were carried out at concentrations that have recently been
studied in all-atom explicit-solvent MD simulations by Petrov and
Zagrovic (PLoS Comput. Biol.2014, 5, e1003638). The anomalously strong intermolecular interactions
seen in the MD study were reproduced in the COFFDROP simulations;
a simple scaling of COFFDROP’s nonbonded parameters, however,
produced results in better accordance with experiment. Overall, our
results suggest that potential functions derived from simulations
of pairwise amino acid interactions might be of quite broad applicability,
with COFFDROP likely to be especially useful for modeling unfolded
or intrinsically disordered proteins.
Collapse
Affiliation(s)
- Casey T Andrews
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| |
Collapse
|
206
|
Nisoli C, Bishop AR. Thermomechanical stability and mechanochemical response of DNA: A minimal mesoscale model. J Chem Phys 2014; 141:115101. [DOI: 10.1063/1.4895724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Cristiano Nisoli
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A. R. Bishop
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| |
Collapse
|
207
|
Maffeo C, Ngo TT, Ha T, Aksimentiev A. A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment. J Chem Theory Comput 2014; 10:2891-2896. [PMID: 25136266 PMCID: PMC4132850 DOI: 10.1021/ct500193u] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2014] [Indexed: 01/02/2023]
Abstract
A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT14 fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.
Collapse
Affiliation(s)
- Christopher Maffeo
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Thuy T.
M. Ngo
- Center
for Biophysics and Computational Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| | - Taekjip Ha
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- The
Howard Hughes Medical Institute, Chevy Chase, Maryland, United
States
| | - Aleksei Aksimentiev
- Department
of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
- Beckman
Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, Illinois, United States
| |
Collapse
|
208
|
Villani G. Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study. J Phys Chem B 2014; 118:5439-52. [PMID: 24813562 DOI: 10.1021/jp502792r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.
Collapse
Affiliation(s)
- Giovanni Villani
- Istituto di Chimica dei Composti OrganoMetallici, ICCOM-UOS Pisa Area della Ricerca del CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
| |
Collapse
|
209
|
Hinckley DM, Freeman GS, Whitmer JK, de Pablo JJ. An experimentally-informed coarse-grained 3-Site-Per-Nucleotide model of DNA: structure, thermodynamics, and dynamics of hybridization. J Chem Phys 2014; 139:144903. [PMID: 24116642 DOI: 10.1063/1.4822042] [Citation(s) in RCA: 150] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
A new 3-Site-Per-Nucleotide coarse-grained model for DNA is presented. The model includes anisotropic potentials between bases involved in base stacking and base pair interactions that enable the description of relevant structural properties, including the major and minor grooves. In an improvement over available coarse-grained models, the correct persistence length is recovered for both ssDNA and dsDNA, allowing for simulation of non-canonical structures such as hairpins. DNA melting temperatures, measured for duplexes and hairpins by integrating over free energy surfaces generated using metadynamics simulations, are shown to be in quantitative agreement with experiment for a variety of sequences and conditions. Hybridization rate constants, calculated using forward-flux sampling, are also shown to be in good agreement with experiment. The coarse-grained model presented here is suitable for use in biological and engineering applications, including nucleosome positioning and DNA-templated engineering.
Collapse
Affiliation(s)
- Daniel M Hinckley
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
| | | | | | | |
Collapse
|
210
|
Ingólfsson HI, Lopez CA, Uusitalo JJ, de Jong DH, Gopal SM, Periole X, Marrink SJ. The power of coarse graining in biomolecular simulations. WILEY INTERDISCIPLINARY REVIEWS. COMPUTATIONAL MOLECULAR SCIENCE 2014; 4:225-248. [PMID: 25309628 PMCID: PMC4171755 DOI: 10.1002/wcms.1169] [Citation(s) in RCA: 325] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Computational modeling of biological systems is challenging because of the multitude of spatial and temporal scales involved. Replacing atomistic detail with lower resolution, coarse grained (CG), beads has opened the way to simulate large-scale biomolecular processes on time scales inaccessible to all-atom models. We provide an overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity. A few state-of-the-art examples of protein folding, membrane protein gating and self-assembly, DNA hybridization, and modeling of carbohydrate fibers are used to illustrate the power and diversity of current CG modeling.
Collapse
Affiliation(s)
- Helgi I Ingólfsson
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Cesar A Lopez
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Jaakko J Uusitalo
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Djurre H de Jong
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Srinivasa M Gopal
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Xavier Periole
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| | - Siewert J Marrink
- Groningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of GroningenGroningen, The Netherlands
| |
Collapse
|
211
|
Rovigatti L, Smallenburg F, Romano F, Sciortino F. Gels of DNA nanostars never crystallize. ACS NANO 2014; 8:3567-74. [PMID: 24646041 DOI: 10.1021/nn501138w] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Using state-of-the-art numerical techniques, we show that, upon lowering the temperature, tetravalent DNA nanostars form a thermodynamically stable, fully bonded equilibrium gel. In contrast to atomic and molecular network formers, in which the disordered liquid is always metastable with respect to some crystalline phase, we find that the DNA nanostar gel has a lower free energy than the diamond crystal structure in a wide range of concentrations. This unconventional behavior, here verified for the first time in a realistic model, arises from the large arm flexibility of the DNA nanostars, a property that can be tuned by design. Our results confirm the thermodynamic stability of the recently experimentally realized DNA hydrogels.
Collapse
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma , Piazzale A. Moro 2, 00185 Roma, Italy
| | | | | | | |
Collapse
|
212
|
Rovigatti L, Bomboi F, Sciortino F. Accurate phase diagram of tetravalent DNA nanostars. J Chem Phys 2014. [DOI: 10.1063/1.4870467] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
213
|
Abstract
By focusing on essential features, while averaging over less important details, coarse-grained (CG) models provide significant computational and conceptual advantages with respect to more detailed models. Consequently, despite dramatic advances in computational methodologies and resources, CG models enjoy surging popularity and are becoming increasingly equal partners to atomically detailed models. This perspective surveys the rapidly developing landscape of CG models for biomolecular systems. In particular, this review seeks to provide a balanced, coherent, and unified presentation of several distinct approaches for developing CG models, including top-down, network-based, native-centric, knowledge-based, and bottom-up modeling strategies. The review summarizes their basic philosophies, theoretical foundations, typical applications, and recent developments. Additionally, the review identifies fundamental inter-relationships among the diverse approaches and discusses outstanding challenges in the field. When carefully applied and assessed, current CG models provide highly efficient means for investigating the biological consequences of basic physicochemical principles. Moreover, rigorous bottom-up approaches hold great promise for further improving the accuracy and scope of CG models for biomolecular systems.
Collapse
Affiliation(s)
- W G Noid
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
| |
Collapse
|
214
|
Růžička Š, Allen MP. Collective translational and rotational Monte Carlo moves for attractive particles. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 89:033307. [PMID: 24730967 DOI: 10.1103/physreve.89.033307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Indexed: 06/03/2023]
Abstract
Virtual move Monte Carlo is a Monte Carlo (MC) cluster algorithm forming clusters via local energy gradients and approximating the collective kinetic or dynamic motion of attractive colloidal particles. We carefully describe, analyze, and test the algorithm. To formally validate the algorithm through highlighting its symmetries, we present alternative and compact ways of selecting and accepting clusters which illustrate the formal use of abstract concepts in the design of biased MC techniques: the superdetailed balance and the early rejection scheme. A brief and comprehensive summary of the algorithms is presented, which makes them accessible without needing to understand the details of the derivation.
Collapse
Affiliation(s)
- Štěpán Růžička
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Michael P Allen
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
215
|
Doye JPK, Ouldridge TE, Louis AA, Romano F, Šulc P, Matek C, Snodin BEK, Rovigatti L, Schreck JS, Harrison RM, Smith WPJ. Coarse-graining DNA for simulations of DNA nanotechnology. Phys Chem Chem Phys 2013; 15:20395-414. [PMID: 24121860 DOI: 10.1039/c3cp53545b] [Citation(s) in RCA: 139] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse-graining, focussing on those at the nucleotide level that allow the self-assembly processes associated with DNA nanotechnology to be studied. OxDNA, our recently-developed coarse-grained DNA model, is particularly suited to this task, and has opened up this field to systematic study by simulations. We illustrate some of the range of DNA nanotechnology systems to which the model is being applied, as well as the insights it can provide into fundamental biophysical properties of DNA.
Collapse
Affiliation(s)
- Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
216
|
Romano F, Chakraborty D, Doye JPK, Ouldridge TE, Louis AA. Coarse-grained simulations of DNA overstretching. J Chem Phys 2013; 138:085101. [PMID: 23464177 DOI: 10.1063/1.4792252] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23 °C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore, the model reproduces the temperature dependence of the overstretching force well. The mechanism of overstretching is always force-induced melting by unpeeling from the free ends. That we never see S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that S-DNA is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.
Collapse
Affiliation(s)
- Flavio Romano
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | | | | | | | | |
Collapse
|
217
|
Ouldridge TE, Sulc P, Romano F, Doye JPK, Louis AA. DNA hybridization kinetics: zippering, internal displacement and sequence dependence. Nucleic Acids Res 2013; 41:8886-95. [PMID: 23935069 PMCID: PMC3799446 DOI: 10.1093/nar/gkt687] [Citation(s) in RCA: 166] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Although the thermodynamics of DNA hybridization is generally well established, the kinetics of this classic transition is less well understood. Providing such understanding has new urgency because DNA nanotechnology often depends critically on binding rates. Here, we explore DNA oligomer hybridization kinetics using a coarse-grained model. Strand association proceeds through a complex set of intermediate states, with successful binding events initiated by a few metastable base-pairing interactions, followed by zippering of the remaining bonds. But despite reasonably strong interstrand interactions, initial contacts frequently dissociate because typical configurations in which they form differ from typical states of similar enthalpy in the double-stranded equilibrium ensemble. Initial contacts must be stabilized by two or three base pairs before full zippering is likely, resulting in negative effective activation enthalpies. Non-Arrhenius behavior arises because the number of base pairs required for nucleation increases with temperature. In addition, we observe two alternative pathways—pseudoknot and inchworm internal displacement—through which misaligned duplexes can rearrange to form duplexes. These pathways accelerate hybridization. Our results explain why experimentally observed association rates of GC-rich oligomers are higher than rates of AT- rich equivalents, and more generally demonstrate how association rates can be modulated by sequence choice.
Collapse
Affiliation(s)
- Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, Department of Physics, University of Oxford, 1 Keble Road, OX1 3NP, Oxford, UK and Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, OX1 3QZ, Oxford, UK
| | | | | | | | | |
Collapse
|
218
|
Ouldridge TE. Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble. J Chem Phys 2013; 137:144105. [PMID: 23061837 DOI: 10.1063/1.4757267] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
In this paper, we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter 22, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling systems of characteristic finite size. In particular, schemes for extrapolating the results of simulations of a single self-assembling object to the bulk limit are established in three cases: for assembly involving multiple particle species, for systems with one species localized in space and for simulations in the grand canonical ensemble. Furthermore, methodologies are introduced for evaluating the accuracy of these extrapolations. Example systems demonstrate that differences in cluster concentrations between simulations of a single self-assembling structure and bulk studies of the same model under identical conditions can be large, and that convergence on bulk results as system size is increased can be slow and non-trivial.
Collapse
Affiliation(s)
- Thomas E Ouldridge
- Rudolf Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, United Kingdom
| |
Collapse
|
219
|
Dršata T, Lankaš F. Theoretical models of DNA flexibility. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1144] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
220
|
Michele LD, Eiser E. Developments in understanding and controlling self assembly of DNA-functionalized colloids. Phys Chem Chem Phys 2013; 15:3115-29. [DOI: 10.1039/c3cp43841d] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
|
221
|
Matek C, Ouldridge TE, Levy A, Doye JPK, Louis AA. DNA cruciform arms nucleate through a correlated but asynchronous cooperative mechanism. J Phys Chem B 2012; 116:11616-25. [PMID: 22931199 DOI: 10.1021/jp3080755] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Inverted repeat (IR) sequences in DNA can form noncanonical cruciform structures to relieve torsional stress. We use Monte Carlo simulations of a recently developed coarse-grained model of DNA to demonstrate that the nucleation of a cruciform can proceed through a cooperative mechanism. First, a twist-induced denaturation bubble must diffuse so that its midpoint is near the center of symmetry of the IR sequence. Second, bubble fluctuations must be large enough to allow one of the arms to form a small number of hairpin bonds. Once the first arm is partially formed, the second arm can rapidly grow to a similar size. Because bubbles can twist back on themselves, they need considerably fewer bases to resolve torsional stress than the final cruciform state does. The initially stabilized cruciform therefore continues to grow, which typically proceeds synchronously, reminiscent of the S-type mechanism of cruciform formation. By using umbrella sampling techniques, we calculate, for different temperatures and superhelical densities, the free energy as a function of the number of bonds in each cruciform arm along the correlated but asynchronous nucleation pathways we observed in direct simulations.
Collapse
Affiliation(s)
- Christian Matek
- Rudolph Peierls Centre for Theoretical Physics, 1 Keble Road, Oxford OX1 3NP, UK
| | | | | | | | | |
Collapse
|