1
|
Hussain S, Haji-Akbari A. Studying rare events using forward-flux sampling: Recent breakthroughs and future outlook. J Chem Phys 2020; 152:060901. [DOI: 10.1063/1.5127780] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sarwar Hussain
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
| | - Amir Haji-Akbari
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, USA
| |
Collapse
|
2
|
Xiao S, Sharpe DJ, Chakraborty D, Wales DJ. Energy Landscapes and Hybridization Pathways for DNA Hexamer Duplexes. J Phys Chem Lett 2019; 10:6771-6779. [PMID: 31609632 DOI: 10.1021/acs.jpclett.9b02356] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Strand hybridization is not only a fundamental molecular mechanism underlying the biological functions of nucleic acids but is also a key step in the design of efficient nanodevices. Despite recent efforts, the microscopic rules governing the hybridization mechanisms remain largely unknown. In this study, we exploit the energy landscape framework to assess how sequence-specificity modulates the hybridization mechanisms in DNA. We find that GG-tracts hybridize much more rapidly compared to GC-tracts, via either zippering or slithering pathways. For the hybridization of GG-tracts, both zippering and slithering mechanisms appear to be kinetically relevant. In contrast, for the GC-tracts, the zippering mechanism is dominant. Our work reveals that even for the relatively small systems considered, the energy landscapes feature multiple metastable states and kinetic traps, which is at odds with the conventional "all-or-nothing" model of DNA hybridization formulated on the basis of thermodynamic arguments alone. Interestingly, entropic effects are found to play an important role in determining the thermal stability of competing conformational ensembles and in determining the preferred hybridization pathways.
Collapse
Affiliation(s)
- Shiyan Xiao
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Daniel J Sharpe
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| | - Debayan Chakraborty
- Department of Chemistry , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - David J Wales
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge , CB2 1EW , United Kingdom
| |
Collapse
|
3
|
Araque JC, Robert MA. Lattice model of oligonucleotide hybridization in solution. II. Specificity and cooperativity. J Chem Phys 2016; 144:125101. [PMID: 27036478 DOI: 10.1063/1.4943577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Because oligonucleotides are short sequences of nucleic acid bases, their association in solution with complementary strands (hybridization) is often seen to conform to a simple two-state model. However, experimental evidence suggests that, despite their short length, oligonucleotides may hybridize through multiple states involving intermediates. We investigate whether these apparently contradictory scenarios are possible by imposing different levels of sequence specificity on a lattice model of oligonucleotides in solution, which we introduced in Part I [J. C. Araque et al., J. Chem. Phys. 134, 165103 (2011)]. We find that both multiple-intermediate (weakly cooperative) and two-state (strongly cooperative) transitions are possible and that these are directly linked to the level of sequence specificity. Sequences with low specificity hybridize (base-by-base) by way of multiple stable intermediates with increasing number of paired bases. Such intermediate states are weakly cooperative because the energetic gain from adding an additional base pair is outweighed by the conformational entropy loss. Instead, sequences with high specificity hybridize through multiple metastable intermediates which easily bridge the configurational and energetic gaps between single- and double-stranded states. These metastable intermediates interconvert with minimal loss of conformational entropy leading to a strongly cooperative hybridization. The possibility of both scenarios, multiple- and two-states, is therefore encoded in the specificity of the sequence which in turn defines the level of cooperativity.
Collapse
Affiliation(s)
- J C Araque
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
| | - M A Robert
- Department of Chemical and Biomolecular Engineering, Rice University, Houston, Texas 77005, USA
| |
Collapse
|
4
|
He Y, Liwo A, Scheraga HA. Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach. J Chem Phys 2016; 143:243111. [PMID: 26723596 DOI: 10.1063/1.4932082] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Coarse-grained models are useful tools to investigate the structural and thermodynamic properties of biomolecules. They are obtained by merging several atoms into one interaction site. Such simplified models try to capture as much as possible information of the original biomolecular system in all-atom representation but the resulting parameters of these coarse-grained force fields still need further optimization. In this paper, a force field optimization method, which is based on maximum-likelihood fitting of the simulated to the experimental conformational ensembles and least-squares fitting of the simulated to the experimental heat-capacity curves, is applied to optimize the Nucleic Acid united-RESidue 2-point (NARES-2P) model for coarse-grained simulations of nucleic acids recently developed in our laboratory. The optimized NARES-2P force field reproduces the structural and thermodynamic data of small DNA molecules much better than the original force field.
Collapse
Affiliation(s)
- Yi He
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Adam Liwo
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | - Harold A Scheraga
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
5
|
Niranjani G, Murugan R. Theory on the Mechanism of DNA Renaturation: Stochastic Nucleation and Zipping. PLoS One 2016; 11:e0153172. [PMID: 27074030 PMCID: PMC4830621 DOI: 10.1371/journal.pone.0153172] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 03/24/2016] [Indexed: 11/18/2022] Open
Abstract
Renaturation of the complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA renaturation. According to our model there are at least three steps in the renaturation process viz. nonspecific-contact formation, correct-contact formation and nucleation, and zipping. Most of the earlier two-state models combined nucleation with nonspecific-contact formation step. In our model we suggest that it is considerably meaningful when we combine the nucleation with the zipping since nucleation is the initial step of zipping and nucleated and zipping molecules are indistinguishable. Nonspecific contact formation step is a pure three-dimensional diffusion controlled collision process. Whereas nucleation involves several rounds of one-dimensional slithering and internal displacement dynamics of one single strand of DNA on the other complementary strand in the process of searching for the correct-contact and then initiate nucleation. Upon nucleation, the stochastic zipping follows to generate a fully renatured double stranded DNA. It seems that the square-root dependency of the overall renaturation rate constant on the length of reacting single strands originates mainly from the geometric constraints in the diffusion controlled nonspecific-contact formation step. Further the inverse scaling of the renaturation rate on the viscosity of reaction medium also originates from nonspecific contact formation step. On the other hand the inverse scaling of the renaturation rate with the sequence complexity originates from the stochastic zipping which involves several rounds of crossing over the free-energy barrier at microscopic levels. When the sequence of renaturing single strands of DNA is repetitive with less complexity then the cooperative effects will not be noticeable since the parallel zipping will be a dominant enhancing factor. However for DNA strands with high sequence complexity and length one needs to consider the underlying cooperative effects both at microscopic and macroscopic levels to explain various scaling behaviours of the overall renaturation rate.
Collapse
Affiliation(s)
| | - Rajamanickam Murugan
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| |
Collapse
|
6
|
Snodin BEK, Randisi F, Mosayebi M, Šulc P, Schreck JS, Romano F, Ouldridge TE, Tsukanov R, Nir E, Louis AA, Doye JPK. Introducing improved structural properties and salt dependence into a coarse-grained model of DNA. J Chem Phys 2016; 142:234901. [PMID: 26093573 DOI: 10.1063/1.4921957] [Citation(s) in RCA: 210] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We introduce an extended version of oxDNA, a coarse-grained model of deoxyribonucleic acid (DNA) designed to capture the thermodynamic, structural, and mechanical properties of single- and double-stranded DNA. By including explicit major and minor grooves and by slightly modifying the coaxial stacking and backbone-backbone interactions, we improve the ability of the model to treat large (kilobase-pair) structures, such as DNA origami, which are sensitive to these geometric features. Further, we extend the model, which was previously parameterised to just one salt concentration ([Na(+)] = 0.5M), so that it can be used for a range of salt concentrations including those corresponding to physiological conditions. Finally, we use new experimental data to parameterise the oxDNA potential so that consecutive adenine bases stack with a different strength to consecutive thymine bases, a feature which allows a more accurate treatment of systems where the flexibility of single-stranded regions is important. We illustrate the new possibilities opened up by the updated model, oxDNA2, by presenting results from simulations of the structure of large DNA objects and by using the model to investigate some salt-dependent properties of DNA.
Collapse
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
| | - Ferdinando Randisi
- Life Sciences Interface Doctoral Training Center, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Majid Mosayebi
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Petr Šulc
- Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10065, USA
| | - 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
| | - Thomas E Ouldridge
- Department of Mathematics, Imperial College, 180 Queen's Gate, London SW7 2AZ, United Kingdom
| | - Roman Tsukanov
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Eyal Nir
- Department of Chemistry and the Ilse Katz Institute for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, 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
| |
Collapse
|
7
|
|
8
|
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: 135] [Impact Index Per Article: 12.3] [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
|
9
|
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
|
10
|
Seifpour A, Dahl SR, Lin B, Jayaraman A. Molecular simulation study of the assembly of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2013.765569] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
11
|
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
|
12
|
Šulc P, Romano F, Ouldridge TE, Rovigatti L, Doye JPK, Louis AA. Sequence-dependent thermodynamics of a coarse-grained DNA model. J Chem Phys 2012; 137:135101. [DOI: 10.1063/1.4754132] [Citation(s) in RCA: 215] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
13
|
Linak MC, Tourdot R, Dorfman KD. Moving beyond Watson-Crick models of coarse grained DNA dynamics. J Chem Phys 2012; 135:205102. [PMID: 22128958 DOI: 10.1063/1.3662137] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
DNA produces a wide range of structures in addition to the canonical B-form of double-stranded DNA. Some of these structures are stabilized by Hoogsteen bonds. We developed an experimentally parameterized, coarse-grained model that incorporates such bonds. The model reproduces many of the microscopic features of double-stranded DNA and captures the experimental melting curves for a number of short DNA hairpins, even when the open state forms complicated secondary structures. We demonstrate the utility of the model by simulating the folding of a thrombin aptamer, which contains G-quartets, and strand invasion during triplex formation. Our results highlight the importance of including Hoogsteen bonding in coarse-grained models of DNA.
Collapse
Affiliation(s)
- Margaret C Linak
- Department of Chemical Engineering and Materials Science, University of Minnesota, 421 Washington Ave SE, Minneapolis, Minnesota 55455, USA
| | | | | |
Collapse
|
14
|
Nielsen LM, Hoffmann SV, Brøndsted Nielsen S. Vacuum-ultraviolet circular dichroism reveals DNA duplex formation between short strands of adenine and thymine. Phys Chem Chem Phys 2012; 14:15054-9. [DOI: 10.1039/c2cp42226c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|