1
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Wang X, Huang T, Li L, Xu Y. Effect of temperature on anisotropic bending elasticity of dsRNA: an all-atom molecular dynamics simulation. RSC Adv 2024; 14:17170-17177. [PMID: 38808231 PMCID: PMC11130765 DOI: 10.1039/d4ra02354d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024] Open
Abstract
Employing all-atom molecular dynamics simulations, we examined the temperature-dependent behavior of bending elasticity in double-stranded RNA (dsRNA). Specifically, we focused on the bending persistence length and its constituent components, namely, the tilt and roll stiffness. Our results revealed a near-linear decrease in these stiffness components as a function of temperature, thereby highlighting the increased flexibility of dsRNA at elevated temperatures. Furthermore, our data revealed a significant anisotropy in dsRNA bending elasticity, which diminished with increasing temperature, attributable to marked disparities in tilt and roll stiffness components. We delineated the underlying biophysical mechanisms and corroborated our findings with extant literature. These observations offer salient implications for advancing our understanding of nucleic acid elasticity, and are pertinent to potential medical applications.
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Affiliation(s)
- Xianghong Wang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Tingting Huang
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
| | - Liyun Li
- Department of Physics, Wenzhou University Wenzhou 325035 China
| | - Yanliang Xu
- School of Sino-German Engineering, Shanghai Technical Institute of Electronics and Information Shanghai 201411 China
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2
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Laeremans W, Segers M, Voorspoels A, Carlon E, Hooyberghs J. Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs cgDNA. J Chem Phys 2024; 160:144105. [PMID: 38591677 DOI: 10.1063/5.0197053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 03/19/2024] [Indexed: 04/10/2024] Open
Abstract
Coarse-grained models have emerged as valuable tools to simulate long DNA molecules while maintaining computational efficiency. These models aim at preserving interactions among coarse-grained variables in a manner that mirrors the underlying atomistic description. We explore here a method for testing coarse-grained vs all-atom models using stiffness matrices in Fourier space (q-stiffnesses), which are particularly suited to probe DNA elasticity at different length scales. We focus on a class of coarse-grained rigid base DNA models known as cgDNA and its most recent version, cgDNA+. Our analysis shows that while cgDNA+ closely follows the q-stiffnesses of the all-atom model, the original cgDNA shows some deviations for twist and bending variables, which are rather strong in the q → 0 (long length scale) limit. The consequence is that while both cgDNA and cgDNA+ give a suitable description of local elastic behavior, the former misses some effects that manifest themselves at longer length scales. In particular, cgDNA performs poorly on twist stiffness, with a value much lower than expected for long DNA molecules. Conversely, the all-atom and cgDNA+ twist are strongly length scale dependent: DNA is torsionally soft at a few base pair distances but becomes more rigid at distances of a few dozen base pairs. Our analysis shows that the bending persistence length in all-atom and cgDNA+ is somewhat overestimated.
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Affiliation(s)
- Wout Laeremans
- Soft Matter and Biological Physics, Department of Applied Physics, and Institute for Complex Molecular Systems, Eindhoven University of Technology, P.O. Box 513, 5600MB Eindhoven, Netherlands
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
| | - Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jef Hooyberghs
- UHasselt, Faculty of Sciences, Data Science Institute, Theory Lab, Agoralaan, 3590 Diepenbeek, Belgium
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3
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Zhang Z, Mou X, Zhang Y, He L, Li S. Influence of temperature on bend, twist and twist-bend coupling of dsDNA. Phys Chem Chem Phys 2024; 26:8077-8088. [PMID: 38224130 DOI: 10.1039/d3cp04932a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Abstract
The temperature-dependent bend and twist elasticities of dsDNA, as well as their couplings, were explored through all-atom molecular dynamics simulations. Three rotational parameters, tilt, roll, and twist, were employed to assess the bend and twist elasticities through their stiffness matrix. Our analysis indicates that the bend and twist stiffnesses decrease as the temperature rises, primarily owing to entropic influences stemming from thermodynamic fluctuations. Furthermore, the couplings between these rotational parameters also exhibit a decline with increasing temperature, although the roll-twist coupling displays greater strength than the tilt-roll and tilt-twist couplings, attributed to its more robust correction component. We elucidated the influence of temperature on bend and twist elasticities based on the comparisons between various models and existing data.
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Affiliation(s)
- Zihao Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Xuankang Mou
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Yahong Zhang
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, 325035, China.
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4
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Chandrasekhar S, Swope TP, Fadaei F, Hollis DR, Bricker R, Houser D, Portman J, Schmidt TL. Bending Unwinds DNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.579968. [PMID: 38405957 PMCID: PMC10888926 DOI: 10.1101/2024.02.14.579968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
In biology, DNA is often tightly bent to small radii. Solely based on the groove asymmetry, a 30-year-old theoretical paper predicted that such bending should unwind DNA, but this effect has not been directly experimentally quantified so far. We developed a ligation-based assay with nicked DNA circles of variable length, thereby decoupling the twist-dependent ligation efficiency from the large bending strain which dominates conventional circularization assays. We demonstrate that tightly bent DNA indeed unwinds to over 11 base pairs/turn, exactly as predicted. Our discovery requires reassessing the molecular mechanisms and energetics of all processes where DNA is tightly bent or relaxed again, including DNA packaging, gene regulation and expression.
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Affiliation(s)
- Soumya Chandrasekhar
- Department of Physics, Kent State University, Kent, OH, 44242, USA
- Contributed equally
| | - Thomas P. Swope
- Department of Physics, Kent State University, Kent, OH, 44242, USA
- Contributed equally
| | - Fatemeh Fadaei
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Daniel R. Hollis
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Rachel Bricker
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - Draven Houser
- Department of Physics, Kent State University, Kent, OH, 44242, USA
| | - John Portman
- Department of Physics, Kent State University, Kent, OH, 44242, USA
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5
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Qiao YP, Ren CL, Ma YQ. Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick. J Phys Chem B 2023; 127:4015-4021. [PMID: 37126597 DOI: 10.1021/acs.jpcb.2c08618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
It is generally believed that DNA nick is an effective way to release stress in supercoiled DNA, resulting from the twisting motion that individual strands rotate around the axis of the DNA helix. Here, we use MD simulations based on the oxDNA model to investigate the relaxation of 336 bp supercoiled minicircular DNA under DNA nick. Our simulations show that stress release, characterized by the abrupt decrease in linking number, may be induced by two types of DNA motion depending on the nick position. Except for the twisting motion, there is a writhing motion, that is, double strands collectively rotating with one plectoneme removal, which may occur in the process of DNA relaxation with the nick position in the loop region. Moreover, the writhing motion is more likely to occur in the DNA with relatively high hardness, such as C-G pairs. Our simulation results uncover the relationship between structural transformation, stress release, and DNA motion during the dynamic process under DNA nick, indicating the influence of nick position on the relaxation of the supercoiled DNA.
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Affiliation(s)
- Ye-Peng Qiao
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
| | - Yu-Qiang Ma
- National Laboratory of Solid State Microstructures and Department of Physics, Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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6
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Zhang Y, He L, Li S. Temperature dependence of DNA elasticity: An all-atom molecular dynamics simulation study. J Chem Phys 2023; 158:094902. [PMID: 36889965 DOI: 10.1063/5.0138940] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023] Open
Abstract
We used all-atom molecular dynamics simulation to investigate the elastic properties of double-stranded DNA (dsDNA). We focused on the influences of temperature on the stretch, bend, and twist elasticities, as well as the twist-stretch coupling, of the dsDNA over a wide range of temperature. The results showed that the bending and twist persistence lengths, together with the stretch and twist moduli, decrease linearly with temperature. However, the twist-stretch coupling behaves in a positive correction and enhances as the temperature increases. The potential mechanisms of how temperature affects dsDNA elasticity and coupling were investigated by using the trajectories from atomistic simulation, in which thermal fluctuations in structural parameters were analyzed in detail. We analyzed the simulation results by comparing them with previous simulation and experimental data, which are in good agreement. The prediction about the temperature dependence of dsDNA elastic properties provides a deeper understanding of DNA elasticities in biological environments and potentially helps in the further development of DNA nanotechnology.
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Affiliation(s)
- Yahong Zhang
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Linli He
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
| | - Shiben Li
- Department of Physics, Wenzhou University, Wenzhou, Zhejiang 325035, China
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7
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Skoruppa E, Carlon E. Equilibrium fluctuations of DNA plectonemes. Phys Rev E 2022; 106:024412. [PMID: 36109921 DOI: 10.1103/physreve.106.024412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/05/2022] [Indexed: 06/15/2023]
Abstract
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e., over- or underwound. They are ubiquitous in cellular DNA, and their physical properties have attracted significant interest both from the experimental side and from the modeling side. In this paper, we investigate fluctuations of the end-point distance z of supercoiled linear DNA molecules subject to external stretching forces. Our analysis is based on a two-phase model, which describes the supercoiled DNA as composed of a stretched phase and a plectonemic phase. A variety of mechanisms are found to contribute to extension fluctuations, characterized by the variance 〈Δz^{2}〉. We find the dominant contribution to 〈Δz^{2}〉 to originate from phase-exchange fluctuations, the transient shrinking and expansion of plectonemes, which is accompanied by an exchange of molecular length between the two phases. We perform Monte Carlo simulations of the twistable wormlike chain and analyze the fluctuation of various quantities, the results of which are found to agree with the two-phase model predictions. Furthermore, we show that the extension and its variance at high forces are very well captured by the two-phase model, provided that one goes beyond quadratic approximations.
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Affiliation(s)
- Enrico Skoruppa
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Enrico Carlon
- Soft Matter and Biophysics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
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8
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Segers M, Voorspoels A, Sakaue T, Carlon E. Mechanical properties of nucleic acids and the non-local twistable wormlike chain model. J Chem Phys 2022; 156:234105. [PMID: 35732531 DOI: 10.1063/5.0089166] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Mechanical properties of nucleic acids play an important role in many biological processes that often involve physical deformations of these molecules. At sufficiently long length scales (say, above ∼20-30 base pairs), the mechanics of DNA and RNA double helices is described by a homogeneous Twistable Wormlike Chain (TWLC), a semiflexible polymer model characterized by twist and bending stiffnesses. At shorter scales, this model breaks down for two reasons: the elastic properties become sequence-dependent and the mechanical deformations at distal sites get coupled. We discuss in this paper the origin of the latter effect using the framework of a non-local Twistable Wormlike Chain (nlTWLC). We show, by comparing all-atom simulations data for DNA and RNA double helices, that the non-local couplings are of very similar nature in these two molecules: couplings between distal sites are strong for tilt and twist degrees of freedom and weak for roll. We introduce and analyze a simple double-stranded polymer model that clarifies the origin of this universal distal couplings behavior. In this model, referred to as the ladder model, a nlTWLC description emerges from the coarsening of local (atomic) degrees of freedom into angular variables that describe the twist and bending of the molecule. Different from its local counterpart, the nlTWLC is characterized by a length-scale-dependent elasticity. Our analysis predicts that nucleic acids are mechanically softer at the scale of a few base pairs and are asymptotically stiffer at longer length scales, a behavior that matches experimental data.
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Affiliation(s)
- Midas Segers
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Takahiro Sakaue
- Department of Physical Sciences, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara 252-5258, Kanagawa, Japan
| | - Enrico Carlon
- Soft Matter and Biophysics Unit, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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9
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Chhetri KB, Sharma A, Naskar S, Maiti PK. Nanoscale structures and mechanics of peptide nucleic acids. NANOSCALE 2022; 14:6620-6635. [PMID: 35421892 DOI: 10.1039/d1nr04239d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Peptide nucleic acids (PNAs) are charge-neutral polyamide oligomers having extremely favorable thermal stability and high affinity to cell membranes when coupled with cationic cell-penetrating peptides (CPPs), as well as the encouraging antisense and antigene activity in cell-free systems. The study of the mechanical properties of short PNA molecules is rare both in experiments and theoretical calculations. Here, we studied the microscopic structures and elastic properties; namely, persistence length, stretch modulus, twist-stretch coupling, and structural crookedness of double-stranded PNA (dsPNA) and their hybrid derivatives using all-atom MD simulation and compared them with those of double-stranded DNA (dsDNA) and double-stranded RNA (dsRNA). The stretch modulus of the dsPNA is found to be ∼160 pN, an order of magnitude lower than that of dsDNA and smaller than dsRNA, respectively. Similarly, the persistence length of dsPNA is found to be ∼35 nm, significantly smaller than those of dsDNA and dsRNA. The PNA-DNA and PNA-RNA hybrid duplexes have elastic properties lying between that of dsPNA and dsDNA/dsRNA. We argue that the neutral backbones of the PNA make it less stiff than dsDNA and dsRNA molecules. Measurement of structural crookedness and principal component analysis additionally support the bending flexibility of dsPNA. Detailed analysis of the helical-rise coupled to helical-twist indicates that the PNA-DNA hybrid over-winds like dsDNA, while PNA-PNA and PNA-RNA unwind like dsRNA upon stretching. Because of the highly flexible nature of PNA, it can bind other biomolecules by adopting a wide range of conformations and is believed to be crucial for future nanobiotechnology research studies.
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Affiliation(s)
- Khadka B Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Nepal
| | - Akshara Sharma
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Supriyo Naskar
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
| | - Prabal K Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore 560012, India.
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10
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Chhetri KB, Dasgupta C, Maiti PK. Diameter Dependent Melting and Softening of dsDNA Under Cylindrical Confinement. Front Chem 2022; 10:879746. [PMID: 35586267 PMCID: PMC9108266 DOI: 10.3389/fchem.2022.879746] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 04/08/2022] [Indexed: 11/13/2022] Open
Abstract
Carbon nanotubes (CNTs) are considered promising candidates for biomolecular confinement, including DNA encapsulation for gene delivery. Threshold values of diameters have been reported for double-stranded DNA (dsDNA) encapsulation inside CNTs. We have performed all-atom molecular dynamics (MD) simulations of dsDNAs confined inside single-walled CNTs (SWCNTs) at the physiologically relevant temperature of 300 K. We found that the dsDNA can be confined without being denatured only when the diameter of the SWCNT exceeds a threshold value. Below this threshold diameter, the dsDNA gets denatured and melts even at the temperature of 300 K. Our simulations using SWCNTs with chirality indices (20,20) to (30,30) at 300 K found the critical diameter to be 3.25 nm (corresponding to (24,24) chirality). Analyses of the hydrogen bonds (H-bonds), Van der Walls (VdW) energy, and other inter-base interactions show drastic reduction in the number of H-bonds, VdW energy, and electrostatic energies between the bases of dsDNA when it is confined in narrower SWCNTs (up to diameter of 3.12 nm). On the other hand, the higher interaction energy between the dsDNA and the SWCNT surface in narrower SWCNTs assists in the melting of the dsDNA. Electrostatic mapping and hydration status analyses show that the dsDNA is not adequately hydrated and the counter ion distribution is not uniform below the critical diameter of the SWCNT. As properly hydrated counter ions provide stability to the dsDNA, we infer that the inappropriate hydration of counter ions and their non-uniform distribution around the dsDNA cause the melting of the dsDNA inside SWCNTs of diameter below the critical value of 3.25 nm. For confined dsDNAs that do not get denatured, we computed their elastic properties. The persistence length of dsDNA was found to increase by a factor of about two and the torsional stiffness by a factor of 1.5 for confinement inside SWCNTs of diameters up to 3.79 nm, the stretch modulus also following nearly the same trend. Interestingly, for higher diameters of SWCNT, 3.79 nm and above, the dsDNA becomes more flexible, demonstrating that the mechanical properties of the dsDNA under cylindrical confinement depend non-monotonically on the confinement diameter.
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Affiliation(s)
- Khadka B. Chhetri
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- Department of Physics, Prithvinarayan Campus, Tribhuvan University, Pokhara, Nepal
| | - Chandan Dasgupta
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
| | - Prabal K. Maiti
- Center for Condensed Matter Theory, Department of Physics, Indian Institute of Science, Bangalore, India
- *Correspondence: Prabal K. Maiti,
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11
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Lim W, Randisi F, Doye JPK, Louis AA. The interplay of supercoiling and thymine dimers in DNA. Nucleic Acids Res 2022; 50:2480-2492. [PMID: 35188542 PMCID: PMC8934635 DOI: 10.1093/nar/gkac082] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/16/2022] Open
Abstract
Thymine dimers are a major mutagenic photoproduct induced by UV radiation. While they have been the subject of extensive theoretical and experimental investigations, questions of how DNA supercoiling affects local defect properties, or, conversely, how the presence of such defects changes global supercoiled structure, are largely unexplored. Here, we introduce a model of thymine dimers in the oxDNA forcefield, parametrized by comparison to melting experiments and structural measurements of the thymine dimer induced bend angle. We performed extensive molecular dynamics simulations of double-stranded DNA as a function of external twist and force. Compared to undamaged DNA, the presence of a thymine dimer lowers the supercoiling densities at which plectonemes and bubbles occur. For biologically relevant supercoiling densities and forces, thymine dimers can preferentially segregate to the tips of the plectonemes, where they enhance the probability of a localized tip-bubble. This mechanism increases the probability of highly bent and denatured states at the thymine dimer site, which may facilitate repair enzyme binding. Thymine dimer-induced tip-bubbles also pin plectonemes, which may help repair enzymes to locate damage. We hypothesize that the interplay of supercoiling and local defects plays an important role for a wider set of DNA damage repair systems.
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Affiliation(s)
- Wilber Lim
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
| | - Ferdinando Randisi
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
- FabricNano Limited, 192 Drummond St, London NW1 3HP, UK
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
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12
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Kim M, Bae S, Oh I, Yoo J, Kim JS. Sequence-dependent twist-bend coupling in DNA minicircles. NANOSCALE 2021; 13:20186-20196. [PMID: 34847218 DOI: 10.1039/d1nr04672a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Looping of double-stranded DNA molecules with 100-200 base pairs into minicircles, catenanes, and rotaxanes has been suggested as a potential tool for DNA nanotechnologies. However, sharp DNA bending into a minicircle with a diameter of several to ten nanometers occurs with alterations in the DNA helical structure and may lead to defective kink formation that hampers the use of DNA minicircles, catenanes, and rotaxanes in nanoscale DNA applications. Here, we investigated local variations of a helical twist in sharply bent DNA using microsecond-long all-atom molecular dynamics simulations of six different DNA minicircles, focusing on the sequence dependence of the coupling between DNA bending and its helical twist. Twist angles between consecutive base pairs were analyzed at different locations relative to the direction of DNA bending and, among 10 unique dinucleotide steps, we identified four dinucleotide steps with strong twist-bend coupling, the pyrimidine-purine dinucleotide steps of TA/TA, CG/CG, and CA/TG and the purine-purine dinucleotide step of GA/TC. This work suggests the sequence-dependent structural responses of DNA to strong mechanical deformation, providing new molecular-level insights into the structure and stability of sharply bent DNA minicircles for nanoscale applications.
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Affiliation(s)
- Minjung Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Sehui Bae
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
| | - Inrok Oh
- LG Chem Ltd, LG Science Park, Seoul 07796, Republic of Korea
| | - Jejoong Yoo
- Department of Physics, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jun Soo Kim
- Department of Chemistry and Nanoscience, Ewha Womans University, Seoul 03760, Republic of Korea.
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13
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KOH HEEYUEN, LEE JAEGYUNG, LEE JAEYOUNG, KIM RYAN, TABATA OSAMU, JIN-WOO KIM, KIM DONYUN. Design Approaches and Computational Tools for DNA Nanostructures. IEEE OPEN JOURNAL OF NANOTECHNOLOGY 2021; 2:86-100. [PMID: 35756857 PMCID: PMC9232119 DOI: 10.1109/ojnano.2021.3119913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Designing a structure in nanoscale with desired shape and properties has been enabled by structural DNA nanotechnology. Design strategies in this research field have evolved to interpret various aspects of increasingly more complex nanoscale assembly and to realize molecular-level functionality by exploring static to dynamic characteristics of the target structure. Computational tools have naturally been of significant interest as they are essential to achieve a fine control over both shape and physicochemical properties of the structure. Here, we review the basic design principles of structural DNA nanotechnology together with its computational analysis and design tools.
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Affiliation(s)
- HEEYUEN KOH
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
| | - JAE GYUNG LEE
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - JAE YOUNG LEE
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
| | - RYAN KIM
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138 USA
- Bio/Nano Technology Group, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, AR 72701 USA
| | - OSAMU TABATA
- Faculty of Engineering, Kyoto University of Advanced Science, Kyoto 621-8555, Japan
| | - KIM JIN-WOO
- Bio/Nano Technology Group, Institute for Nanoscience and Engineering, University of Arkansas, Fayetteville, AR 72701 USA
- Department of Biological and Agricultural Engineering, University of Arkansas, Fayetteville, AR 72701 USA
- Materials Science and Engineering Program, University of Arkansas, Fayetteville, AR 72701 USA
| | - DO-NYUN KIM
- Institute of Advanced Machines and Design, Seoul National University, Seoul 08826, Republic of Korea
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Engineering Research, Seoul National University, Seoul 08826, Republic of Korea
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14
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Dohnalová H, Lankaš F. Deciphering the mechanical properties of
B‐DNA
duplex. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2021. [DOI: 10.1002/wcms.1575] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Hana Dohnalová
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
| | - Filip Lankaš
- Department of Informatics and Chemistry University of Chemistry and Technology Prague Praha 6 Czech Republic
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15
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Sengar A, Ouldridge TE, Henrich O, Rovigatti L, Šulc P. A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results. Front Mol Biosci 2021; 8:693710. [PMID: 34235181 PMCID: PMC8256390 DOI: 10.3389/fmolb.2021.693710] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
The oxDNA model of Deoxyribonucleic acid has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly documented exemplar simulations that simultaneously provide both an introduction to simulating the model, and a review of the model's fundamental properties. We outline how simulation results can be interpreted in terms of-and feed into our understanding of-less detailed models that operate at larger length scales, and provide guidance on whether simulating a system with oxDNA is worthwhile.
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Affiliation(s)
- A. Sengar
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - T. E. Ouldridge
- Centre for Synthetic Biology, Department of Bioengineering, Imperial College London, London, United Kingdom
| | - O. Henrich
- Department of Physics, SUPA, University of Strathclyde, Glasgow, United Kingdom
| | - L. Rovigatti
- Department of Physics, Sapienza University of Rome, Rome, Italy
- CNR Institute of Complex Systems, Sapienza University of Rome, Rome, Italy
| | - P. Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, Tempe, AZ, United States
- School of Molecular Sciences, Arizona State University, Tempe, AZ, United States
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16
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Skoruppa E, Voorspoels A, Vreede J, Carlon E. Length-scale-dependent elasticity in DNA from coarse-grained and all-atom models. Phys Rev E 2021; 103:042408. [PMID: 34005944 DOI: 10.1103/physreve.103.042408] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 03/25/2021] [Indexed: 12/24/2022]
Abstract
We investigate the influence of nonlocal couplings on the torsional and bending elasticities of DNA. Such couplings have been observed in the past by several simulation studies. Here, we use a description of DNA conformations based on the variables tilt, roll, and twist. Our analysis of both coarse-grained (oxDNA) and all-atom models indicates that these share strikingly similar features: there are strong off-site couplings for tilt-tilt and twist-twist, while they are much weaker in the roll-roll case. By developing an analytical framework to estimate bending and torsional persistence lengths in nonlocal DNA models, we show how off-site interactions generate a length-scale-dependent elasticity. Based on the simulation-generated elasticity data, the theory predicts a significant length-scale-dependent effect on torsional fluctuations but only a modest effect on bending fluctuations. These results are in agreement with experiments probing DNA mechanics from single base pair to kilobase pair scales.
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Affiliation(s)
- Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Aderik Voorspoels
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Jocelyne Vreede
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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17
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Xu W, Dunlap D, Finzi L. Energetics of twisted DNA topologies. Biophys J 2021; 120:3242-3252. [PMID: 33974883 DOI: 10.1016/j.bpj.2021.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/30/2021] [Accepted: 05/05/2021] [Indexed: 11/30/2022] Open
Abstract
Our goal is to review the main theoretical models used to calculate free energy changes associated with common, torsion-induced conformational changes in DNA and provide the resulting equations hoping to facilitate quantitative analysis of both in vitro and in vivo studies. This review begins with a summary of work regarding the energy change of the negative supercoiling-induced B- to L-DNA transition, followed by a discussion of the energetics associated with the transition to Z-form DNA. Finally, it describes the energy changes associated with the formation of DNA curls and plectonemes, which can regulate DNA-protein interactions and promote cross talk between distant DNA elements, respectively. The salient formulas and parameters for each scenario are summarized in table format to facilitate comparison and provide a concise, user-friendly resource.
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Affiliation(s)
- Wenxuan Xu
- Emory University, Department of Physics, Atlanta, Georgia
| | - David Dunlap
- Emory University, Department of Physics, Atlanta, Georgia
| | - Laura Finzi
- Emory University, Department of Physics, Atlanta, Georgia.
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18
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Gutiérrez Fosado YA, Landuzzi F, Sakaue T. Twist dynamics and buckling instability of ring DNA: the effect of groove asymmetry and anisotropic bending. SOFT MATTER 2021; 17:1530-1537. [PMID: 33331374 DOI: 10.1039/d0sm01812k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. In this process, the twist-bend coupling arising from the groove asymmetry in the DNA double helix clearly shows up. In the two scenarios explored, with/without this coupling, the initial perturbation relaxes diffusively. However, there are some marked differences in the value of the diffusion coefficient and the dynamics in both cases. These differences can be explained by assuming the existence of three distinctive time scales; a rapid relaxation of local bending, the slow twist spreading, and the buckling transition taking place in a much longer time scale. In particular, the separation of time scales allows deducing an effective diffusion equation in stage , with a diffusion coefficient influenced by the twist-bend coupling. We also discuss the mapping of the realistic DNA model to the simpler isotropic twistable worm-like chain using the renormalized bending and twist moduli; although useful in many cases, it fails to make a quantitative prediction on the instability mode of buckling transition.
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Affiliation(s)
- Yair Augusto Gutiérrez Fosado
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan.
| | - Fabio Landuzzi
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan.
| | - Takahiro Sakaue
- Department of Physics and Mathematics, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara-shi, Kanagawa 252-5258, Japan. and PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
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19
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Desai PR, Brahmachari S, Marko JF, Das S, Neuman KC. Coarse-grained modelling of DNA plectoneme pinning in the presence of base-pair mismatches. Nucleic Acids Res 2020; 48:10713-10725. [PMID: 33045724 DOI: 10.1093/nar/gkaa836] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 09/14/2020] [Accepted: 09/18/2020] [Indexed: 12/27/2022] Open
Abstract
Damaged or mismatched DNA bases result in the formation of physical defects in double-stranded DNA. In vivo, defects in DNA must be rapidly and efficiently repaired to maintain cellular function and integrity. Defects can also alter the mechanical response of DNA to bending and twisting constraints, both of which are important in defining the mechanics of DNA supercoiling. Here, we use coarse-grained molecular dynamics (MD) simulation and supporting statistical-mechanical theory to study the effect of mismatched base pairs on DNA supercoiling. Our simulations show that plectoneme pinning at the mismatch site is deterministic under conditions of relatively high force (>2 pN) and high salt concentration (>0.5 M NaCl). Under physiologically relevant conditions of lower force (0.3 pN) and lower salt concentration (0.2 M NaCl), we find that plectoneme pinning becomes probabilistic and the pinning probability increases with the mismatch size. These findings are in line with experimental observations. The simulation framework, validated with experimental results and supported by the theoretical predictions, provides a way to study the effect of defects on DNA supercoiling and the dynamics of supercoiling in molecular detail.
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Affiliation(s)
- Parth Rakesh Desai
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA.,Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - John F Marko
- Department of Physics and Astronomy, Northwestern University, Evanston, IL 60208, USA.,Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208, USA
| | - Siddhartha Das
- Department of Mechanical Engineering, University of Maryland, College Park, MD 20742, USA
| | - Keir C Neuman
- Laboratory of Single Molecule Biophysics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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20
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Bores C, Woodson M, Morais MC, Pettitt BM. Effects of Model Shape, Volume, and Softness of the Capsid for DNA Packaging of phi29. J Phys Chem B 2020; 124:10337-10344. [PMID: 33151690 PMCID: PMC7903877 DOI: 10.1021/acs.jpcb.0c07478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Double-stranded DNA is under extreme confinement when packed in phage phi29 with osmotic pressures approaching 60 atm and densities near liquid crystalline. The shape of the capsid determined from experiment is elongated. We consider the effects of the capsid shape and volume on the DNA distribution. We propose simple models for the capsid of phage phi29 to capture volume, shape, and wall flexibility, leading to an accurate DNA density profile. The effect of the packaging motor twisting the DNA on the resulting density distribution has been explored. We find packing motor induced twisting leads to a greater numbers of defects formed. The emergence of defects such as bubbles or large roll angles along the DNA shows a sequence dependence, and the resulting flexibility leads to an inhomogeneous distribution of defects occurring more often at TpA steps and AT-rich regions. In conjunction with capsid elongation, this has effects on the global DNA packing structures.
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Affiliation(s)
- Cecilia Bores
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Michael Woodson
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - Marc C Morais
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
| | - B Montgomery Pettitt
- University of Texas Medical Branch, 301 University Boulevard, Galveston, Texas 77555, United States
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21
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Chhabra H, Mishra G, Cao Y, Prešern D, Skoruppa E, Tortora MMC, Doye JPK. Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures. J Chem Theory Comput 2020; 16:7748-7763. [PMID: 33164531 DOI: 10.1021/acs.jctc.0c00661] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
To study the elastic properties of rodlike DNA nanostructures, we perform long simulations of these structures using the oxDNA coarse-grained model. By analyzing the fluctuations in these trajectories, we obtain estimates of the bend and twist persistence lengths and the underlying bend and twist elastic moduli and couplings between them. Only on length scales beyond those associated with the spacings between the interhelix crossovers do the bending fluctuations behave like those of a wormlike chain. The obtained bending persistence lengths are much larger than that for double-stranded DNA and increase nonlinearly with the number of helices, whereas the twist moduli increase approximately linearly. To within the numerical error in our data, the twist-bend coupling constants are of order zero. That the bending persistence lengths that we obtain are generally somewhat higher than in experiment probably reflects both that the simulated origamis have no assembly defects and that the oxDNA extensional modulus for double-stranded DNA is too large.
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Affiliation(s)
- Hemani Chhabra
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Garima Mishra
- Department of Physics, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Yijing Cao
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Domen Prešern
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Maxime M C Tortora
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom.,Laboratory of Biology and Modeling of the Cell, École Normale Supérieure de Lyon, 46, allée d'Italie, 69364 Lyon Cedex 07, France
| | - Jonathan P K Doye
- Physical & Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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22
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Bores C, Pettitt BM. Structure and the role of filling rate on model dsDNA packed in a phage capsid. Phys Rev E 2020; 101:012406. [PMID: 32069548 DOI: 10.1103/physreve.101.012406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Indexed: 06/10/2023]
Abstract
The conformation of DNA inside bacteriophages is of paramount importance for understanding packaging and ejection mechanisms. Models describing the structure of the confined macromolecule have depicted highly ordered conformations, such as spooled or toroidal arrangements that focus on reproducing experimental results obtained by averaging over thousands of configurations. However, it has been seen that more disordered states, including DNA kinking and the presence of domains with different DNA orientation can also accurately reproduce many of the structural experiments. In this work we have compared the results obtained through different simulated filling rates. We find a rate dependence for the resulting constrained states showing different anisotropic configurations. We present a quantitative analysis of the density distribution and the DNA orientation across the capsid showing excellent agreement with structural experiments. Second, we have analyzed the correlations within the capsid, finding evidence of the presence of domains characterized by aligned segments of DNA characterized by the structure factor. Finally, we have measured the number and distribution of DNA defects such as the emergence of bubbles and kinks as function of the filling rate. We find the slower the rate the fewer kink defects that appear and they would be unlikely at experimental filling rates with our model parameters. DNA domains of various orientation get larger with slower rates.
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Affiliation(s)
- Cecilia Bores
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston Tx, 77555, USA
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston Tx, 77555, USA
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23
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Velasco-Berrelleza V, Burman M, Shepherd JW, Leake MC, Golestanian R, Noy A. SerraNA: a program to determine nucleic acids elasticity from simulation data. Phys Chem Chem Phys 2020; 22:19254-19266. [DOI: 10.1039/d0cp02713h] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly.
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Affiliation(s)
| | | | | | - Mark C. Leake
- Department of Physics
- University of York
- York
- UK
- Department of Biology
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS)
- Göttingen
- Germany
- Rudolf Peierls Center for Theoretical Physics
- University of Oxford
| | - Agnes Noy
- Department of Physics
- University of York
- York
- UK
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24
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Zhai C, Li T, Shi H, Yeo J. Discovery and design of soft polymeric bio-inspired materials with multiscale simulations and artificial intelligence. J Mater Chem B 2020; 8:6562-6587. [DOI: 10.1039/d0tb00896f] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Establishing the “Materials 4.0” paradigm requires intimate knowledge of the virtual space in materials design.
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Affiliation(s)
- Chenxi Zhai
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Tianjiao Li
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Haoyuan Shi
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
| | - Jingjie Yeo
- J2 Lab for Engineering Living Materials
- Sibley School of Mechanical and Aerospace Engineering
- Cornell University
- Ithaca
- USA
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25
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Snodin BEK, Schreck JS, Romano F, Louis AA, Doye JPK. Coarse-grained modelling of the structural properties of DNA origami. Nucleic Acids Res 2019; 47:1585-1597. [PMID: 30605514 PMCID: PMC6379721 DOI: 10.1093/nar/gky1304] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 11/17/2018] [Accepted: 12/20/2018] [Indexed: 01/12/2023] Open
Abstract
We use the oxDNA coarse-grained model to provide a detailed characterization of the fundamental structural properties of DNA origami, focussing on archetypal 2D and 3D origami. The model reproduces well the characteristic pattern of helix bending in a 2D origami, showing that it stems from the intrinsic tendency of anti-parallel four-way junctions to splay apart, a tendency that is enhanced both by less screened electrostatic interactions and by increased thermal motion. We also compare to the structure of a 3D origami whose structure has been determined by cryo-electron microscopy. The oxDNA average structure has a root-mean-square deviation from the experimental structure of 8.4 Å, which is of the order of the experimental resolution. These results illustrate that the oxDNA model is capable of providing detailed and accurate insights into the structure of DNA origami, and has the potential to be used to routinely pre-screen putative origami designs and to investigate the molecular mechanisms that regulate the properties of DNA origami.
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Affiliation(s)
- Benedict E K Snodin
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
| | - John S Schreck
- Department of Chemical Engineering, Columbia University, 500 W 120th Street, New York, NY 10027, USA
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universit Ca' Foscari, Via Torino 155, 30172 Venezia Mestre, Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK
| | - Jonathan P K Doye
- Physical, and Theoretical Chemistry Laboratory, Department of Chemistry, South Parks Road, Oxford OX1 3QZ, UK
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26
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Temperature-dependence of the bending elastic constant of DNA and extension of the two-state model. Tests and new insights. Biophys Chem 2019; 251:106146. [DOI: 10.1016/j.bpc.2019.106146] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/28/2019] [Accepted: 04/01/2019] [Indexed: 12/15/2022]
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27
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Nomidis SK, Caraglio M, Laleman M, Phillips K, Skoruppa E, Carlon E. Twist-bend coupling, twist waves, and the shape of DNA loops. Phys Rev E 2019; 100:022402. [PMID: 31574750 DOI: 10.1103/physreve.100.022402] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2019] [Indexed: 06/10/2023]
Abstract
By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately 100 base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an imposed bending stress, as recently found in DNA minicircles and observed in nucleosomal DNA. These twist oscillations, here referred to as twist waves, are due to the coupling between twist and bending deformations, which in turn originates from the asymmetry between DNA major and minor grooves. We introduce a simple analytical variational shape that reproduces the exact loop energy up to the fourth significant digit and is in very good agreement with shapes obtained from coarse-grained simulations. We, finally, analyze the loop dynamics at room temperature, and show that the twist waves are robust against thermal fluctuations. They perform a normal diffusive motion, whose origin is briefly discussed.
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Affiliation(s)
- S K Nomidis
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - M Caraglio
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - M Laleman
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - K Phillips
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - E Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - E Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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28
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Nomidis SK, Skoruppa E, Carlon E, Marko JF. Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond. Phys Rev E 2019; 99:032414. [PMID: 30999490 DOI: 10.1103/physreve.99.032414] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Indexed: 12/12/2022]
Abstract
The simplest model of DNA mechanics describes the double helix as a continuous rod with twist and bend elasticity. Recent work has discussed the relevance of a little-studied coupling G between twisting and bending, known to arise from the groove asymmetry of the DNA double helix. Here the effect of G on the statistical mechanics of long DNA molecules subject to applied forces and torques is investigated. We present a perturbative calculation of the effective torsional stiffness C_{eff} for small twist-bend coupling. We find that the "bare" G is "screened" by thermal fluctuations, in the sense that the low-force, long-molecule effective free energy is that of a model with G=0 but with long-wavelength bending and twisting rigidities that are shifted by G-dependent amounts. Using results for torsional and bending rigidities for freely fluctuating DNA, we show how our perturbative results can be extended to a nonperturbative regime. These results are in excellent agreement with numerical calculations for Monte Carlo "triad" and molecular dynamics "oxDNA" models, characterized by different degrees of coarse graining, validating the perturbative and nonperturbative analyses. While our theory is in generally good quantitative agreement with experiment, the predicted torsional stiffness does systematically deviate from experimental data, suggesting that there are as-yet-uncharacterized aspects of DNA twisting-stretching mechanics relevant to low-force, long-molecule mechanical response, which are not captured by widely used coarse-grained models.
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Affiliation(s)
- Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium.,Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - Enrico Skoruppa
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
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29
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Caraglio M, Skoruppa E, Carlon E. Overtwisting induces polygonal shapes in bent DNA. J Chem Phys 2019; 150:135101. [PMID: 30954045 DOI: 10.1063/1.5084950] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
By combining analytical results and simulations of various coarse-grained models, we investigate the minimal energy shape of DNA minicircles which are torsionally constrained by an imposed over or undertwist. We show that twist-bend coupling, a cross interaction term discussed in the recent DNA literature, induces minimal energy shapes with a periodic alternation of parts with high and low curvature resembling rounded polygons. We briefly discuss the possible experimental relevance of these findings. We finally show that the twist and bending energies of minicircles are governed by renormalized stiffness constants, rather than the bare ones. This has important consequences for the analysis of experiments involving circular DNA meant to determine DNA elastic constants.
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Affiliation(s)
- Michele Caraglio
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Skoruppa
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Enrico Carlon
- Laboratory for Soft Matter and Biophysics, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
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30
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Skoruppa E, Nomidis SK, Marko JF, Carlon E. Bend-Induced Twist Waves and the Structure of Nucleosomal DNA. PHYSICAL REVIEW LETTERS 2018; 121:088101. [PMID: 30192578 PMCID: PMC6132066 DOI: 10.1103/physrevlett.121.088101] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Indexed: 05/14/2023]
Abstract
Recent work indicates that twist-bend coupling plays an important role in DNA micromechanics. Here we investigate its effect on bent DNA. We provide an analytical solution of the minimum-energy shape of circular DNA, showing that twist-bend coupling induces sinusoidal twist waves. This solution is in excellent agreement with both coarse-grained simulations of minicircles and nucleosomal DNA data, which is bent and wrapped around histone proteins in a superhelical conformation. Our analysis shows that the observed twist oscillation in nucleosomal DNA, so far attributed to the interaction with the histone proteins, is an intrinsic feature of free bent DNA, and should be observable in other protein-DNA complexes.
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Affiliation(s)
- Enrico Skoruppa
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Stefanos K Nomidis
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
- Flemish Institute for Technological Research (VITO), Boeretang 200, B-2400 Mol, Belgium
| | - John F Marko
- Department of Physics and Astronomy, and Department of Molecular Biosciences, Northwestern University, Evanston, Illinois 60208, USA
| | - Enrico Carlon
- KU Leuven, Institute for Theoretical Physics, Celestijnenlaan 200D, 3001 Leuven, Belgium
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Pereira MCF, Brackley CA, Lintuvuori JS, Marenduzzo D, Orlandini E. Entropic elasticity and dynamics of the bacterial chromosome: A simulation study. J Chem Phys 2018; 147:044908. [PMID: 28764377 DOI: 10.1063/1.4995992] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the compressional elasticity of the bacterial nucleoid (DNA plus associated proteins), where DNA is confined into a cylindrical container and subjected to the action of a "piston"-a spherical bead to which an external force is applied. We quantify the effect of steric interactions (excluded volume) on the force-extension curves as the polymer is compressed. We find that non-DNA-binding proteins, even at low densities, exert an osmotic force which can be a lot larger than the entropic force exerted by the compressed DNA. The trends we observe are qualitatively robust with respect to changes in protein sizes and are similar for neutral and charged proteins (and DNA). We also quantify the dynamics of DNA expansion following removal of the "piston": while the expansion is well fitted by power laws, the apparent exponent depends on protein concentration and protein-DNA interaction in a significant way. We further highlight an interesting kinetic process which we observe during the expansion of DNA interacting with DNA-binding proteins when the interaction strength is intermediate: the proteins bind while the DNA is packaged by the compression force, but they "pop-off" one-by-one as the force is removed, leading to a slow unzipping kinetics. Finally, we quantify the importance of supercoiling, which is an important feature of bacterial DNA in vivo.
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Affiliation(s)
- M C F Pereira
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - C A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - J S Lintuvuori
- Laboratoire de Physique des Solides, CNRS, Univ. Paris-Sud, Universite Paris-Saclay, 91405 Orsay Cedex, France
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - E Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova, 35131 PD, Italy
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Tortora MMC, Doye JPK. Incorporating particle flexibility in a density functional description of nematics and cholesterics. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1464226] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Maxime M. C. Tortora
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, United Kingdom
| | - Jonathan P. K. Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford , Oxford, United Kingdom
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