1
|
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.
Collapse
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
| |
Collapse
|
2
|
Qiao YP, Ren CL. Correlated Hybrid DNA Structures Explored by the oxDNA Model. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:109-117. [PMID: 38154122 DOI: 10.1021/acs.langmuir.3c02231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Thermodynamically, perfect DNA hybridization can be formed between probes and their corresponding targets due to the favorable energy. However, this is not the case dynamically. Here, we use molecular dynamics (MD) simulations based on the oxDNA model to investigate the process of DNA microarray hybridization. In general, correlated hybrid DNA structures are formed, including one probe associated with several targets as well as one target hybrid with multiple probes leading to the target-mediated hybridization. The formation of these two types of correlated structures largely depends on the surface coverage of the DNA microarray. Moreover, DNA sequence, DNA length, and spacer length have an impact on the structural formation. Our findings shed light on the dynamics of DNA hybridization, which is important for the application of DNA microarray.
Collapse
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
| |
Collapse
|
3
|
Miller LM, Draper BE, Barnes LF, Ofoegbu PC, Jarrold MF. Analysis of Megadalton-Sized DNA by Charge Detection Mass Spectrometry: Entropic Trapping and Shearing in Nanoelectrospray. Anal Chem 2023. [PMID: 37267126 DOI: 10.1021/acs.analchem.3c01027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The analysis of nucleic acids by conventional mass spectrometry is complicated by counter ions which cause mass heterogeneity and limit the size of the DNA that can be analyzed. In this work, we overcome this limitation using charge detection mass spectrometry to analyze megadalton-sized DNA. Using positive mode electrospray, we find two dramatically different charge distributions for DNA plasmids. A low charge population that charges like compact DNA origami and a much higher charge population, with charges that extend over a broad range. For the high-charge population, the deviation between the measured mass and mass expected from the DNA sequence is consistently around 1%. For the low-charge population, the deviation is larger and more variable. The high-charge population is attributed to the supercoiled plasmid in a random coil configuration, with the broad charge distribution resulting from the rich variety of geometries the random coil can adopt. High-resolution measurements show that the mass distribution shifts to slightly lower mass with increasing charge. The low-charge population is attributed to a condensed form of the plasmid. We suggest that the condensed form results from entropic trapping where the random coil must undergo a geometry change to squeeze through the Taylor cone and enter an electrospray droplet. For the larger plasmids, shearing (mechanical breakup) occurs during electrospray or in the electrospray interface. Shearing is reduced by lowering the salt concentration.
Collapse
Affiliation(s)
- Lohra M Miller
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Benjamin E Draper
- Megadalton Solutions Inc, 3750 E Bluebird Ln, Bloomington, Indiana 47401, United States
| | - Lauren F Barnes
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Polycarp C Ofoegbu
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| | - Martin F Jarrold
- Chemistry Department, Indiana University, 800 E Kirkwood Ave, Bloomington, Indiana 47405, United States
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Sleiman JL, Burton RH, Caraglio M, Gutierrez Fosado YA, Michieletto D. Geometric Predictors of Knotted and Linked Arcs. ACS POLYMERS AU 2022; 2:341-350. [PMID: 36254317 PMCID: PMC9562465 DOI: 10.1021/acspolymersau.2c00021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Inspired by how certain proteins “sense”
knots and
entanglements in DNA molecules, here, we ask if local geometric features
that may be used as a readout of the underlying topology of generic
polymers exist. We perform molecular simulations of knotted and linked
semiflexible polymers and study four geometric measures to predict
topological entanglements: local curvature, local density, local 1D
writhe, and nonlocal 3D writhe. We discover that local curvature is
a poor predictor of entanglements. In contrast, segments with maximum
local density or writhe correlate as much as 90% of the time with
the shortest knotted and linked arcs. We find that this accuracy is
preserved across different knot types and also under significant spherical
confinement, which is known to delocalize essential crossings in knotted
polymers. We further discover that nonlocal 3D writhe is the best
geometric readout of the knot location. Finally, we discuss how these
geometric features may be used to computationally analyze entanglements
in generic polymer melts and gels.
Collapse
Affiliation(s)
- Joseph L. Sleiman
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Robin H. Burton
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Michele Caraglio
- Institut für Theoretische Physik, Universität Innsbruck, Technikerstraße 21A, A-6020 Innsbruck, Austria
| | - Yair Augusto Gutierrez Fosado
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| |
Collapse
|
7
|
Tagliabue A, Micheletti C, Mella M. Tunable Knot Segregation in Copolyelectrolyte Rings Carrying a Neutral Segment. ACS Macro Lett 2021; 10:1365-1370. [PMID: 35549022 DOI: 10.1021/acsmacrolett.1c00453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We use Langevin dynamics simulations to study the knotting properties of copolyelectrolyte rings carrying neutral segments. We show that by solely tuning the relative length of the neutral and charged blocks, one can achieve different combinations of knot contour position and size. Strikingly, the latter is shown to vary nonmonotonically with the length of the neutral segment; at the same time, the knot switches from being pinned at the block's edge to becoming trapped inside it. Model calculations relate both effects to the competition between two adversarial mechanisms: the energy gain of localizing one or more of the knot's essential crossings on the neutral segment and the entropic cost of such localization. Tuning the length of the neutral segment sets the balance between the two mechanisms and hence the number of localized essential crossings, which in turn modulates the knot's size. This general principle ought to be useful in more complex systems, such as multiblock copolyelectrolytes, to achieve a more granular control of topological constraints.
Collapse
Affiliation(s)
- Andrea Tagliabue
- Dipartimento di Scienza ed Alta Tecnologia, Universitá degli Studi dell’Insubria, via Valleggio 11, 22100, Como, Italy
| | - Cristian Micheletti
- SISSA (Scuola Internazionale Superiore di Studi Avanzati), via Bonomea 265, 34136, Trieste, Italy
| | - Massimo Mella
- Dipartimento di Scienza ed Alta Tecnologia, Universitá degli Studi dell’Insubria, via Valleggio 11, 22100, Como, Italy
| |
Collapse
|
8
|
Roca J, Dyson S, Segura J, Valdés A, Martínez-García B. Keeping intracellular DNA untangled: A new role for condensin? Bioessays 2021; 44:e2100187. [PMID: 34761394 DOI: 10.1002/bies.202100187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 12/25/2022]
Abstract
The DNA-passage activity of topoisomerase II accidentally produces DNA knots and interlinks within and between chromatin fibers. Fortunately, these unwanted DNA entanglements are actively removed by some mechanism. Here we present an outline on DNA knot formation and discuss recent studies that have investigated how intracellular DNA knots are removed. First, although topoisomerase II is able to minimize DNA entanglements in vitro to below equilibrium values, it is unclear whether such capacity performs equally in vivo in chromatinized DNA. Second, DNA supercoiling could bias topoisomerase II to untangle the DNA. However, experimental evidence indicates that transcriptional supercoiling of intracellular DNA boosts knot formation. Last, cohesin and condensin could tighten DNA entanglements via DNA loop extrusion (LE) and force their dissolution by topoisomerase II. Recent observations indicate that condensin activity promotes the removal of DNA knots during interphase and mitosis. This activity might facilitate the spatial organization and dynamics of chromatin.
Collapse
Affiliation(s)
- Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Silvia Dyson
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| | - Antonio Valdés
- Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona, Spain
| |
Collapse
|
9
|
Orlandini E, Micheletti C. Topological and physical links in soft matter systems. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:013002. [PMID: 34547745 DOI: 10.1088/1361-648x/ac28bf] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Linking, or multicomponent topological entanglement, is ubiquitous in soft matter systems, from mixtures of polymers and DNA filaments packedin vivoto interlocked line defects in liquid crystals and intertwined synthetic molecules. Yet, it is only relatively recently that theoretical and experimental advancements have made it possible to probe such entanglements and elucidate their impact on the physical properties of the systems. Here, we review the state-of-the-art of this rapidly expanding subject and organize it as follows. First, we present the main concepts and notions, from topological linking to physical linking and then consider the salient manifestations of molecular linking, from synthetic to biological ones. We next cover the main physical models addressing mutual entanglements in mixtures of polymers, both linear and circular. Finally, we consider liquid crystals, fluids and other non-filamentous systems where topological or physical entanglements are observed in defect or flux lines. We conclude with a perspective on open challenges.
Collapse
Affiliation(s)
- Enzo Orlandini
- Department of Physics and Astronomy, University of Padova and Sezione INFN, Via Marzolo 8, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, Trieste, Italy
| |
Collapse
|
10
|
Herschberg T, Carrillo JMY, Sumpter BG, Panagiotou E, Kumar R. Topological Effects Near Order–Disorder Transitions in Symmetric Diblock Copolymer Melts. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00780] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tom Herschberg
- Department of Computer Science and Engineering, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403, United States
| | - Jan-Michael Y. Carrillo
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Bobby G. Sumpter
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eleni Panagiotou
- Department of Mathematics, University of Tennessee at Chattanooga, Chattanooga, Tennessee 37403, United States
| | - Rajeev Kumar
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Suma A, Stopar A, Nicholson AW, Castronovo M, Carnevale V. Global and local mechanical properties control endonuclease reactivity of a DNA origami nanostructure. Nucleic Acids Res 2020; 48:4672-4680. [PMID: 32043111 PMCID: PMC7229852 DOI: 10.1093/nar/gkaa080] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/24/2020] [Accepted: 01/29/2020] [Indexed: 01/17/2023] Open
Abstract
We used coarse-grained molecular dynamics simulations to characterize the global and local mechanical properties of a DNA origami triangle nanostructure. The structure presents two metastable conformations separated by a free energy barrier that is lowered upon omission of four specific DNA staples (defect). In contrast, only one stable conformation is present upon removing eight staples. The metastability is explained in terms of the intrinsic conformations of the three trapezoidal substructures. We computationally modeled the local accessibility to endonucleases, to predict the reactivity of twenty sites, and found good agreement with the experimental data. We showed that global fluctuations affect local reactivity: the removal of the DNA staples increased the computed accessibility to a restriction enzyme, at sites as distant as 40 nm, due to an increase in global fluctuation. These results raise the intriguing possibility of the rational engineering of allosterically modulated DNA origami.
Collapse
Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA.,Department of Biology, Temple University, Philadelphia, PA 19122, USA.,Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Alex Stopar
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.,Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy
| | - Allen W Nicholson
- Department of Biology, Temple University, Philadelphia, PA 19122, USA
| | - Matteo Castronovo
- Department of Biology, Temple University, Philadelphia, PA 19122, USA.,Department of Chemical Science and Technologies, University of Rome, Tor Vergata, Via della Ricerca Scientifica, 00133 Rome, Italy.,School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Vincenzo Carnevale
- Institute for Computational Molecular Science, Temple University, Philadelphia, PA 19122, USA.,Department of Biology, Temple University, Philadelphia, PA 19122, USA
| |
Collapse
|
14
|
Valdés A, Coronel L, Martínez-García B, Segura J, Dyson S, Díaz-Ingelmo O, Micheletti C, Roca J. Transcriptional supercoiling boosts topoisomerase II-mediated knotting of intracellular DNA. Nucleic Acids Res 2020; 47:6946-6955. [PMID: 31165864 PMCID: PMC6649788 DOI: 10.1093/nar/gkz491] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/09/2019] [Accepted: 05/22/2019] [Indexed: 12/04/2022] Open
Abstract
Recent studies have revealed that the DNA cross-inversion mechanism of topoisomerase II (topo II) not only removes DNA supercoils and DNA replication intertwines, but also produces small amounts of DNA knots within the clusters of nucleosomes that conform to eukaryotic chromatin. Here, we examine how transcriptional supercoiling of intracellular DNA affects the occurrence of these knots. We show that although (−) supercoiling does not change the basal DNA knotting probability, (+) supercoiling of DNA generated in front of the transcribing complexes increases DNA knot formation over 25-fold. The increase of topo II-mediated DNA knotting occurs both upon accumulation of (+) supercoiling in topoisomerase-deficient cells and during normal transcriptional supercoiling of DNA in TOP1 TOP2 cells. We also show that the high knotting probability (Pkn ≥ 0.5) of (+) supercoiled DNA reflects a 5-fold volume compaction of the nucleosomal fibers in vivo. Our findings indicate that topo II-mediated DNA knotting could be inherent to transcriptional supercoiling of DNA and other chromatin condensation processes and establish, therefore, a new crucial role of topoisomerase II in resetting the knotting–unknotting homeostasis of DNA during chromatin dynamics.
Collapse
Affiliation(s)
- Antonio Valdés
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Lucia Coronel
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Belén Martínez-García
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Joana Segura
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Sílvia Dyson
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Ofelia Díaz-Ingelmo
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| | - Cristian Micheletti
- Scuola Internazionale Superiore di Studi Avanzati (SISSA), 34136 Trieste, Italy
| | - Joaquim Roca
- Molecular Biology Institute of Barcelona (IBMB), Spanish National Research Council (CSIC), Barcelona 08028, Spain
| |
Collapse
|
15
|
Sun T, Mirzoev A, Minhas V, Korolev N, Lyubartsev AP, Nordenskiöld L. A multiscale analysis of DNA phase separation: from atomistic to mesoscale level. Nucleic Acids Res 2019; 47:5550-5562. [PMID: 31106383 PMCID: PMC6582353 DOI: 10.1093/nar/gkz377] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 04/26/2019] [Accepted: 05/09/2019] [Indexed: 12/17/2022] Open
Abstract
DNA condensation and phase separation is of utmost importance for DNA packing in vivo with important applications in medicine, biotechnology and polymer physics. The presence of hexagonally ordered DNA is observed in virus capsids, sperm heads and in dinoflagellates. Rigorous modelling of this process in all-atom MD simulations is presently difficult to achieve due to size and time scale limitations. We used a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA phase separation induced by the three-valent cobalt(III)-hexammine (CoHex3+). Solvent-mediated effective potentials for a CG model of DNA were extracted from all-atom MD simulations. Simulations of several hundred 100-bp-long CG DNA oligonucleotides in the presence of explicit CoHex3+ ions demonstrated aggregation to a liquid crystalline hexagonally ordered phase. Following further coarse-graining and extraction of effective potentials, we conducted modelling at mesoscale level. In agreement with electron microscopy observations, simulations of an 10.2-kb-long DNA molecule showed phase separation to either a toroid or a fibre with distinct hexagonal DNA packing. The mechanism of toroid formation is analysed in detail. The approach used here is based only on the underlying all-atom force field and uses no adjustable parameters and may be generalised to modelling chromatin up to chromosome size.
Collapse
Affiliation(s)
- Tiedong Sun
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander Mirzoev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Vishal Minhas
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| | - Alexander P Lyubartsev
- Department of Materials and Environmental Chemistry, Stockholm University, 10691 Stockholm, Sweden
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore 637551
| |
Collapse
|
16
|
Niewieczerzał S, Sulkowska JI. Supercoiling in a Protein Increases its Stability. PHYSICAL REVIEW LETTERS 2019; 123:138102. [PMID: 31697559 DOI: 10.1103/physrevlett.123.138102] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 06/10/2023]
Abstract
The supercoiling motif is the most complex type of nontrivial topology found in proteins with at least one disulfide bond and, to the best of our knowledge, it has not been studied before. We show that a protein from extremophilic species with such a motif can fold; however, the supercoiling changes a smooth landscape observed in reduced conditions into a two-state folding process in the oxidative conditions, with a deep intermediate state. The protein takes advantage of the hairpinlike motif to overcome the topological barrier and thus to supercoil. We find that the depth of the supercoiling motif, i.e., the length of the threaded terminus, has a crucial impact on the folding rates of the studied protein. We show that fluctuations of the minimal surface area can be used to measure local stability, and we find that supercoiling introduces stability into the protein. We suggest that the supercoiling motif enables the studied protein to live in physically extreme conditions, which are detrimental to most life on Earth.
Collapse
Affiliation(s)
- Szymon Niewieczerzał
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | - Joanna I Sulkowska
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| |
Collapse
|
17
|
Ziraldo R, Hanke A, Levene SD. Kinetic pathways of topology simplification by Type-II topoisomerases in knotted supercoiled DNA. Nucleic Acids Res 2019; 47:69-84. [PMID: 30476194 PMCID: PMC6326819 DOI: 10.1093/nar/gky1174] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 11/02/2018] [Indexed: 11/13/2022] Open
Abstract
The topological state of covalently closed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\Delta Lk$ relative to unknotted relaxed DNA. DNA topoisomerases are essential enzymes that control the topology of DNA in all cells. In particular, type-II topoisomerases change both $K$ and $\Delta Lk$ by a duplex-strand-passage mechanism and have been shown to simplify the topology of DNA to levels below thermal equilibrium at the expense of ATP hydrolysis. It remains a key question how small enzymes are able to preferentially select strand passages that result in topology simplification in much larger DNA molecules. Using numerical simulations, we consider the non-equilibrium dynamics of transitions between topological states $(K,\Delta Lk)$ in DNA induced by type-II topoisomerases. For a biological process that delivers DNA molecules in a given topological state $(K,\Delta Lk)$ at a constant rate we fully characterize the pathways of topology simplification by type-II topoisomerases in terms of stationary probability distributions and probability currents on the network of topological states $(K,\Delta Lk)$. In particular, we observe that type-II topoisomerase activity is significantly enhanced in DNA molecules that maintain a supercoiled state with constant torsional tension. This is relevant for bacterial cells in which torsional tension is maintained by enzyme-dependent homeostatic mechanisms such as DNA-gyrase activity.
Collapse
Affiliation(s)
- Riccardo Ziraldo
- Department of Bioengineering, University of Texas at Dallas, TX 75080, USA
| | - Andreas Hanke
- Department of Physics and Astronomy, University of Texas Rio Grande Valley, Brownsville, TX 78520, USA
| | - Stephen D Levene
- Department of Bioengineering, University of Texas at Dallas, TX 75080, USA.,Department of Biological Sciences, University of Texas at Dallas, Richardson, TX 75080, USA.,Department of Physics, University of Texas at Dallas, Richardson, TX 75080, USA
| |
Collapse
|
18
|
Suma A, Poppleton E, Matthies M, Šulc P, Romano F, Louis AA, Doye JPK, Micheletti C, Rovigatti L. TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami. J Comput Chem 2019; 40:2586-2595. [PMID: 31301183 DOI: 10.1002/jcc.26029] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/20/2019] [Accepted: 06/22/2019] [Indexed: 12/11/2022]
Abstract
Simulations of nucleic acids at different levels of structural details are increasingly used to complement and interpret experiments in different fields, from biophysics to medicine and materials science. However, the various structural models currently available for DNA and RNA and their accompanying suites of computational tools can be very rarely used in a synergistic fashion. The tacoxDNA webserver and standalone software package presented here are a step toward a long-sought interoperability of nucleic acids models. The webserver offers a simple interface for converting various common input formats of DNA structures and setting up molecular dynamics (MD) simulations. Users can, for instance, design DNA rings with different topologies, such as knots, with and without supercoiling, by simply providing an XYZ coordinate file of the DNA centre-line. More complex DNA geometries, as designable in the cadnano, CanDo and Tiamat tools, can also be converted to all-atom or oxDNA representations, which can then be used to run MD simulations. Though the latter are currently geared toward the native and LAMMPS oxDNA representations, the open-source package is designed to be further expandable. TacoxDNA is available at http://tacoxdna.sissa.it. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Antonio Suma
- Institute for Computational Molecular Science, Temple University, Philadelphia, Pennsylvania, 19122.,SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Erik Poppleton
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Michael Matthies
- Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, 01062, Dresden, Germany
| | - Petr Šulc
- Center for Molecular Design and Biomimetics, The Biodesign Institute, Arizona State University, 1001, South McAllister Avenue, Tempe, Arizona 85281
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi, Universitá Ca Foscari di Venezia, 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, University of Oxford, South Parks Road, Oxford, OX1 3QZ, UK
| | - Cristian Micheletti
- SISSA-Scuola Internazionale Superiore di Studi Avanzati, Via Bonomea, 265, 34136, Trieste, Italy
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Universitá di Roma, Piazzale A. Moro, 2, 00185, Rome, Italy.,CNR-ISC, Uos Sapienza, Piazzale A. Moro, 2, 00185, Rome, Italy
| |
Collapse
|
19
|
Forte G, Caraglio M, Marenduzzo D, Orlandini E. Plectoneme dynamics and statistics in braided polymers. Phys Rev E 2019; 99:052503. [PMID: 31212427 DOI: 10.1103/physreve.99.052503] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Indexed: 06/09/2023]
Abstract
Braids composed of two interwoven polymer chains exhibit a "buckling" transition whose origin has been explained through the onset of plectonemic structures. Here we study, by a combination of simulation and analytics, the dynamics of plectoneme formation and their statistics in steady state. The introduction of an order parameter-the plectonemic fraction-allows us to map out the phase boundary between the straight-braid phase and the plectonemic one. We then monitor the formation and the growth of plectonemes, observing events typical of phase separation kinetics for liquid-gas systems (fusion, fission, and one-dimensional Ostwald ripening) but also of DNA supercoiling dynamics (plectonemic hopping). Finally, we propose a stochastic field theory for the coupled dynamics of twist and local writhe which explains the phenomenology found with Brownian dynamics simulations as well as the power laws underlying the coarsening of plectonemes.
Collapse
Affiliation(s)
- Giada Forte
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - Michele Caraglio
- Soft Matter and Biophysics section, KU Leuven, Celestijnenlaan 200D, 3001 Leuven, Belgium
| | - Davide Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|