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Sengupta S, Bhattacharjee SM, Mishra G. Large bubble drives circular DNA melting. Phys Chem Chem Phys 2024. [PMID: 39027987 DOI: 10.1039/d4cp01536c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulations. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.
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Affiliation(s)
- Souradeep Sengupta
- Department of Physics, Ashoka University, Sonipat, Haryana - 131029, India.
| | | | - Garima Mishra
- Department of Physics, Ashoka University, Sonipat, Haryana - 131029, India.
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Al Qanobi A, Marenduzzo D, Ali I. Simulations of DNA denaturation dynamics under constrained conditions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:295101. [PMID: 35512678 DOI: 10.1088/1361-648x/ac6d39] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
We study the dynamics of double-stranded DNA (dsDNA) denaturation using Brownian dynamics simulations. We use a coarse-grained single nucleotide model for dsDNA which considers the helix structure. We compare the melting dynamics for free DNA of length 300 base pairs with that of a DNA of the same length but fixed from one end-mimicking DNA tethered to a substrate. We find that free DNA melts at faster rate because the entropic gain associated with denaturation is larger. Additionally, we insert the DNA in nanochannels of different widths to study the influence of the confinement on the melting dynamics. Our results suggest that there is no significant difference in the critical temperature or rate of melting when the channel width⩾Rg/2, whereRgis the radius of gyration of DNA. Instead, at channel width ofRg/4 we only see partial denaturation at the free DNA melting temperature. Surprisingly, this trend is reversed at higher temperature, and we find that at 110 °C tight confinement results in faster melting. This is due to the fact that confinement promotes segregation of the single-stranded segment, thereby acting as an effective entropic force aiding denaturation.
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Affiliation(s)
- A Al Qanobi
- Department of Physics, College of Science, Sultan Qaboos University, PO Box 36, Al-Khod 123, Oman
| | - D Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom
| | - I Ali
- Department of Physics, College of Science, Sultan Qaboos University, PO Box 36, Al-Khod 123, Oman
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Smrek J, Garamella J, Robertson-Anderson R, Michieletto D. Topological tuning of DNA mobility in entangled solutions of supercoiled plasmids. SCIENCE ADVANCES 2021; 7:eabf9260. [PMID: 33980492 PMCID: PMC8115916 DOI: 10.1126/sciadv.abf9260] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/26/2021] [Indexed: 05/04/2023]
Abstract
Ring polymers in dense solutions are among the most intriguing problems in polymer physics. Because of its natural occurrence in circular form, DNA has been extensively used as a proxy to study the fundamental physics of ring polymers in different topological states. Yet, torsionally constrained-such as supercoiled-topologies have been largely neglected so far. The applicability of existing theoretical models to dense supercoiled DNA is thus unknown. Here, we address this gap by coupling large-scale molecular dynamics simulations with differential dynamic microscopy of entangled supercoiled DNA plasmids. We find that, unexpectedly, larger supercoiling increases the size of entangled plasmids and concomitantly induces an enhancement in DNA mobility. These findings are reconciled as due to supercoiling-driven asymmetric and double-folded plasmid conformations that reduce interplasmid entanglements and threadings. Our results suggest a way to topologically tune DNA mobility via supercoiling, thus enabling topological control over the (micro)rheology of DNA-based complex fluids.
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Affiliation(s)
- Jan Smrek
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Jonathan Garamella
- Department of Physics and Biophysics, University of San Diego, San Diego, CA 92110, USA
| | | | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK.
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine University of Edinburgh, Edinburgh EH4 2XU, UK
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Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling. Proc Natl Acad Sci U S A 2021; 118:1905215118. [PMID: 33649196 DOI: 10.1073/pnas.1905215118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide-resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an "action at a distance" on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps.
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Chevizovich D, Michieletto D, Mvogo A, Zakiryanov F, Zdravković S. A review on nonlinear DNA physics. ROYAL SOCIETY OPEN SCIENCE 2020; 7:200774. [PMID: 33391787 PMCID: PMC7735367 DOI: 10.1098/rsos.200774] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 10/23/2020] [Indexed: 06/12/2023]
Abstract
The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard-Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of 'self-trapping' of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo, possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.
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Affiliation(s)
- Dalibor Chevizovich
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Alain Mvogo
- Laboratory of Biophysics, Department of Physics, Faculty of Science, University of Yaounde I, PO Box 812, Cameroon
| | - Farit Zakiryanov
- Bashkir State University, 32 Zali Validi Street, 450076 Ufa, Republic of Bashkortostan, Russia
| | - Slobodan Zdravković
- Institut za nuklearne nauke Vinča, Univerzitet u Beogradu, 11001 Beograd, Serbia
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Abstract
Chromosome organisation is increasingly recognised as an essential component of genome regulation, cell fate and cell health. Within the realm of transposable elements (TEs) however, the spatial information of how genomes are folded is still only rarely integrated in experimental studies or accounted for in modelling. Whilst polymer physics is recognised as an important tool to understand the mechanisms of genome folding, in this commentary we discuss its potential applicability to aspects of TE biology. Based on recent works on the relationship between genome organisation and TE integration, we argue that existing polymer models may be extended to create a predictive framework for the study of TE integration patterns. We suggest that these models may offer orthogonal and generic insights into the integration profiles (or "topography") of TEs across organisms. In addition, we provide simple polymer physics arguments and preliminary molecular dynamics simulations of TEs inserting into heterogeneously flexible polymers. By considering this simple model, we show how polymer folding and local flexibility may generically affect TE integration patterns. The preliminary discussion reported in this commentary is aimed to lay the foundations for a large-scale analysis of TE integration dynamics and topography as a function of the three-dimensional host genome.
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Sicard F, Destainville N, Rousseau P, Tardin C, Manghi M. Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles. Phys Rev E 2020; 101:012403. [PMID: 32069623 DOI: 10.1103/physreve.101.012403] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Indexed: 06/10/2023]
Abstract
We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.
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Affiliation(s)
- François Sicard
- Department of Chemistry, King's College London, SE1 1DB London, United Kingdom
| | - Nicolas Destainville
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
| | - Philippe Rousseau
- Laboratoire de Microbiologie et Génetique Moléculaires, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, France
| | - Catherine Tardin
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, France
| | - Manoel Manghi
- Laboratoire de Physique Théorique, IRSAMC, Université de Toulouse, CNRS, UPS, France
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Michieletto D, Colì D, Marenduzzo D, Orlandini E. Nonequilibrium Theory of Epigenomic Microphase Separation in the Cell Nucleus. PHYSICAL REVIEW LETTERS 2019; 123:228101. [PMID: 31868408 DOI: 10.1103/physrevlett.123.228101] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/05/2019] [Indexed: 06/10/2023]
Abstract
Understanding the spatial organization of the genome in the cell nucleus is one of the current grand challenges in biophysics. Certain biochemical-or epigenetic-marks that are deposited along the genome are thought to play an important, yet poorly understood, role in determining genome organization and cell identity. The physical principles underlying the interplay between epigenetic dynamics and genome folding remain elusive. Here we propose and study a theory that assumes a coupling between epigenetic mark and genome densities, and which can be applied at the scale of the whole nucleus. We show that equilibrium models are not compatible with experiments and a qualitative agreement is recovered by accounting for nonequilibrium processes that can stabilize microphase separated epigenomic domains. We finally discuss the potential biophysical origin of these terms.
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Affiliation(s)
- Davide Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
- Centre for Mathematical Biology, and Department of Mathematical Sciences, University of Bath, North Rd, Bath BA2 7AY, United Kingdom
| | - Davide Colì
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università degli Studi di Padova, I-35131 Padova, Italy
| | - 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
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Michieletto D, Lusic M, Marenduzzo D, Orlandini E. Physical principles of retroviral integration in the human genome. Nat Commun 2019; 10:575. [PMID: 30718508 PMCID: PMC6362086 DOI: 10.1038/s41467-019-08333-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 12/13/2018] [Indexed: 12/26/2022] Open
Abstract
Certain retroviruses, including HIV, insert their DNA in a non-random fraction of the host genome via poorly understood selection mechanisms. Here, we develop a biophysical model for retroviral integration as stochastic and quasi-equilibrium topological reconnections between polymers. We discover that physical effects, such as DNA accessibility and elasticity, play important and universal roles in this process. Our simulations predict that integration is favoured within nucleosomal and flexible DNA, in line with experiments, and that these biases arise due to competing energy barriers associated with DNA deformations. By considering a long chromosomal region in human T-cells during interphase, we discover that at these larger scales integration sites are predominantly determined by chromatin accessibility. Finally, we propose and solve a reaction-diffusion problem that recapitulates the distribution of HIV hot-spots within T-cells. With few generic assumptions, our model can rationalise experimental observations and identifies previously unappreciated physical contributions to retroviral integration site selection.
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Affiliation(s)
- D. Michieletto
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - M. Lusic
- Department of Infectious Diseases, Integrative Virology, Heidelberg University Hospital and German Center for Infection Research, Im Neuenheimer Feld 344, 69120 Heidelberg, Germany
| | - D. Marenduzzo
- SUPA, School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD UK
| | - E. Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Universitá di Padova, Via Marzolo 8, 35131 Padova, Italy
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