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Yi J, Yeou S, Lee NK. DNA Bending Force Facilitates Z-DNA Formation under Physiological Salt Conditions. J Am Chem Soc 2022; 144:13137-13145. [PMID: 35839423 PMCID: PMC9335521 DOI: 10.1021/jacs.2c02466] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Z-DNA, a noncanonical helical structure of double-stranded DNA (dsDNA), plays pivotal roles in various biological processes, including transcription regulation. Mechanical stresses on dsDNA, such as twisting and stretching, help to form Z-DNA. However, the effect of DNA bending, one of the most common dsDNA deformations, on Z-DNA formation is utterly unknown. Here, we show that DNA bending induces the formation of Z-DNA, that is, more Z-DNA is formed as the bending force becomes stronger. We regulated the bending force on dsDNA by using D-shaped DNA nanostructures. The B-Z transition was observed by single-molecule fluorescence resonance energy transfer. We found that as the bending force became stronger, Z-DNA was formed at lower Mg2+ concentrations. When dsDNA contained cytosine methylations, the B-Z transition occurred at 78 mM Mg2+ (midpoint) in the absence of the bending force. However, the B-Z transition occurred at a 28-fold lower Mg2+ concentration (2.8 mM) in the presence of the bending force. Monte Carlo simulation suggested that the B-Z transition stabilizes the bent form via the formation of the B-Z junction with base extrusion, which effectively releases the bending stress on DNA. Our results clearly show that the bending force facilitates the B-Z transition under physiological salt conditions.
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Affiliation(s)
- Jaehun Yi
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Sanghun Yeou
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
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2
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Yeou S, Hwang J, Yi J, Kim C, Kim SK, Lee NK. Cytosine methylation regulates DNA bendability depending on the curvature. Chem Sci 2022; 13:7516-7525. [PMID: 35872822 PMCID: PMC9242020 DOI: 10.1039/d1sc07115g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/01/2022] [Indexed: 11/21/2022] Open
Abstract
Cytosine methylation plays an essential role in many biological processes, such as nucleosome inactivation and regulation of gene expression. The modulation of DNA mechanics may be one of the regulatory mechanisms influenced by cytosine methylation. However, it remains unclear how methylation influences DNA mechanics. Here, we show that methylation has contrasting effects on the bending property of dsDNA depending on DNA curvature. We directly applied bending force on 30 base pairs of dsDNA using a D-shaped DNA nanostructure and measured the degree of bending using single-molecule fluorescence resonance energy transfer without surface immobilization. When dsDNA is weakly bent, methylation increases the stiffness of dsDNA. The stiffness of dsDNA increased by approximately 8% with a single methylation site for 30 bp dsDNA. When dsDNA is highly bent by a strong force, it forms a kink, i.e., a sharp bending of dsDNA. Under strong bending, methylation destabilizes the non-kink form compared with the kink form, which makes dsDNA near the kink region apparently more bendable. However, if the kink region is methylated, the kink form is destabilized, and dsDNA becomes stiffer. As a result, methylation increases the stiffness of weakly bent dsDNA and concurrently can promote kink formation, which may stabilize the nucleosome structure. Our results provide new insight into the effect of methylation, showing that cytosine methylation has opposite effects on DNA mechanics depending on its curvature and methylation location.
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Affiliation(s)
- Sanghun Yeou
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jihee Hwang
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Jaehun Yi
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Cheolhee Kim
- National Science Museum Daejeon 34143 Republic of Korea
| | - Seong Keun Kim
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
| | - Nam Ki Lee
- Department of Chemistry, Seoul National University 08832 Seoul Republic of Korea
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3
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Pyne ALB, Noy A, Main KHS, Velasco-Berrelleza V, Piperakis MM, Mitchenall LA, Cugliandolo FM, Beton JG, Stevenson CEM, Hoogenboom BW, Bates AD, Maxwell A, Harris SA. Base-pair resolution analysis of the effect of supercoiling on DNA flexibility and major groove recognition by triplex-forming oligonucleotides. Nat Commun 2021; 12:1053. [PMID: 33594049 PMCID: PMC7887228 DOI: 10.1038/s41467-021-21243-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 01/16/2021] [Indexed: 12/16/2022] Open
Abstract
In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.
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Affiliation(s)
- Alice L B Pyne
- Department of Materials Science and Engineering, University of Sheffield, Sheffield, UK.
- London Centre for Nanotechnology, University College London, London, UK.
| | - Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, UK.
| | - Kavit H S Main
- London Centre for Nanotechnology, University College London, London, UK
- UCL Cancer Institute, University College London, London, UK
| | | | - Michael M Piperakis
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Chemistry, University of Reading, Whiteknights, Reading, UK
| | | | - Fiorella M Cugliandolo
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
- Department of Pathology, Division of Immunology, University of Cambridge, Cambridge, UK
| | - Joseph G Beton
- London Centre for Nanotechnology, University College London, London, UK
- Department of Crystallography, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, UK
| | | | - Bart W Hoogenboom
- London Centre for Nanotechnology, University College London, London, UK
- Department of Physics and Astronomy, University College London, London, UK
| | - Andrew D Bates
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
| | - Anthony Maxwell
- Department of Biological Chemistry, John Innes Centre, Norwich, UK
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, Leeds, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, UK.
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4
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Jeong J, Kim HD. Base-Pair Mismatch Can Destabilize Small DNA Loops through Cooperative Kinking. PHYSICAL REVIEW LETTERS 2019; 122:218101. [PMID: 31283336 PMCID: PMC7819736 DOI: 10.1103/physrevlett.122.218101] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Indexed: 05/13/2023]
Abstract
Base-pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule fluorescence resonance energy transfer, we measured the lifetimes of tightly bent DNA loops with and without base-pair mismatch. Surprisingly, for loops captured by stackable sticky ends which leave single-stranded DNA breaks (or nicks) upon annealing, the mismatch decreased the loop lifetime despite reducing the overall bending stress, and the decrease was largest when the mismatch was placed at the DNA midpoint. These findings suggest that base-pair mismatch increases bending stress at the opposite side of the loop through an allosteric mechanism known as cooperative kinking. Based on this mechanism, we present a three-state model that explains the apparent dichotomy between thermodynamic and kinetic stability.
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5
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Simulation of DNA Supercoil Relaxation. Biophys J 2017; 110:2176-84. [PMID: 27224483 DOI: 10.1016/j.bpj.2016.03.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 03/24/2016] [Accepted: 03/28/2016] [Indexed: 01/17/2023] Open
Abstract
Several recent single-molecule experiments observe the response of supercoiled DNA to nicking endonucleases and topoisomerases. Typically in these experiments, indirect measurements of supercoil relaxation are obtained by observing the motion of a large micron-sized bead. The bead, which also serves to manipulate DNA, experiences significant drag and thereby obscures supercoil dynamics. Here we employ our discrete wormlike chain model to bypass experimental limitations and simulate the dynamic response of supercoiled DNA to a single strand nick. From our simulations, we make three major observations. First, extension is a poor dynamic measure of supercoil relaxation; in fact, the linking number relaxes so fast that it cannot have much impact on extension. Second, the rate of linking number relaxation depends upon its initial partitioning into twist and writhe as determined by tension. Third, the extensional response strongly depends upon the initial position of plectonemes.
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6
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:145-155. [PMID: 28035245 PMCID: PMC5153831 DOI: 10.1007/s12551-016-0241-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 01/09/2023] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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7
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Noy A, Sutthibutpong T, A Harris S. Protein/DNA interactions in complex DNA topologies: expect the unexpected. Biophys Rev 2016; 8:233-243. [PMID: 27738452 PMCID: PMC5039213 DOI: 10.1007/s12551-016-0208-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/13/2016] [Indexed: 12/31/2022] Open
Abstract
DNA supercoiling results in compacted DNA structures that can bring distal sites into close proximity. It also changes the local structure of the DNA, which can in turn influence the way it is recognised by drugs, other nucleic acids and proteins. Here, we discuss how DNA supercoiling and the formation of complex DNA topologies can affect the thermodynamics of DNA recognition. We then speculate on the implications for transcriptional control and the three-dimensional organisation of the genetic material, using examples from our own simulations and from the literature. We introduce and discuss the concept of coupling between the multiple length-scales associated with hierarchical nuclear structural organisation through DNA supercoiling and topology.
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Affiliation(s)
- Agnes Noy
- Department of Physics, Biological Physical Sciences Institute, University of York, York, YO10 5DD UK
| | - Thana Sutthibutpong
- Theoretical and Computational Physics Group, Department of Physics, King Mongkut University of Technology Thonburi, 126 Pracha Uthit Road, Bang Mod, Thung Khru, Bangkok, Thailand 10140
| | - Sarah A Harris
- School of Physics and Astronomy, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT ; Astbury Centre for Structural and Molecular Biology, University of Leeds, 192 Woodhouse Lane, Leeds, UK LS2 9JT
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8
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Abstract
Sharp bending of double-stranded DNA (dsDNA) plays an essential role in genome structure and function. However, the elastic limit of dsDNA bending remains controversial. Here, we measured the opening rates of small dsDNA loops with contour lengths ranging between 40 and 200 bp using single-molecule Fluorescence Resonance Energy Transfer. The relationship of loop lifetime to loop size revealed a critical transition in bending stress. Above the critical loop size, the loop lifetime changed with loop size in a manner consistent with elastic bending stress, but below it, became less sensitive to loop size, indicative of softened dsDNA. The critical loop size increased from ∼60 bp to ∼100 bp with the addition of 5 mM magnesium. We show that our result is in quantitative agreement with the kinkable worm-like chain model, and furthermore, can reproduce previously reported looping probabilities of dsDNA over the range between 50 and 200 bp. Our findings shed new light on the energetics of sharply bent dsDNA.
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Affiliation(s)
- Tung T Le
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
| | - Harold D Kim
- School of Physics, Georgia Institute of Technology, 837 State Street, Atlanta, GA 30332, USA
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9
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Zheng H, Xiao M, Yan Q, Ma Y, Xiao SJ. Small circular DNA molecules act as rigid motifs to build DNA nanotubes. J Am Chem Soc 2014; 136:10194-7. [PMID: 25000226 DOI: 10.1021/ja504050r] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Small circular DNA molecules with designed lengths, for example 64 and 96 nucleotides (nt), after hybridization with a few 32-nt staple strands respectively, can act as rigid motifs for the construction of DNA nanotubes with excellent uniformity in ring diameter. Unlike most native DNA nanotubes, which consist of longitudinal double helices, nanotubes assembled from circular DNAs are constructed from lateral double helices. Of the five types of DNA nanotubes designed here, four are built by alternating two different rings of the same ring size, while one is composed of all the same 96-nt rings. Nanotubes constructed from the same 96-nt rings are 10-100 times shorter than those constructed from two different 96-nt rings, because there are fewer hinge joints on the rings.
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Affiliation(s)
- Hongning Zheng
- Nanjing National Laboratory of Microstructures, State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University , Nanjing 210093, Jiangsu, China
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10
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Abstract
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with ∼100 base pairs, is addressed. Three minicircles with different radii and almost equal contents of AT and GC pairs are investigated. The DNA sequences are modeled by a mesoscopic Hamiltonian which describes the essential interactions in the helix at the level of the base pair and incorporates twisting and bending degrees of freedom. Helix unwinding and bubble formation patterns are consistently computed by a path integral method that sums over a large number of molecule configurations compatible with the model potential. The path ensembles are determined, as a function of temperature, by minimizing the free energy of the system. Fluctuational openings appear along the helix to release the stress due to the bending of the molecule backbone. In agreement with the experimental findings, base pair disruptions are found with larger probability in the smallest minicircle of 66 bps whose bending angle is ∼6°. For this minicircle, a sizeable untwisting is obtained with the helical repeat showing a step-like increase at T = 315 K. The method can be generalized to determine the bubble probability profiles of open ends linear sequences.
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Affiliation(s)
- Marco Zoli
- School of Science and Technology - CNISM, Università di Camerino, I-62032 Camerino, Italy.
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11
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Abstract
During the past decade, the issue of strong bending of the double helix has attracted a lot of attention. Here, we overview the major experimental and theoretical developments in the field sorting out reliably established facts from speculations and unsubstantiated claims. Theoretical analysis shows that sharp bends or kinks have to facilitate strong bending of the double helix. It remains to be determined what is the critical curvature of DNA that prompts the appearance of the kinks. Different experimental and computational approaches to the problem are analyzed. We conclude that there is no reliable evidence that any anomalous behavior of the double helix happens when DNA fragments in the range of 100 bp are circularized without torsional stress. The anomaly starts at the fragment length of about 70 bp when sharp bends or kinks emerge in essentially every molecule. Experimental data and theoretical analysis suggest that kinks may represent openings of isolated base pairs, which had been experimentally detected in linear DNA molecules. The calculation suggests that although the probability of these openings in unstressed DNA is close to 10−5, it increases sharply in small DNA circles reaching 1 open bp per circle of 70 bp.
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12
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Vologodskii A, Du Q, Frank-Kamenetskii MD. Bending of short DNA helices. ARTIFICIAL DNA, PNA & XNA 2013; 4:1-3. [PMID: 23406786 DOI: 10.4161/adna.23892] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In their recent Science paper, Vafabakhsh and Ha claim that DNA duplexes at the range of 100 bp experience anomalous flexibility, much greater than the flexibility of large DNA molecules. ( 1) However, careful reevaluation of their data leads to the conclusion that the presented data do not warrant the authors' claim.
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13
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Lionberger TA, Demurtas D, Witz G, Dorier J, Lillian T, Meyhöfer E, Stasiak A. Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Res 2011; 39:9820-32. [PMID: 21917856 PMCID: PMC3239204 DOI: 10.1093/nar/gkr666] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In cells, DNA is routinely subjected to significant levels of bending and twisting. In some cases, such as under physiological levels of supercoiling, DNA can be so highly strained, that it transitions into non-canonical structural conformations that are capable of relieving mechanical stress within the template. DNA minicircles offer a robust model system to study stress-induced DNA structures. Using DNA minicircles on the order of 100 bp in size, we have been able to control the bending and torsional stresses within a looped DNA construct. Through a combination of cryo-EM image reconstructions, Bal31 sensitivity assays and Brownian dynamics simulations, we have been able to analyze the effects of biologically relevant underwinding-induced kinks in DNA on the overall shape of DNA minicircles. Our results indicate that strongly underwound DNA minicircles, which mimic the physical behavior of small regulatory DNA loops, minimize their free energy by undergoing sequential, cooperative kinking at two sites that are located about 180° apart along the periphery of the minicircle. This novel form of structural cooperativity in DNA demonstrates that bending strain can localize hyperflexible kinks within the DNA template, which in turn reduces the energetic cost to tightly loop DNA.
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Affiliation(s)
- Troy A Lionberger
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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Mitchell JS, Laughton CA, Harris SA. Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Res 2011; 39:3928-38. [PMID: 21247872 PMCID: PMC3089460 DOI: 10.1093/nar/gkq1312] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Although DNA is frequently bent and supercoiled in the cell, much of the available information on DNA structure at the atomistic level is restricted to short linear sequences. We report atomistic molecular dynamics (MD) simulations of a series of DNA minicircles containing between 65 and 110 bp which we compare with a recent biochemical study of structural distortions in these tight DNA loops. We have observed a wealth of non-canonical DNA structures such as kinks, denaturation bubbles and wrinkled conformations that form in response to bending and torsional stress. The simulations show that bending alone is sufficient to induce the formation of kinks in circles containing only 65 bp, but we did not observe any defects in simulations of larger torsionally relaxed circles containing 110 bp over the same MD timescales. We also observed that under-winding in minicircles ranging in size from 65 to 110 bp leads to the formation of single stranded bubbles and wrinkles. These calculations are used to assess the ability of atomistic MD simulations to determine the structure of bent and supercoiled DNA.
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Affiliation(s)
- J S Mitchell
- Polymer IRC, School of Physics and Astronomy, University of Leeds, Leeds West Yorkshire, Leeds, LS2 9JT, UK
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Geggier S, Kotlyar A, Vologodskii A. Temperature dependence of DNA persistence length. Nucleic Acids Res 2010; 39:1419-26. [PMID: 20952402 PMCID: PMC3045604 DOI: 10.1093/nar/gkq932] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
We have determined the temperature dependence of DNA persistence length, a, using two different methods. The first approach was based on measuring the j-factors of short DNA fragments at various temperatures. Fitting the measured j-factors by the theoretical equation allowed us to obtain the values of a for temperatures between 5°C and 42°C. The second approach was based on measuring the equilibrium distribution of the linking number between the strands of circular DNA at different temperatures. The major contribution into the distribution variance comes from the fluctuations of DNA writhe in the nicked circular molecules which are specified by the value of a. The computation-based analysis of the measured variances was used to obtain the values of a for temperatures up to 60°C. We found a good agreement between the results obtained by these two methods. Our data show that DNA persistence length strongly depends on temperature and accounting for this dependence is important in quantitative comparison between experimental results obtained at different temperatures.
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Affiliation(s)
- Stephanie Geggier
- Department of Chemistry, New York University, New York, NY 10003, USA
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