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Chen SWW, Banneville AS, Teulon JM, Timmins J, Pellequer JL. Nanoscale surface structures of DNA bound to Deinococcus radiodurans HU unveiled by atomic force microscopy. NANOSCALE 2020; 12:22628-22638. [PMID: 33150905 DOI: 10.1039/d0nr05320a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The Deinococcus radiodurans protein HU (DrHU) was shown to be critical for nucleoid activities, yet its functional and structural properties remain largely unexplored. We have applied atomic force microscopy (AFM) imaging to study DrHU binding to pUC19-DNA in vitro and analyzed the topographic structures formed at the nanoscale. At the single-molecule level, AFM imaging allows visualization of super-helical turns on naked DNA surfaces and characterization of free DrHU molecules observed as homodimers. When enhancing the molecular surface structures of AFM images by the Laplacian weight filter, the distribution of bound DrHUs was visibly varied as a function of the DrHU/DNA molar ratio. At a low molar ratio, DrHU binding was found to reduce the volume of condensed DNA configuration by about 50%. We also show that DrHU is capable of bridging distinct DNA segments. Moreover, at a low molar ratio, the binding orientation of individual DrHU dimers could be perceived on partially "open" DNA configuration. At a high molar ratio, DrHU stiffened the DNA molecule and enlarged the spread of the open DNA configuration. Furthermore, a lattice-like pattern could be seen on the surface of DrHU-DNA complex, indicating that DrHU multimerization had occurred leading to the formation of a higher order architecture. Together, our results show that the functional plasticity of DrHU in mediating DNA organization is subject to both the conformational dynamics of DNA molecules and protein abundance.
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Affiliation(s)
- Shu-Wen W Chen
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale (IBS), F-38000 Grenoble, France.
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Kim Y, Chae MK, Lee NK, Jung Y, Johner A. Irreversible Adsorption of Wormlike Chains: Alignment Effects. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00748] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yunha Kim
- Department
of Physics, Sejong University, Seoul 05006, South Korea
| | - Min-Kyung Chae
- Department
of Physics, Sejong University, Seoul 05006, South Korea
| | - Nam-Kyung Lee
- Department
of Physics, Sejong University, Seoul 05006, South Korea
- Institute Charles
Sadron, CNRS 23 Rue du Loess, 67034 Cedex 2, Strasbourg, France
| | - Youngkyun Jung
- Supercomputing
Center, Korea Institute of Science and Technology Information, Daejeon 34141, Korea
| | - Albert Johner
- Institute Charles
Sadron, CNRS 23 Rue du Loess, 67034 Cedex 2, Strasbourg, France
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Buyukdagli S, Blossey R. Correlation-induced DNA adsorption on like-charged membranes. Phys Rev E 2016; 94:042502. [PMID: 27841536 DOI: 10.1103/physreve.94.042502] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Indexed: 11/07/2022]
Abstract
The adsorption of DNA or other polyelectrolyte molecules on charged membranes is a recurrent motif in soft matter and bionanotechnological systems. Two typical situations encountered are the deposition of single DNA chains onto substrates for further analysis, e.g., by force microscopy, or the pulling of polyelectrolytes into membrane nanopores, as in sequencing applications. In this paper, we present a theoretical analysis of such scenarios based on the self-consistent field theory approach, which allows us to address the important effect of charge correlations. We calculate the grand potential of a stiff polyelectrolyte immersed in an electrolyte in contact with a negatively charged dielectric membrane. For the sake of conciseness, we neglect conformational polymer fluctuations and model the molecule as a rigid charged line. At strongly charged membranes, the adsorbed counterions enhance the screening ability of the interfacial region. In the presence of highly charged polymers such as double-stranded DNA molecules close to the membrane, this enhanced interfacial screening dominates the mean-field level DNA-membrane repulsion and results in the adsorption of the DNA molecule to the surface. This picture provides a simple explanation for the recently observed DNA binding onto similarly charged substrates [G. L.-Caballero et al., Soft Matter 10, 2805 (2014)1744-683X10.1039/c3sm52428k] and points out charge correlations as a non-negligible ingredient of polymer-surface interactions.
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Affiliation(s)
| | - Ralf Blossey
- Université Lille 1, CNRS, UGSF UMR8576, 59000 Lille, France
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Baschnagel J, Meyer H, Wittmer J, Kulić I, Mohrbach H, Ziebert F, Nam GM, Lee NK, Johner A. Semiflexible Chains at Surfaces: Worm-Like Chains and beyond. Polymers (Basel) 2016; 8:E286. [PMID: 30974563 PMCID: PMC6432221 DOI: 10.3390/polym8080286] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/29/2016] [Accepted: 07/29/2016] [Indexed: 12/27/2022] Open
Abstract
We give an extended review of recent numerical and analytical studies on semiflexible chains near surfaces undertaken at Institut Charles Sadron (sometimes in collaboration) with a focus on static properties. The statistical physics of thin confined layers, strict two-dimensional (2D) layers and adsorption layers (both at equilibrium with the dilute bath and from irreversible chemisorption) are discussed for the well-known worm-like-chain (WLC) model. There is mounting evidence that biofilaments (except stable d-DNA) are not fully described by the WLC model. A number of augmented models, like the (super) helical WLC model, the polymorphic model of microtubules (MT) and a model with (strongly) nonlinear flexural elasticity are presented, and some aspects of their surface behavior are analyzed. In many cases, we use approaches different from those in our previous work, give additional results and try to adopt a more general point of view with the hope to shed some light on this complex field.
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Affiliation(s)
- Jörg Baschnagel
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
| | - Hendrik Meyer
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
| | - Joachim Wittmer
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
| | - Igor Kulić
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
| | - Hervé Mohrbach
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
- Equipe BioPhysStat Université de Lorraine, 1 boulevard Arago, 57070 Metz, France.
| | - Falko Ziebert
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 3, 79104 Freiburg, Germany.
| | - Gi-Moon Nam
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
- Department of Physics, Sejong University, Neundongro 209, Seoul 05006, Korea.
| | - Nam-Kyung Lee
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
- Department of Physics, Sejong University, Neundongro 209, Seoul 05006, Korea.
| | - Albert Johner
- Institut Charles Sadron, CNRS-UdS, 23 rue du Loess, BP 84047, 67034 Strasbourg cedex 2, France.
- Department of Physics, Sejong University, Neundongro 209, Seoul 05006, Korea.
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Fathizadeh A, Schiessel H, Ejtehadi MR. Molecular Dynamics Simulation of Supercoiled DNA Rings. Macromolecules 2014. [DOI: 10.1021/ma501660w] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Arman Fathizadeh
- School
of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Institute
for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Helmut Schiessel
- Instituut-Lorentz
for Theoretical Physics, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - Mohammad Reza Ejtehadi
- Department
of Physics, Sharif University of Technology, P.O. Box 11155-8639, Tehran, Iran
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Schmatko T, Muller P, Maaloum M. Surface charge effects on the 2D conformation of supercoiled DNA. SOFT MATTER 2014; 10:2520-2529. [PMID: 24647451 DOI: 10.1039/c3sm53071j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We have adsorbed plasmid pUc19 DNA on a supported bilayer. By varying the fraction of cationic lipids in the membrane, we have tuned the surface charge. Plasmid conformations were imaged by Atomic Force Microscopy (AFM). We performed two sets of experiments: deposition from salt free solution on charged bilayers and deposition from salty solutions on neutral bilayers. Both sets show similar trends: at low surface charge density or low bulk salt concentration, the internal electrostatic repulsion forces plasmids to adopt completely opened structures, while at high surface charge density or higher bulk salt concentration, usual supercoiled plectonemes are observed. We experimentally demonstrate the equivalence of surface screening by mobile interfacial charges and bulk screening from salt ions. At low to medium screening, the electrostatic repulsion at plasmid crossings is predominant, leading to a number of crossovers decreasing linearly with the characteristic screening length. We compare our data with an analytical 2D-equilibrated model developed recently for the system and extract the DNA effective charge density when strands are adsorbed at the surface.
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Affiliation(s)
- Tatiana Schmatko
- Institut Charles Sadron, CNRS UPR 22 et Université de Strasbourg, 23 rue du loess, BP 84047 67034 Strasbourg Cedex2, France.
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Iacomino G, Picariello G, Stillitano I, D'Agostino L. Nuclear aggregates of polyamines in a radiation-induced DNA damage model. Int J Biochem Cell Biol 2013; 47:11-9. [PMID: 24291171 DOI: 10.1016/j.biocel.2013.11.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 10/24/2013] [Accepted: 11/12/2013] [Indexed: 01/04/2023]
Abstract
Polyamines (PA) are believed to protect DNA minimizing the effect of radiation damage either by inducing DNA compaction and aggregation or acting as scavengers of free radicals. Using an in vitro pDNA double strand breakage assay based on gel electrophoretic mobility, we compared the protective capability of PA against γ-radiation with that of compounds generated by the supramolecular self-assembly of nuclear polyamines and phosphates, named Nuclear Aggregates of Polyamines (NAPs). Both unassembled PA and in vitro produced NAPs (ivNAPs) were ineffective in conferring pDNA protection at the sub-mM concentration. Single PA showed an appreciable protective effect only at high (mM) concentrations. However, concentrations of spermine (4+) within a critical range (0.481 mM) induced pDNA precipitation, an event that was not observed with NAPs-pDNA interaction. We conclude that the interaction of individual PA is ineffective to assure DNA protection, simultaneously preserving the flexibility and charge density of the double strand. Furthermore, data obtained by testing polyamine and ivNAPS with the current radiation-induced DNA damage model support the concept that PA-phosphate aggregates are the only forms through which PA interact with DNA.
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Bohr J, Olsen KW. Total positive curvature of circular DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:052714. [PMID: 24329303 DOI: 10.1103/physreve.88.052714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 08/15/2013] [Indexed: 06/03/2023]
Abstract
The properties of double-stranded DNA and other chiral molecules depend on the local geometry, i.e., on curvature and torsion, yet the paths of closed chain molecules are globally restricted by topology. When both of these characteristics are to be incorporated in the description of circular chain molecules, e.g., plasmids, it is shown to have implications for the total positive curvature integral. For small circular micro-DNAs it follows as a consequence of Fenchel's inequality that there must exist a minimum length for the circular plasmids to be double stranded. It also follows that all circular micro-DNAs longer than the minimum length must be concave, a result that is consistent with typical atomic force microscopy images of plasmids. Predictions for the total positive curvature of circular micro-DNAs are given as a function of length, and comparisons with circular DNAs from the literature are presented.
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Affiliation(s)
- Jakob Bohr
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Kasper W Olsen
- DTU Nanotech, Building 345Ø, Ørsteds Plads, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
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