1
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Harnett J, Weir S, Michieletto D. Effects of monovalent and divalent cations on the rheology of entangled DNA. SOFT MATTER 2024; 20:3980-3986. [PMID: 38686506 PMCID: PMC11095498 DOI: 10.1039/d3sm00957b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 04/19/2024] [Indexed: 05/02/2024]
Abstract
In this paper we investigate the effects of varying cation valency and concentration on the rheology of entangled λDNA solutions. We show that monovalent cations moderately increase the viscoelasticty of the solutions mainly by stabilising linear concatenation of λDNA "monomers" via hybridisation of their sticky ends. On the contrary, divalent cations have a far more complex and dramatic effect on the rheology of the solution and we observe evidence of inter-molecular DNA-DNA bridging by Mg2+. We argue that these results may be interesting in the context of dense solutions of single and double stranded DNA, e.g. in vivo or in biotechnology applications such as DNA origami and DNA hydrogels.
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Affiliation(s)
- Jennifer Harnett
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - Simon Weir
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh, EH9 3FD, UK.
| | - 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 Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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2
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Dai L, Hu X, Ji M, Ma N, Xing H, Zhu JJ, Min Q, Tian Y. Programming the morphology of DNA origami crystals by magnesium ion strength. Proc Natl Acad Sci U S A 2023; 120:e2302142120. [PMID: 37399399 PMCID: PMC10334761 DOI: 10.1073/pnas.2302142120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/31/2023] [Indexed: 07/05/2023] Open
Abstract
Harnessing the programmable nature of DNA origami for controlling structural features in crystalline materials affords opportunities to bring crystal engineering to a remarkable level. However, the challenge of crystallizing a single type of DNA origami unit into varied structural outcomes remains, given the requirement for specific DNA designs for each targeted structure. Here, we show that crystals with distinct equilibrium phases and shapes can be realized using a single DNA origami morphology with an allosteric factor to modulate the binding coordination. As a result, origami crystals undergo phase transitions from a simple cubic lattice to a simple hexagonal (SH) lattice and eventually to a face-centered cubic (FCC) lattice. After selectively removing internal nanoparticles from DNA origami building blocks, the body-centered tetragonal and chalcopyrite lattice are derived from the SH and FCC lattices, respectively, revealing another phase transition involving crystal system conversions. The rich phase space was realized through the de novo synthesis of crystals under varying solution environments, followed by the individual characterizations of the resulting products. Such phase transitions can lead to associated transitions in the shape of the resulting products. Hexagonal prism crystals, crystals characterized by triangular facets, and twinned crystals are observed to form from SH and FCC systems, which have not previously been experimentally realized by DNA origami crystallization. These findings open a promising pathway toward accessing a rich phase space with a single type of building block and wielding other instructions as tools to develop crystalline materials with tunable properties.
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Affiliation(s)
- Lizhi Dai
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Min Ji
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ningning Ma
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Hang Xing
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, College of Chemistry and Chemical Engineering, Hunan University, Changsha410082, China
| | - Jun-Jie Zhu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, National Laboratory of Solid State Microstructures, Jiangsu Key Laboratory of Artificial Functional Materials, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing210023, China
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3
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Ober MF, Baptist A, Wassermann L, Heuer-Jungemann A, Nickel B. In situ small-angle X-ray scattering reveals strong condensation of DNA origami during silicification. Nat Commun 2022; 13:5668. [PMID: 36167861 PMCID: PMC9515200 DOI: 10.1038/s41467-022-33083-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/31/2022] [Indexed: 11/09/2022] Open
Abstract
Silicification of DNA origami structures increases their stability and provides chemical protection. Yet, it is unclear whether the whole DNA framework is embedded or if silica just forms an outer shell and how silicification affects the origami's internal structure. Employing in situ small-angle X-ray scattering (SAXS), we show that addition of silica precursors induces substantial condensation of the DNA origami at early reaction times by almost 10 %. Subsequently, the overall size of the silicified DNA origami increases again due to increasing silica deposition. We further identify the SAXS Porod invariant as a reliable, model-free parameter for the evaluation of the amount of silica formation at a given time. Contrast matching of the DNA double helix Lorentzian peak reveals silica growth also inside the origami. The less polar silica forming within the origami structure, replacing more than 40 % of the internal hydration water, causes a hydrophobic effect: condensation. DNA origami objects with flat surfaces show a strong tendency towards aggregation during silicification, presumably driven by the same entropic forces causing condensation. Maximally condensed origami displayed thermal stability up to 60 °C. Our studies provide insights into the silicification reaction allowing for the formulation of optimized reaction protocols.
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Affiliation(s)
- Martina F Ober
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany
| | - Anna Baptist
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Lea Wassermann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Amelie Heuer-Jungemann
- Max Planck Institute of Biochemistry and CeNS, Ludwig-Maximilians-Universität München, Am Klopferspitz 18, 82152, Martinsried, Germany.
| | - Bert Nickel
- Faculty of Physics and CeNS, Ludwig-Maximilians-Universität München, Geschwister-Scholl-Platz 1, 80539, Munich, Germany.
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4
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Bespalova M, Behjatian A, Karedla N, Walker-Gibbons R, Krishnan M. Opto-Electrostatic Determination of Nucleic Acid Double-Helix Dimensions and the Structure of the Molecule–Solvent Interface. Macromolecules 2022; 55:6200-6210. [PMID: 35910310 PMCID: PMC9330769 DOI: 10.1021/acs.macromol.2c00657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A DNA molecule is
highly electrically charged in solution. The
electrical potential at the molecular surface is known to vary strongly
with the local geometry of the double helix and plays a pivotal role
in DNA–protein interactions. Further out from the molecular
surface, the electrical field propagating into the surrounding electrolyte
bears fingerprints of the three-dimensional arrangement of the charged
atoms in the molecule. However, precise extraction of the structural
information encoded in the electrostatic “far field”
has remained experimentally challenging. Here, we report an optical
microscopy-based approach that detects the field distribution surrounding
a charged molecule in solution, revealing geometric features such
as the radius and the average rise per basepair of the double helix
with up to sub-Angstrom precision, comparable with traditional molecular
structure determination techniques like X-ray crystallography and
nuclear magnetic resonance. Moreover, measurement of the helical radius
furnishes an unprecedented view of both hydration and the arrangement
of cations at the molecule–solvent interface. We demonstrate
that a probe in the electrostatic far field delivers structural and
chemical information on macromolecules, opening up a new dimension
in the study of charged molecules and interfaces in solution.
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Affiliation(s)
- Maria Bespalova
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Narain Karedla
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Rowan Walker-Gibbons
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
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5
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The Effects of Flexibility on dsDNA–dsDNA Interactions. Life (Basel) 2022; 12:life12050699. [PMID: 35629366 PMCID: PMC9147707 DOI: 10.3390/life12050699] [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: 04/07/2022] [Revised: 05/02/2022] [Accepted: 05/06/2022] [Indexed: 11/29/2022] Open
Abstract
A detailed understanding of the physical mechanism of ion-mediated dsDNA interactions is important in biological functions such as DNA packaging and homologous pairing. We report the potential of mean force (PMF) or the effective solvent mediated interactions between two parallel identical dsDNAs as a function of interhelical separation in 0.15 M NaCl solution. Here, we study the influence of flexibility of dsDNAs on the effective interactions by comparing PMFs between rigid models and flexible ones. The role of flexibility of dsDNA pairs in their association is elucidated by studying the energetic properties of Na+ ions as well as the fluctuations of ions around dsDNAs. The introduction of flexibility of dsDNAs softens the vdW contact wall and induces more counterion fluctuations around dsDNAs. In addition, flexibility facilitates the Na+ ions dynamics affecting their distribution. The results quantify the extent of attraction influenced by dsDNA flexibility and further emphasize the importance of non-continuum solvation approaches.
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6
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Behjatian A, Krishnan M. Electrostatic free energies carry structural information on nucleic acid molecules in solution. J Chem Phys 2022; 156:134201. [DOI: 10.1063/5.0080008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Over the last several decades, a range of experimental techniques from x-ray crystallography and atomic force microscopy to nuclear magnetic resonance and small angle x-ray scattering have probed nucleic acid structure and conformation with high resolution both in the condensed state and in solution. We present a computational study that examines the prospect of using electrostatic free energy measurements to detect 3D conformational properties of nucleic acid molecules in solution. As an example, we consider the conformational difference between A- and B-form double helices whose structures differ in the values of two key parameters—the helical radius and rise per basepair. Mapping the double helix onto a smooth charged cylinder reveals that electrostatic free energies for molecular helices can, indeed, be described by two parameters: the axial charge spacing and the radius of a corresponding equivalent cylinder. We show that electrostatic free energies are also sensitive to the local structure of the molecular interface with the surrounding electrolyte. A free energy measurement accuracy of 1%, achievable using the escape time electrometry (ET e) technique, could be expected to offer a measurement precision on the radius of the double helix of approximately 1 Å. Electrostatic free energy measurements may, therefore, not only provide information on the structure and conformation of biomolecules but could also shed light on the interfacial hydration layer and the size and arrangement of counterions at the molecular interface in solution.
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Affiliation(s)
- Ali Behjatian
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Madhavi Krishnan
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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7
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Liu YF, Ran SY. Divalent metal ions and intermolecular interactions facilitate DNA network formation. Colloids Surf B Biointerfaces 2020; 194:111117. [PMID: 32512310 DOI: 10.1016/j.colsurfb.2020.111117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/30/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023]
Abstract
The interactions between divalent metal ions and DNA are crucial for basic life processes. These interactions are also important in advanced technological products such as DNA-based ion sensors. Current polyelectrolyte theories cannot describe these interactions well and do not consider the corresponding dynamics. In this study, we report the single-molecule dynamics of the binding of divalent metal ions to a single DNA molecule and the morphology characterization of the complex. We found that most of the divalent metal ions (Mn2+, Zn2+, Co2+, Ni2+, and Cd2+), except Mg2+ and Ca2+, could cause monomolecular DNA condensation. For transition metal ions, different ionic strengths were required to induce the compaction, and different shortening speeds were displayed in the dynamics, indicating ionic specificity. Atomic force microscopy revealed that the morphologies of the metal ion-DNA complexes were affected by the ionic strength of the metal ion, DNA chain length, and DNA concentration. At low metal ion concentration, DNA tended to adopt a random coil conformation. Increasing the ionic strength led to network-like condensed structures, suggesting that divalent metal ions can induce attraction between DNA molecules. Furthermore, higher DNA concentration and longer chain length enhanced intermolecular interactions and consequently resulted in network structures with a higher degree of interconnectivity.
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Affiliation(s)
- Yin-Feng Liu
- Department of Physics, Wenzhou University, Wenzhou 325035, China
| | - Shi-Yong Ran
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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8
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Plumridge A, Andresen K, Pollack L. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. J Am Chem Soc 2019; 142:109-119. [PMID: 31804813 DOI: 10.1021/jacs.9b04461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence-dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion, and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs and may explain their distinct recognition by protein partners.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
| | - Kurt Andresen
- Department of Physics , Gettysburg College , Gettysburg , Pennsylvania 17325 , United States
| | - Lois Pollack
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
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9
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Roodhuizen JA, Hendrikx PJTM, Hilbers PAJ, de Greef TFA, Markvoort AJ. Counterion-Dependent Mechanisms of DNA Origami Nanostructure Stabilization Revealed by Atomistic Molecular Simulation. ACS NANO 2019; 13:10798-10809. [PMID: 31502824 PMCID: PMC6764110 DOI: 10.1021/acsnano.9b05650] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/09/2019] [Indexed: 05/18/2023]
Abstract
The DNA origami technique has proven to have tremendous potential for therapeutic and diagnostic applications like drug delivery, but the relatively low concentrations of cations in physiological fluids cause destabilization and degradation of DNA origami constructs preventing in vivo applications. To reveal the mechanisms behind DNA origami stabilization by cations, we performed atomistic molecular dynamics simulations of a DNA origami rectangle in aqueous solvent with varying concentrations of magnesium and sodium as well as polyamines like oligolysine and spermine. We explored the binding of these ions to DNA origami in detail and found that the mechanism of stabilization differs between ion types considerably. While sodium binds weakly and quickly exchanges with the solvent, magnesium and spermine bind close to the origami with spermine also located in between helices, stabilizing the crossovers characteristic for DNA origami and reducing repulsion of parallel helices. In contrast, oligolysine of length ten prevents helix repulsion by binding to adjacent helices with its flexible side chains, spanning the gap between the helices. Shorter oligolysine molecules with four subunits are weak stabilizers as they lack both the ability to connect helices and to prevent helix repulsion. This work thus shows how the binding modes of ions influence the stabilization of DNA origami nanostructures on a molecular level.
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Affiliation(s)
- Job A.
L. Roodhuizen
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex
Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Philip J. T. M. Hendrikx
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex
Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Peter A. J. Hilbers
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex
Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Tom F. A. de Greef
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex
Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- Institute
for Molecules and Materials, Radboud University, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
- E-mail:
| | - Albert J. Markvoort
- Computational Biology Group, Department of Biomedical Engineering and Institute for Complex
Molecular Systems, Department of Biomedical Engineering, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
- E-mail:
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10
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Mansel BW, Irani AH, Ryan TM, McGillivray DJ, Chen HL, Williams MAK. Resolving solution conformations of the model semi-flexible polyelectrolyte homogalacturonan using molecular dynamics simulations and small-angle x-ray scattering. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2019; 42:19. [PMID: 30788674 DOI: 10.1140/epje/i2019-11776-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Accepted: 01/04/2019] [Indexed: 05/27/2023]
Abstract
The conformation of polyelectrolytes in the solution state has long been of interest in polymer science. Herein we utilize all atom molecular dynamics simulations (MD) and small-angle x-ray scattering experiments (SAXS) to elucidate the molecular structure of the model polyelectrolyte homogalacturonan. Several degrees of polymerization were studied and in addition partial methylesterification of the otherwise charge-carrying carboxyl groups was used in order to generate samples with varying intra-chain charge distributions. It is shown that at length scales above around 1nm the conformation of isolated chains has surprisingly little dependence on the charge distribution or the concentration of attendant monovalent salts, reflective of the intrinsic stiffness of the saccharide rings and the dynamical constraints of the glycosidic linkage. Indeed the conformation of isolated chains over all accessible length scales is well described by the atomic coordinates available from fibre diffraction studies. Furthermore, in more concentrated systems it is shown that, after careful analysis of the SAXS data, the form of the inter-particle effects heralded by the emergence of a so-called polyelectrolyte peak, can be extracted, and that this phenomena can be reproduced by multiple chain MD simulations.
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Affiliation(s)
- Bradley W Mansel
- Department of Chemical Engineering, National Tsing Hua University, 30013, Hsinchu, Taiwan.
| | - Amir Hossein Irani
- Institute of Fundamental Sciences, Massey University, 4474, Palmerston North, New Zealand
| | | | - Duncan J McGillivray
- School of Chemical Sciences, University of Auckland, Private Bag 90219, Auckland, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, 6140, Wellington, New Zealand
| | - Hsin-Lung Chen
- Department of Chemical Engineering, National Tsing Hua University, 30013, Hsinchu, Taiwan
| | - Martin A K Williams
- Institute of Fundamental Sciences, Massey University, 4474, Palmerston North, New Zealand
- The MacDiarmid Institute for Advanced Materials and Nanotechnology, 6140, Wellington, New Zealand
- Riddet Institute, Massey University, 4474, Palmerston North, New Zealand
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11
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Erlenbach N, Grünewald C, Krstic B, Heckel A, Prisner TF. "End-to-end" stacking of small dsRNA. RNA (NEW YORK, N.Y.) 2019; 25:239-246. [PMID: 30404925 PMCID: PMC6348986 DOI: 10.1261/rna.068130.118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 11/06/2018] [Indexed: 05/08/2023]
Abstract
PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.
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Affiliation(s)
- Nicole Erlenbach
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Christian Grünewald
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Bisera Krstic
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Alexander Heckel
- Institute of Organic Chemistry and Chemical Biology, Goethe University, D-60438 Frankfurt am Main, Germany
| | - Thomas F Prisner
- Institute of Physical and Theoretical Chemistry, Center of Biomolecular Magnetic Resonance, Goethe University, D-60438 Frankfurt am Main, Germany
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12
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Wang Y, Gao T, Li S, Xia W, Zhang W, Yang G. Direct Demonstration of DNA Compaction Mediated by Divalent Counterions. J Phys Chem B 2018; 123:79-85. [PMID: 30540472 DOI: 10.1021/acs.jpcb.8b09398] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We unambiguously demonstrated DNA attraction and its regulation mediated by divalent cations Mg2+ and Ca2+ by tethering a DNA single chain at various pH solutions. It is found that DNA is compacted when the pH of the solution containing these divalent counterions is decreased below 5. When the pH of the medium is ∼4, DNA is in an unstable transition state, being able to switch between compact and extensible states. We can also regulate the DNA attraction through a cyclic process of DNA compaction and unraveling by alternating the pH of the solution between 3 and 8. The corresponding change of morphology of DNA modulated by pH is also confirmed by atomic force microscopy (AFM). In the theoretical aspect, the present experimental finding is consistent with the coarse-grained simulation of Langevin dynamics on the effect of pH on DNA in a solution of divalent counterions.
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Affiliation(s)
- Yanwei Wang
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
| | - Tianyong Gao
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
| | - Shuhang Li
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
| | - Wenyan Xia
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
| | - Wei Zhang
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
| | - Guangcan Yang
- Department of Physics , Wenzhou University , Wenzhou 325035 , China
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13
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Li M, Wang W, Yin P. A General Approach to Access Morphologies of Polyoxometalates in Solution by Using SAXS: An Ab Initio Modeling Protocol. Chemistry 2018; 24:6639-6644. [PMID: 29473664 DOI: 10.1002/chem.201800344] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Indexed: 11/08/2022]
Abstract
Herein, we reported a general protocol for an ab initio modeling approach to deduce structure information of polyoxometalates (POMs) in solutions from scattering data collected by the small-angle X-ray scattering (SAXS) technique. To validate the protocol, the morphologies of a serious of known POMs in either aqueous or organic solvents were analyzed. The obtained particle morphologies were compared and confirmed with previous reported crystal structures. To extend the feasibility of the protocol to an unknown system of aqueous solutions of Na2 MoO4 with the pH ranging from -1 to 8.35, the formation of {Mo36 } clusters was probed, identified, and confirmed by SAXS. The approach was further optimized with a multi-processing capability to achieve fast analysis of experimental data, thereby, facilitating in situ studies of formations of POMs in solutions. The advantage of this approach is to generate intuitive 3D models of POMs in solutions without confining information such as symmetries and possible sizes.
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Affiliation(s)
- Mu Li
- South China Advanced Institute for Soft Matter Science and Technology and State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640, P.R. China
| | - Weiyu Wang
- South China Advanced Institute for Soft Matter Science and Technology and State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640, P.R. China
| | - Panchao Yin
- South China Advanced Institute for Soft Matter Science and Technology and State Key Laboratory of Luminescent Materials and Devices, South China University of Technology, Guangzhou, 510640, P.R. China
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14
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Raghuwanshi VS, Garusinghe UM, Ilavsky J, Batchelor WJ, Garnier G. Effect of nanoparticles size and polyelectrolyte on nanoparticles aggregation in a cellulose fibrous matrix. J Colloid Interface Sci 2018; 510:190-198. [DOI: 10.1016/j.jcis.2017.09.064] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 09/15/2017] [Accepted: 09/15/2017] [Indexed: 11/25/2022]
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15
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Zhang JS, Zhang X, Zhang ZL, Tan ZJ. Potential of mean force between oppositely charged nanoparticles: A comprehensive comparison between Poisson-Boltzmann theory and Monte Carlo simulations. Sci Rep 2017; 7:14145. [PMID: 29074886 PMCID: PMC5658377 DOI: 10.1038/s41598-017-14636-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 10/12/2017] [Indexed: 01/31/2023] Open
Abstract
Ion-mediated interactions between like-charged polyelectrolytes have been paid much attention, and the Poisson-Boltzmann (PB) theory has been shown to fail in qualitatively predicting multivalent ion-mediated like-charge attraction. However, inadequate attention has been paid to the ion-mediated interactions between oppositely charged polyelectrolytes. In this work, the potentials of mean force (PMF) between oppositely charged nanoparticles in 1:1 and 2:2 salt solutions were investigated by Monte Carlo simulations and the PB theory. Our calculations show that the PMFs between oppositely charged nanoparticles are generally attractive in 1:1 and 2:2 salt solutions and that such attractive PMFs become weaker at higher 1:1 or 2:2 salt concentrations. The comprehensive comparisons show that the PB theory can quantitatively predict the PMFs between oppositely charged nanoparticles in 1:1 salt solutions, except for the slight deviation at very high 1:1 salt concentration. However, for 2:2 salt solutions, the PB theory generally overestimates the attractive PMF between oppositely charged nanoparticles, and this overestimation becomes more pronounced for nanoparticles with higher charge density and for higher 2:2 salt concentration. Our microscopic analyses suggest that the overestimation of the PB theory on the attractive PMFs for 2:2 salt solutions is attributed to the underestimation of divalent ions bound to nanoparticles.
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Affiliation(s)
- Jin-Si Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Zhong-Liang Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro & Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China.
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16
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Buyukdagli S, Ala-Nissila T. Multivalent cation induced attraction of anionic polymers by like-charged pores. J Chem Phys 2017; 147:144901. [DOI: 10.1063/1.4994018] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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17
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Buyukdagli S. Like-charge attraction and opposite-charge decomplexation between polymers and DNA molecules. Phys Rev E 2017; 95:022502. [PMID: 28297861 DOI: 10.1103/physreve.95.022502] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Indexed: 11/07/2022]
Abstract
We scrutinize the effect of polyvalent ions on polymer-DNA interactions. We extend a recently developed test-charge theory [S. Buyukdagli et al., Phys. Rev. E 94, 042502 (2016)1539-375510.1103/PhysRevE.94.042502] to the case of a stiff polymer interacting with a DNA molecule in an electrolyte mixture. The theory accounts for one-loop level electrostatic correlation effects such as the ionic cloud deformation around the strongly charged DNA molecule as well as image-charge forces induced by the low DNA permittivity. Our model can reproduce and explain various characteristics of the experimental phase diagrams for polymer solutions. First, the addition of polyvalent cations to the electrolyte solution results in the attraction of the negatively charged polymer by the DNA molecule. The glue of the like-charge attraction is the enhanced shielding of the polymer charges by the dense counterion layer at the DNA surface. Second, through the shielding of the DNA-induced electrostatic potential, mono- and polyvalent cations of large concentration both suppress the like-charge attraction. Within the same formalism, we also predict a new opposite-charge repulsion effect between the DNA molecule and a positively charged polymer. In the presence of polyvalent anions such as sulfate or phosphate, their repulsion by the DNA charges leads to the charge screening deficiency of the region around the DNA molecule. This translates into a repulsive force that results in the decomplexation of the polymer from DNA. This opposite-charge repulsion phenomenon can be verified by current experiments and the underlying mechanism can be beneficial to gene therapeutic applications where the control over polymer-DNA interactions is the key factor.
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18
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Kewalramani S, Guerrero-García G, Moreau LM, Zwanikken JW, Mirkin CA, Olvera de la Cruz M, Bedzyk MJ. Electrolyte-Mediated Assembly of Charged Nanoparticles. ACS CENTRAL SCIENCE 2016; 2:219-24. [PMID: 27163052 PMCID: PMC4850508 DOI: 10.1021/acscentsci.6b00023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2016] [Indexed: 05/23/2023]
Abstract
Solutions at high salt concentrations are used to crystallize or segregate charged colloids, including proteins and polyelectrolytes via a complex mechanism referred to as "salting-out". Here, we combine small-angle X-ray scattering (SAXS), molecular dynamics (MD) simulations, and liquid-state theory to show that salting-out is a long-range interaction, which is controlled by electrolyte concentration and colloid charge density. As a model system, we analyze Au nanoparticles coated with noncomplementary DNA designed to prevent interparticle assembly via Watson-Crick hybridization. SAXS shows that these highly charged nanoparticles undergo "gas" to face-centered cubic (FCC) to "glass-like" transitions with increasing NaCl or CaCl2 concentration. MD simulations reveal that the crystallization is concomitant with interparticle interactions changing from purely repulsive to a "long-range potential well" condition. Liquid-state theory explains this attraction as a sum of cohesive and depletion forces that originate from the interelectrolyte ion and electrolyte-ion-nanoparticle positional correlations. Our work provides fundamental insights into the effect of ionic correlations in the salting-out mechanism and suggests new routes for the crystallization of colloids and proteins using concentrated salts.
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Affiliation(s)
- Sumit Kewalramani
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
| | - Guillermo
I. Guerrero-García
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
- Instituto
de Física, Universidad Autónoma
de San Luis Potosí, Àlvaro Obregón 64, 78000 San Luis Potosí, San Luis Potosí, Mexico
| | - Liane M. Moreau
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
| | - Jos W. Zwanikken
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
| | - Chad A. Mirkin
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Monica Olvera de la Cruz
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
- Department
of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Physics
and Astronomy Department, Northwestern University, Evanston, Illinois 60208, United States
| | - Michael J. Bedzyk
- Materials
Science and Engineering Department, Northwestern
University, Evanston, Illinois 60208, United
States
- Physics
and Astronomy Department, Northwestern University, Evanston, Illinois 60208, United States
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19
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Wang FH, Wu YY, Tan ZJ. Salt contribution to the flexibility of single-stranded nucleic acid offinite length. Biopolymers 2016; 99:370-81. [PMID: 23529689 DOI: 10.1002/bip.22189] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/18/2012] [Indexed: 12/15/2022]
Abstract
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na(+) and Mg(2+)-dependent persistence length l(p)'s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l(p) as a function of [Na(+)], [Mg(2+)] and chain length.
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Affiliation(s)
- Feng-Hua Wang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
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20
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Meisburger SP, Sutton JL, Chen H, Pabit SA, Kirmizialtin S, Elber R, Pollack L. Polyelectrolyte properties of single stranded DNA measured using SAXS and single-molecule FRET: Beyond the wormlike chain model. Biopolymers 2016; 99:1032-45. [PMID: 23606337 DOI: 10.1002/bip.22265] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 04/11/2013] [Indexed: 12/28/2022]
Abstract
Nucleic acids are highly charged polyelectrolytes that interact strongly with salt ions. Rigid, base-paired regions are successfully described with wormlike chain models, but nonbase-paired single stranded regions have fundamentally different polymer properties because of their greater flexibility. Recently, attention has turned to single stranded nucleic acids due to the growing recognition of their biological importance, as well as the availability of sophisticated experimental techniques sensitive to the conformation of individual molecules. We investigate polyelectrolyte properties of poly(dT), an important and widely studied model system for flexible single stranded nucleic acids, in physiologically important mixed mono- and divalent salt. We report measurements of the form factor and interparticle interactions using SAXS, end-to-end distances using smFRET, and number of excess ions using ASAXS. We present a coarse-grained model that accounts for flexibility, excluded volume, and electrostatic interactions in these systems. Predictions of the model are validated against experiment. We also discuss the state of all-atom, explicit solvent molecular dynamics simulations of poly(dT), the next step in understanding the complexities of ion interactions with these highly charged and flexible polymers.
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Affiliation(s)
- Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY
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21
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Meisburger SP, Pabit SA, Pollack L. Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements. Biophys J 2016; 108:2886-95. [PMID: 26083928 DOI: 10.1016/j.bpj.2015.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Revised: 04/30/2015] [Accepted: 05/11/2015] [Indexed: 10/23/2022] Open
Abstract
Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To understand these biological processes, knowledge of solvent structure around the nucleic acids is critical. Yet, because they are often disordered, ions and water evade detection by x-ray crystallography and other high-resolution methods. Small-angle x-ray scattering (SAXS) is uniquely sensitive to the spatial correlations between solutes and the surrounding solvent. Thus, SAXS provides an experimental constraint to guide or test emerging solvation theories. However, the interpretation of SAXS profiles is nontrivial because of the difficulty in separating the scattering signals of each component: the macromolecule, ions, and hydration water. Here, we demonstrate methods for robustly deconvoluting these signals, facilitating a more straightforward comparison with theory. Using SAXS data collected on an absolute intensity scale for short DNA duplexes in solution with Na(+), K(+), Rb(+), or Cs(+) counterions, we mathematically decompose the scattering profiles into components (DNA, water, and ions) and validate the decomposition using anomalous scattering measurements. In addition, we generate a library of physically motivated ion atmosphere models and rank them by agreement with the scattering data. The best-fit models have relatively compact ion atmospheres when compared to predictions from the mean-field Poisson-Boltzmann theory of electrostatics. Thus, the x-ray scattering methods presented here provide a valuable measurement of the global structure of the ion atmosphere that can be used to test electrostatics theories that go beyond the mean-field approximation.
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Affiliation(s)
- Steve P Meisburger
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York
| | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
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22
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Zhang X, Zhang JS, Shi YZ, Zhu XL, Tan ZJ. Potential of mean force between like-charged nanoparticles: Many-body effect. Sci Rep 2016; 6:23434. [PMID: 26997415 PMCID: PMC4800448 DOI: 10.1038/srep23434] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/07/2016] [Indexed: 11/26/2022] Open
Abstract
Ion-mediated interaction is important for the properties of polyelectrolytes such as colloids and nucleic acids. The effective pair interactions between two polyelectrolytes have been investigated extensively, but the many-body effect for multiple polyelectrolytes still remains elusive. In this work, the many-body effect in potential of mean force (PMF) between like-charged nanoparticles in various salt solutions has been comprehensively examined by Monte Carlo simulation and the nonlinear Poisson-Boltzmann theory. Our calculations show that, at high 1:1 salt, the PMF is weakly repulsive and appears additive, while at low 1:1 salt, the additive assumption overestimates the repulsive many-body PMF. At low 2:2 salt, the pair PMF appears weakly repulsive while the many-body PMF can become attractive. In contrast, at high 2:2 salt, the pair PMF is apparently attractive while the many-body effect can cause a weaker attractive PMF than that from the additive assumption. Our microscopic analyses suggest that the elusive many-body effect is attributed to ion-binding which is sensitive to ion concentration, ion valence, number of nanoparticles and charges on nanoparticles.
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Affiliation(s)
- Xi Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro &Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Jin-Si Zhang
- Center for Theoretical Physics and Key Laboratory of Artificial Micro &Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Ya-Zhou Shi
- Center for Theoretical Physics and Key Laboratory of Artificial Micro &Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
| | - Xiao-Long Zhu
- Department of Physics, School of Physics &Information Engineering, Jianghan University, Wuhan 430056, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro &Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430072, China
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23
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Yin P, Wu B, Mamontov E, Daemen LL, Cheng Y, Li T, Seifert S, Hong K, Bonnesen PV, Keum JK, Ramirez-Cuesta AJ. X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates. J Am Chem Soc 2016; 138:2638-43. [DOI: 10.1021/jacs.5b11465] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Panchao Yin
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Bin Wu
- Department
of Physics and Astronomy, Joint Institute of Neutron Science, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Eugene Mamontov
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Luke L. Daemen
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Yongqiang Cheng
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Tao Li
- X-ray
Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Soenke Seifert
- X-ray
Science Division, Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois 60439, United States
| | - Kunlun Hong
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Peter V. Bonnesen
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jong Kahk Keum
- Center
for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Anibal J. Ramirez-Cuesta
- Chemical
and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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24
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Li J, Wijeratne SS, Qiu X, Kiang CH. DNA under Force: Mechanics, Electrostatics, and Hydration. NANOMATERIALS (BASEL, SWITZERLAND) 2015; 5:246-267. [PMID: 28347009 PMCID: PMC5312857 DOI: 10.3390/nano5010246] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 01/16/2015] [Accepted: 02/12/2015] [Indexed: 11/16/2022]
Abstract
Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.
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Affiliation(s)
- Jingqiang Li
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Sithara S Wijeratne
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
| | - Xiangyun Qiu
- Department of Physics, George Washington University, Washington, DC 20052, USA.
| | - Ching-Hwa Kiang
- Department of Physics and Astronomy, Rice University, Houston, TX 77005, USA.
- Department of Bioengineering, Rice University, Houston, TX 77005, USA.
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25
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Qiu X, Giannini J, Howell SC, Xia Q, Ke F, Andresen K. Ion competition in condensed DNA arrays in the attractive regime. Biophys J 2014; 105:984-92. [PMID: 23972850 DOI: 10.1016/j.bpj.2013.07.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Revised: 06/30/2013] [Accepted: 07/01/2013] [Indexed: 10/26/2022] Open
Abstract
Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt(3+) Hexammine, or Co(3+)Hex) and one nonDNA-condensing ion (Mg(2+)) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co(3+)Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg(2+), the Co(3+)Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg(2+) and Co(3+)Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co(3+)Hex. It is also observed that only ∼20% DNA charge neutralization by Co(3+)Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions.
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Affiliation(s)
- Xiangyun Qiu
- Department of Physics, George Washington University, Washington, DC, USA.
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26
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Howell SC, Andresen K, Jimenez-Useche I, Yuan C, Qiu X. Elucidating internucleosome interactions and the roles of histone tails. Biophys J 2014; 105:194-9. [PMID: 23823239 DOI: 10.1016/j.bpj.2013.05.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 04/19/2013] [Accepted: 05/06/2013] [Indexed: 12/11/2022] Open
Abstract
The nucleosome is the first level of genome organization and regulation in eukaryotes where negatively charged DNA is wrapped around largely positively charged histone proteins. Interaction between nucleosomes is dominated by electrostatics at long range and guided by specific contacts at short range, particularly involving their flexible histone tails. We have thus quantified how internucleosome interactions are modulated by salts (KCl, MgCl2) and histone tail deletions (H3, H4 N-terminal), using small-angle x-ray scattering and theoretical modeling. We found that measured effective charges at low salts are ∼1/5th of the theoretically predicted renormalized charges and that H4 tail deletion suppresses the attraction at high salts to a larger extent than H3 tail deletion.
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Affiliation(s)
- Steven C Howell
- Department of Physics, George Washington University, Washington, DC, USA
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27
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Kornyshev AA, Leikin S. Helical structure determines different susceptibilities of dsDNA, dsRNA, and tsDNA to counterion-induced condensation. Biophys J 2013; 104:2031-41. [PMID: 23663846 DOI: 10.1016/j.bpj.2013.03.033] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Revised: 03/06/2013] [Accepted: 03/18/2013] [Indexed: 11/18/2022] Open
Abstract
Recent studies of counterion-induced condensation of nucleic acid helices into aggregates produced several puzzling observations. For instance, trivalent cobalt hexamine ions condensed double-stranded (ds) DNA oligomers but not their more highly charged dsRNA counterparts. Divalent alkaline earth metal ions condensed triple-stranded (ts) DNA oligomers but not dsDNA. Here we show that these counterintuitive experimental results can be rationalized within the electrostatic zipper model of interactions between molecules with helical charge motifs. We report statistical mechanical calculations that reveal dramatic and nontrivial interplay between the effects of helical structure and thermal fluctuations on electrostatic interaction between oligomeric nucleic acids. Combining predictions for oligomeric and much longer helices, we also interpret recent experimental studies of the role of counterion charge, structure, and chemistry. We argue that an electrostatic zipper attraction might be a major or even dominant force in nucleic acid condensation.
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Affiliation(s)
- Alexei A Kornyshev
- Department of Chemistry, Imperial College London, London, United Kingdom
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28
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Jimenez-Useche I, Ke J, Tian Y, Shim D, Howell SC, Qiu X, Yuan C. DNA methylation regulated nucleosome dynamics. Sci Rep 2013; 3:2121. [PMID: 23817195 PMCID: PMC3698496 DOI: 10.1038/srep02121] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 06/17/2013] [Indexed: 01/05/2023] Open
Abstract
A strong correlation between nucleosome positioning and DNA methylation patterns has been reported in literature. However, the mechanistic model accounting for the correlation remains elusive. In this study, we evaluated the effects of specific DNA methylation patterns on modulating nucleosome conformation and stability using FRET and SAXS. CpG dinucleotide repeats at 10 bp intervals were found to play different roles in nucleosome stability dependent on their methylation states and their relative nucleosomal locations. An additional (CpG)5 stretch located in the nucleosomal central dyad does not alter the nucleosome conformation, but significant conformational differences were observed between the unmethylated and methylated nucleosomes. These findings suggest that the correlation between nucleosome positioning and DNA methylation patterns can arise from the variations in nucleosome stability dependent on their sequence and epigenetic content. This knowledge will help to reveal the detailed role of DNA methylation in regulating chromatin packaging and gene transcription.
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29
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Ravikumar KM, Huang W, Yang S. Fast-SAXS-pro: a unified approach to computing SAXS profiles of DNA, RNA, protein, and their complexes. J Chem Phys 2013; 138:024112. [PMID: 23320673 DOI: 10.1063/1.4774148] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
A generalized method, termed Fast-SAXS-pro, for computing small angle x-ray scattering (SAXS) profiles of proteins, nucleic acids, and their complexes is presented. First, effective coarse-grained structure factors of DNA nucleotides are derived using a simplified two-particle-per-nucleotide representation. Second, SAXS data of a 18-bp double-stranded DNA are measured and used for the calibration of the scattering contribution from excess electron density in the DNA solvation layer. Additional test on a 25-bp DNA duplex validates this SAXS computational method and suggests that DNA has a different contribution from its hydration surface to the total scattering compared to RNA and protein. To account for such a difference, a sigmoidal function is implemented for the treatment of non-uniform electron density across the surface of a protein/nucleic-acid complex. This treatment allows differential scattering from the solvation layer surrounding protein/nucleic-acid complexes. Finally, the applications of this Fast-SAXS-pro method are demonstrated for protein/DNA and protein/RNA complexes.
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Affiliation(s)
- Krishnakumar M Ravikumar
- Center for Proteomics and Department of Pharmacology, Case Western Reserve University, Cleveland, Ohio 44106-4988, USA
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30
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DNA self-assembly: from chirality to evolution. Int J Mol Sci 2013; 14:8252-70. [PMID: 23591841 PMCID: PMC3645741 DOI: 10.3390/ijms14048252] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Revised: 03/03/2013] [Accepted: 03/21/2013] [Indexed: 01/12/2023] Open
Abstract
Transient or long-term DNA self-assembly participates in essential genetic functions. The present review focuses on tight DNA-DNA interactions that have recently been found to play important roles in both controlling DNA higher-order structures and their topology. Due to their chirality, double helices are tightly packed into stable right-handed crossovers. Simple packing rules that are imposed by DNA geometry and sequence dictate the overall architecture of higher order DNA structures. Close DNA-DNA interactions also provide the missing link between local interactions and DNA topology, thus explaining how type II DNA topoisomerases may sense locally the global topology. Finally this paper proposes that through its influence on DNA self-assembled structures, DNA chirality played a critical role during the early steps of evolution.
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31
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Sim AYL, Lipfert J, Herschlag D, Doniach S. Salt dependence of the radius of gyration and flexibility of single-stranded DNA in solution probed by small-angle x-ray scattering. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:021901. [PMID: 23005779 DOI: 10.1103/physreve.86.021901] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Indexed: 06/01/2023]
Abstract
Short single-stranded nucleic acids are ubiquitous in biological processes; understanding their physical properties provides insights to nucleic acid folding and dynamics. We used small-angle x-ray scattering to study 8-100 residue homopolymeric single-stranded DNAs in solution, without external forces or labeling probes. Poly-T's structural ensemble changes with increasing ionic strength in a manner consistent with a polyelectrolyte persistence length theory that accounts for molecular flexibility. For any number of residues, poly-A is consistently more elongated than poly-T, likely due to the tendency of A residues to form stronger base-stacking interactions than T residues.
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Affiliation(s)
- Adelene Y L Sim
- Applied Physics Department, Stanford University, Stanford, California 94305, USA
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32
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Pezeshkian W, Nikoofard N, Norouzi D, Mohammad-Rafiee F, Fazli H. Distribution of counterions and interaction between two similarly charged dielectric slabs: roles of charge discreteness and dielectric inhomogeneity. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 85:061925. [PMID: 23005145 DOI: 10.1103/physreve.85.061925] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Indexed: 06/01/2023]
Abstract
The distribution of counterions and the electrostatic interaction between two similarly charged dielectric slabs is studied in the strong coupling limit. Dielectric inhomogeneities and discreteness of charge on the slabs have been taken into account. It is found that the amount of dielectric constant difference between the slabs and the environment, and the discreteness of charge on the slabs have opposing effects on the equilibrium distribution of the counterions. At small interslab separations, increasing the amount of dielectric constant difference increases the tendency of the counterions toward the middle of the intersurface space between the slabs and the discreteness of charge pushes them to the surfaces of the slabs. In the limit of point charges, independent of the strength of dielectric inhomogeneity, counterions distribute near the surfaces of the slabs. The interaction between the slabs is attractive at low temperatures and its strength increases with the dielectric constant difference. At room temperature, the slabs may completely attract each other, reach to an equilibrium separation, or have two equilibrium separations with a barrier in between, depending on the system parameters.
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Affiliation(s)
- Weria Pezeshkian
- Department of Physics, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan 45137-66731, Iran
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33
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Mao Y, Zhang J. Understanding thermodynamic competitivity between biopolymer folding and misfolding under large-scale intermolecular interactions. J Am Chem Soc 2011; 134:631-9. [PMID: 22126310 DOI: 10.1021/ja209534c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cooperativity is a hallmark of spontaneous biopolymer folding. The presence of intermolecular interactions could create off-pathway misfolding structures and suppress folding cooperativity. This raises the hypothesis that thermodynamic competitivity between off-pathway misfolding and on-pathway folding may intervene with cooperativity and govern biopolymer folding dynamics under conditions permitting large-scale intermolecular interactions. Here we report direct imaging and theoretical modeling of thermodynamic competitivity between biopolymer folding and misfolding under such conditions, using a two-dimensional array of proton-fueled DNA molecular motors packed at the maximal density as a model system. Time-resolved liquid-phase atomic force microscopy with enhanced phase contrast revealed that the misfolding and folding intermediates transiently self-organize into spatiotemporal patterns on the nanoscale in thermodynamic states far away from equilibrium as a result of thermodynamic competitivity. Computer simulations using a novel cellular-automaton network model provide quantitative insights into how large-scale intermolecular interactions correlate the structural dynamics of individual biomolecules together at the systems level.
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Affiliation(s)
- Youdong Mao
- Dana-Farber Cancer Institute, Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts 02215, USA.
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34
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Manning GS. Counterion condensation theory of attraction between like charges in the absence of multivalent counterions. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:1-18. [PMID: 22197905 DOI: 10.1140/epje/i2011-11132-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 12/07/2011] [Indexed: 05/31/2023]
Abstract
There is abundant experimental evidence suggesting the existence of attractive interactions among identically charged polyelectrolytes in ordinary salt solutions. The presence of multivalent counterions is not required. We review the relevant literature in detail and conclude that it merits more attention than it has received. We discuss also some recent observations of a low ionic strength attraction of negatively charged DNA to the region of a negatively charged glass nanoslit where the floor of the nanoslit meets the walls, again in the absence of multivalent ions. On the theoretical side, it has become clear that purely electrostatic interactions require the presence of multivalent counterions if they are to generate like-charge attraction. Any theory of like-charge attraction in the absence of multivalent counterions must therefore contain a non-electrostatic component. We point out that counterion condensation theory, which has predicted like-charge polyelectrolyte attraction in an intermediate range of distances in ordinary 1:1 salt conditions, contains both electrostatic and non-electrostatic elements. The non-electrostatic component of the theory is the modeling constraint that the counterions fall into two explicit populations, condensed and uncondensed. As reviewed in the paper, this physically motivated constraint is supported by strong experimental evidence. We proceed to offer an explanation of the nanoslit observations by showing in an idealized model that the line of intersection of two intersecting planes is a virtual polyelectrolyte. Since we have previously developed a counterion condensation theory of attraction of two like-charged polyelectrolytes, our suggestion is that the DNA is attracted to the virtual polyelectrolytes that may be located in the nanoslit where floor meets walls. We present the detailed calculations needed to document this suggestion: an extension of previous theory to the case of polyelectrolytes with like but not identical charges; the demonstration of counterion condensation on a plane with bare charge density greater than an explicitly exhibited critical value; a calculation of the free energy of the plane; a calculation of the interaction of a line charge polyelectrolyte with a like-charged plane; and the detailed demonstration that the line of intersection of two planes is a virtual polyelectrolyte.
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Affiliation(s)
- G S Manning
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854-8087, USA.
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35
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Blose JM, Pabit SA, Meisburger SP, Li L, Jones CD, Pollack L. Effects of a protecting osmolyte on the ion atmosphere surrounding DNA duplexes. Biochemistry 2011; 50:8540-7. [PMID: 21882885 DOI: 10.1021/bi200710m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Osmolytes are small, chemically diverse, organic solutes that function as an essential component of cellular stress response. Protecting osmolytes enhance protein stability via preferential exclusion, and nonprotecting osmolytes, such as urea, destabilize protein structures. Although much is known about osmolyte effects on proteins, less is understood about osmolyte effects on nucleic acids and their counterion atmospheres. Nonprotecting osmolytes destabilize nucleic acid structures, but effects of protecting osmolytes depend on numerous factors including the type of nucleic acid and the complexity of the functional fold. To begin quantifying protecting osmolyte effects on nucleic acid interactions, we used small-angle X-ray scattering (SAXS) techniques to monitor DNA duplexes in the presence of sucrose. This protecting osmolyte is a commonly used contrast matching agent in SAXS studies of protein-nucleic acid complexes; thus, it is important to characterize interaction changes induced by sucrose. Measurements of interactions between duplexes showed no dependence on the presence of up to 30% sucrose, except under high Mg(2+) conditions where stacking interactions were disfavored. The number of excess ions associated with DNA duplexes, reported by anomalous small-angle X-ray scattering (ASAXS) experiments, was sucrose independent. Although protecting osmolytes can destabilize secondary structures, our results suggest that ion atmospheres of individual duplexes remain unperturbed by sucrose.
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Affiliation(s)
- Joshua M Blose
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, United States
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36
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Abstract
Positively charged ions, atoms, or molecules compensate the high negative charge of the nucleic acid backbone. Their presence is critical to the biological function of DNA and RNA. This review focuses on experimental studies probing (a) interactions between small ions and nucleic acids and (b) ion-mediated interactions between nucleic acid duplexes. Experimental results on these simple model systems can be compared with specific theoretical models to validate their predictions. Small angle X-ray scattering (SAXS) provides unique insight into these interactions. Anomalous SAXS reports the spatial correlations of condensed (e.g., locally concentrated) counterions to individual DNA or RNA duplexes. SAXS very effectively reports interactions between nucleic acid helices, which range from strongly repulsive to strongly attractive depending on the ionic species present. The sign and strength of interparticle interactions are easily deduced from dramatic changes in the scattering profiles of interacting duplexes.
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Affiliation(s)
- Lois Pollack
- School of Applied & Engineering Physics, Cornell University, Ithaca, NY 14853, USA.
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37
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Fenley MO, Russo C, Manning GS. Theoretical assessment of the oligolysine model for ionic interactions in protein-DNA complexes. J Phys Chem B 2011; 115:9864-72. [PMID: 21751805 DOI: 10.1021/jp204915y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The observed salt dependence of charged ligand binding to polyelectrolytes, such as proteins to DNA or antithrombin to heparin, is often interpreted by means of the "oligolysine model." We review this model as derived entirely within the framework of the counterion condensation theory of polyelectrolytes with no introduction of outside assumptions. We update its comparison with experimental data on the structurally simple systems for which it was originally intended. We then compute the salt dependence of the binding free energy for a variety of protein-DNA complexes with nonlinear Poisson-Boltzmann (NLPB) simulation methods. The results of the NLPB calculations confirm the central prediction of the oligolysine model that the net charge density of DNA remains invariant to protein binding. Specifically, when a cationic protein residue penetrates the layer of counterions condensed on DNA, a counterion is released to bulk solution, and when an anionic protein residue penetrates the condensed counterion layer, an additional counterion is condensed from bulk solution. We also conclude, however, that the cumulative effect of charged protein residues distant from the binding interface makes a significant contribution to the salt dependence of binding, an observation not accommodated by the oligolysine model.
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Affiliation(s)
- Marcia O Fenley
- Institute of Molecular Biophysics+, Florida State University, Tallahassee, Florida 32306, USA.
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38
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Li L, Pabit SA, Meisburger SP, Pollack L. Double-stranded RNA resists condensation. PHYSICAL REVIEW LETTERS 2011; 106:108101. [PMID: 21469837 PMCID: PMC3156472 DOI: 10.1103/physrevlett.106.108101] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Indexed: 05/02/2023]
Abstract
Much attention has been focused on DNA condensation because of its fundamental biological importance. The recent discovery of new roles for RNA duplexes demands efficient packaging of double-stranded RNA for therapeutics. Here we report measurements of short DNA and RNA duplexes in the presence of trivalent ions. Under conditions where UV spectroscopy indicates condensation of DNA duplexes into (insoluble) precipitates, RNA duplexes remain soluble. Small angle x-ray scattering results suggest that the differing surface topologies of RNA and DNA may be crucial in generating the attractive forces that result in precipitation.
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Affiliation(s)
- Li Li
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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39
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Maffeo C, Schöpflin R, Brutzer H, Stehr R, Aksimentiev A, Wedemann G, Seidel R. DNA-DNA interactions in tight supercoils are described by a small effective charge density. PHYSICAL REVIEW LETTERS 2010; 105:158101. [PMID: 21230940 PMCID: PMC3170404 DOI: 10.1103/physrevlett.105.158101] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Indexed: 05/21/2023]
Abstract
DNA-DNA interactions are important for genome compaction and transcription regulation. In studies of such complex processes, DNA is often modeled as a homogeneously charged cylinder and its electrostatic interactions are calculated within the framework of the Poisson-Boltzmann equation. Commonly, a charge adaptation factor is used to address limitations of this theoretical approach. Despite considerable theoretical and experimental efforts, a rigorous quantitative assessment of this parameter is lacking. Here, we comprehensively characterized DNA-DNA interactions in the presence of monovalent ions by analyzing the supercoiling behavior of single DNA molecules held under constant tension. Both a theoretical model and coarse-grained simulations of this process revealed a surprisingly small effective DNA charge of 40% of the nominal charge density, which was additionally supported by all-atom molecular dynamics simulations.
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Affiliation(s)
| | | | | | | | | | | | - Ralf Seidel
- To whom correspondence should be addressed: ; ;
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40
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Wong GCL, Pollack L. Electrostatics of strongly charged biological polymers: ion-mediated interactions and self-organization in nucleic acids and proteins. Annu Rev Phys Chem 2010; 61:171-89. [PMID: 20055668 DOI: 10.1146/annurev.physchem.58.032806.104436] [Citation(s) in RCA: 171] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Charges on biological polymers in physiologically relevant solution conditions are strongly screened by water and salt solutions containing counter-ions. However, the entropy of these counterions can result in surprisingly strong interactions between charged objects in water despite short screening lengths, via coupling between osmotic and electrostatic interactions. Widespread work in theory, experiment, and computation has been carried out to gain a fundamental understanding of the rich, yet sometimes counterintuitive, behavior of these polyelectrolyte systems. Examples of polyelectrolyte association in biology include DNA packaging and RNA folding, as well as aggregation and self-organization phenomena in different disease states.
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Affiliation(s)
- Gerard C L Wong
- Materials Science and Engineering Department, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA.
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41
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Várnai P, Timsit Y. Differential stability of DNA crossovers in solution mediated by divalent cations. Nucleic Acids Res 2010; 38:4163-72. [PMID: 20215439 PMCID: PMC2896531 DOI: 10.1093/nar/gkq150] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNA–DNA interactions that are required for such functions. In nature, DNA helices minimize electrostatic repulsion between double helices in several ways. Within crystals, B-DNA forms either right-handed crossovers by groove–backbone interaction or left-handed crossovers by groove–groove juxtaposition. We evaluated the stability of such crossovers at various ionic concentrations using large-scale atomistic molecular dynamics simulations. Our results show that right-handed DNA crossovers are thermodynamically stable in solution in the presence of divalent cations. Attractive forces at short-range stabilize such crossover structures with inter-axial separation of helices less than 20 Å. Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only. Surprisingly, left-handed crossovers, assembled by sequence-independent juxtaposition of the helices, appear unstable even at the highest concentration of Mg2+studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in differential stabilization of crossover structures. These results may serve as a rational basis to understand the role DNA crossovers play in biological processes.
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Affiliation(s)
- Péter Várnai
- Department of Chemistry and Biochemistry, University of Sussex, Brighton, BN1 9QJ, UK.
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42
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Mastroianni AJ, Sivak DA, Geissler PL, Alivisatos AP. Probing the conformational distributions of subpersistence length DNA. Biophys J 2009; 97:1408-17. [PMID: 19720029 DOI: 10.1016/j.bpj.2009.06.031] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2009] [Revised: 06/09/2009] [Accepted: 06/11/2009] [Indexed: 10/20/2022] Open
Abstract
We have measured the bending elasticity of short double-stranded DNA (dsDNA) chains through small-angle x-ray scattering from solutions of dsDNA-linked dimers of gold nanoparticles. This method, which does not require exertion of external forces or binding to a substrate, reports on the equilibrium distribution of bending fluctuations, not just an average value (as in ensemble fluorescence resonance energy transfer) or an extreme value (as in cyclization), and in principle provides a more robust data set for assessing the suitability of theoretical models. Our experimental results for dsDNA comprising 42-94 basepairs are consistent with a simple wormlike chain model of dsDNA elasticity, whose behavior we have determined from Monte Carlo simulations that explicitly represent nanoparticles and their alkane tethers. A persistence length of 50 nm (150 basepairs) gave a favorable comparison, consistent with the results of single-molecule force-extension experiments on much longer dsDNA chains, but in contrast to recent suggestions of enhanced flexibility at these length scales.
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43
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Pabit SA, Qiu X, Lamb JS, Li L, Meisburger SP, Pollack L. Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA. Nucleic Acids Res 2009; 37:3887-96. [PMID: 19395592 PMCID: PMC2709557 DOI: 10.1093/nar/gkp257] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The recent discovery of the RNA interference mechanism emphasizes the biological importance of short, isolated, double-stranded (ds) RNA helices and calls for a complete understanding of the biophysical properties of dsRNA. However, most previous studies of the electrostatics of nucleic acid duplexes have focused on DNA. Here, we present a comparative investigation of electrostatic effects in RNA and DNA. Using resonant (anomalous) and non-resonant small-angle X-ray scattering, we characterized the charge screening efficiency and counterion distribution around short (25 bp) dsDNA and RNA molecules of comparable sequence. Consistent with theoretical predictions, we find counterion mediated screening to be more efficient for dsRNA than dsDNA. Furthermore, the topology of the RNA A-form helix alters the spatial distribution of counterions relative to B-form DNA. The experimental results reported here agree well with ion-size-corrected non-linear Poisson-Boltzmann calculations. We propose that differences in electrostatic properties aid in selective recognition of different types of short nucleic acid helices by target binding partners.
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Affiliation(s)
- Suzette A Pabit
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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44
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Sambriski E, Schwartz D, de Pablo J. A mesoscale model of DNA and its renaturation. Biophys J 2009; 96:1675-90. [PMID: 19254530 PMCID: PMC2717267 DOI: 10.1016/j.bpj.2008.09.061] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/30/2008] [Indexed: 11/26/2022] Open
Abstract
A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.
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Affiliation(s)
- E.J. Sambriski
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - D.C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory for Genetics, University of Wisconsin-Madison, Madison, Wisconsin
| | - J.J. de Pablo
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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45
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Sambriski EJ, Ortiz V, de Pablo JJ. Sequence effects in the melting and renaturation of short DNA oligonucleotides: structure and mechanistic pathways. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:034105. [PMID: 21817250 PMCID: PMC3886633 DOI: 10.1088/0953-8984/21/3/034105] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The renaturation/denaturation of DNA oligonucleotides is characterized in the context of expanded ensemble (EXE) and transition path sampling (TPS) simulations. Free energy profiles have been determined from EXE for DNA sequences of varying composition, chain length, and ionic strength. TPS simulations within a Langevin dynamics formalism have been carried out to obtain further information of the transition state for renaturation. Simulation results reveal that free energy profiles are strikingly similar for the various DNA sequences considered in this work. Taking intact double-stranded DNA to have an extent of reaction ξ = 1.0, the maximum of the free energy profile appears at ξ≈0.15, corresponding to ∼2 base pairs. In terms of chain length, the free energy barrier of longer oligonucleotides (30 versus 15 base pairs) is higher and slightly narrower, due to increased sharpness associated with the transition. Low ionic strength tends to decrease free energy barriers, whereby increasing strand rigidity facilitates reassociation. Two mechanisms for DNA reassociation emerge from our analysis of the transition state ensemble. Repetitive sequences tend to reassociate through a non-specific pathway involving molecular slithering. In contrast, random sequences associate through a more restrictive pathway involving the formation of specific contacts, which then leads to overall molecular zippering. In both random and repetitive sequences, the distribution of contacts suggests that nucleation is favored for sites located within the middle region of the chain. The prevalent extent of reaction for the transition state is ξ≈0.25, and the critical size of the nucleus as obtained from our analysis involves ∼4 base pairs.
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Affiliation(s)
- E. J. Sambriski
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - V. Ortiz
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
| | - J. J. de Pablo
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin 53706 USA
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46
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McPhie MG, Nägele G. Nonmonotonic density dependence of the diffusion of DNA fragments in low-salt suspensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 78:060401. [PMID: 19256789 DOI: 10.1103/physreve.78.060401] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2008] [Indexed: 05/27/2023]
Abstract
The high linear charge density of 20-base-pair oligomers of DNA is shown to lead to a striking nonmonotonic dependence of the long-time self-diffusion on the concentration of DNA in low-salt conditions. This generic nonmonotonic behavior results from the strong coupling between the electrostatic and solvent-mediated hydrodynamic interactions, from the renormalization of these electrostatic interactions at large separations, and specifically from the dominance of the far-field hydrodynamic interactions caused by the strong repulsion between the DNA fragments.
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Affiliation(s)
- Mathieu G McPhie
- Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany
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47
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Qiu X, Andresen K, Lamb JS, Kwok LW, Pollack L. Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations. PHYSICAL REVIEW LETTERS 2008; 101:228101. [PMID: 19113524 PMCID: PMC2843915 DOI: 10.1103/physrevlett.101.228101] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Indexed: 05/18/2023]
Abstract
We have investigated the energetics of DNA condensation by multivalent polyamine cations. Solution small angle x-ray scattering was used to monitor interactions between short 25 base pair dsDNA strands in the free supernatant DNA phase that coexists with the condensed DNA phase. Interestingly, when tetravalent spermine is used, significant inter-DNA repulsion is observed in the free phase, in contrast with the presumed inter-DNA attraction in the coexisting condensed phase. DNA condensation thus appears to be a discrete, first-order-like, transition from a repulsive gaseous to an attractive condensed solid phase, in accord with the reported all-or-none condensation of giant DNA. We further quantify the electrostatic repulsive potentials in the free DNA phase and estimate the number of additional spermine cations that bind to DNA upon condensation.
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Affiliation(s)
- Xiangyun Qiu
- School of Applied and Engineering Physics, Cornell University, Ithaca, New York 14853, USA
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48
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Abstract
Many genetic processes depend on proteins interacting with specific sequences on DNA. Despite the large excess of nonspecific DNA in the cell, proteins can locate their targets rapidly. After initial nonspecific binding, they are believed to find the target site by 1D diffusion ("sliding") interspersed by 3D dissociation/reassociation, a process usually referred to as facilitated diffusion. The 3D events combine short intrasegmental "hops" along the DNA contour, intersegmental "jumps" between nearby DNA segments, and longer volume "excursions." The impact of DNA conformation on the search pathway is, however, still unknown. Here, we show direct evidence that DNA coiling influences the specific association rate of EcoRV restriction enzymes. Using optical tweezers together with a fast buffer exchange system, we obtained association times of EcoRV on single DNA molecules as a function of DNA extension, separating intersegmental jumping from other search pathways. Depending on salt concentration, targeting rates almost double when the DNA conformation is changed from fully extended to a coiled configuration. Quantitative analysis by an extended facilitated diffusion model reveals that only a fraction of enzymes are ready to bind to DNA. Generalizing our results to the crowded environment of the cell we predict a major impact of intersegmental jumps on target localization speed on DNA.
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49
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Zhang F, Skoda MWA, Jacobs RMJ, Zorn S, Martin RA, Martin CM, Clark GF, Weggler S, Hildebrandt A, Kohlbacher O, Schreiber F. Reentrant condensation of proteins in solution induced by multivalent counterions. PHYSICAL REVIEW LETTERS 2008; 101:148101. [PMID: 18851577 DOI: 10.1103/physrevlett.101.148101] [Citation(s) in RCA: 152] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Indexed: 05/26/2023]
Abstract
Negatively charged globular proteins in solution undergo a condensation upon adding trivalent counterions between two critical concentrations C and C, C <C. This reentrant condensation behavior above C is caused by short-ranged electrostatic interactions between multivalent cations and acidic residues, mechanistically different from the case of DNA. Small-angle x-ray scattering indicates a short-ranged attraction between counterion-bound proteins near C and C. Monte Carlo simulations (under these strong electrostatic coupling conditions) support an effective inversion of charge on surface side chains through binding of the multivalent counterions.
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Affiliation(s)
- F Zhang
- Institut für Angewandte Physik, Universität Tübingen, Auf der Morgenstelle 10, 72076 Tübingen, Germany
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50
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Abstract
RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA folding kinetics even for small RNA systems such as hairpins and pseudoknots, (c) the intraloop interactions and sequence-dependent loop free energy, and (d) the strong nonadditivity of chain entropy in RNA pseudoknot and other tertiary folds. Several related issues, which have not been thoroughly resolved, require combined approaches with thermodynamic and kinetic experiments, statistical mechanical modeling, and all-atom computer simulations.
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Affiliation(s)
- Shi-Jie Chen
- Department of Physics and Astronomy and Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, USA.
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