1
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Baral S, Liu C, Chakraborty UK, Kubo K, Mao X, Coates GW, Chen P. Single-chain polymerization dynamics and conformational mechanics of conjugated polymers. Chem 2021. [DOI: 10.1016/j.chempr.2021.05.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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2
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Milchev A, Egorov SA, Binder K. Phase Separation in a Binary Mixture of Semiflexible Polymers Confined in a Repulsive Sphere. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Andrey Milchev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Sergei A. Egorov
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22901, United States
| | - Kurt Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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3
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Villaluenga JPG, Vidal J, Cao-García FJ. Noncooperative thermodynamics and kinetic models of ligand binding to polymers: Connecting McGhee-von Hippel model with the Tonks gas model. Phys Rev E 2020; 102:012407. [PMID: 32795076 DOI: 10.1103/physreve.102.012407] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 06/18/2020] [Indexed: 11/07/2022]
Abstract
Ligand binding to polymers modifies the physical and chemical properties of the polymers, leading to physical, chemical, and biological implications. McGhee and von Hippel obtained the equilibrium coverage as a function of the ligand affinity, through the computation of the possible binding sites for the ligand. Here, we complete this theory deriving the kinetic model for the ligand-binding dynamics and the associated equilibrium chemical potential, which turns out to be of the Tonks gas model type. At low coverage, the Tonks chemical potential becomes the Fermi chemical potential and even the ideal gas chemical potential. We also discuss kinetic models associated with these chemical potentials. These results clarify the kinetic models of ligand binding, their relations with the chemical potentials, and their range of validity. Our results highlight the inaccuracy of ideal and simplified kinetic approaches for medium and high coverages.
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Affiliation(s)
- Juan P G Villaluenga
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Jules Vidal
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain
| | - Francisco Javier Cao-García
- Departamento de Estructura de la Materia, Física Térmica y Electrónica, Universidad Complutense de Madrid, Pza. de Ciencias, 1, 28040 Madrid, Spain.,Instituto Madrileño de Estudios Avanzados en Nanociencia, IMDEA Nanociencia, C/Faraday, 9, 28049 Madrid, Spain
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4
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Innes-Gold SN, Pincus PA, Stevens MJ, Saleh OA. Polyelectrolyte Conformation Controlled by a Trivalent-Rich Ion Jacket. PHYSICAL REVIEW LETTERS 2019; 123:187801. [PMID: 31763890 DOI: 10.1103/physrevlett.123.187801] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/02/2019] [Indexed: 06/10/2023]
Abstract
The configuration of charged polymers is heavily dependent on interactions with surrounding salt ions, typically manifesting as a sensitivity to the bulk ionic strength. Here, we use single-molecule mechanical measurements to show that a charged polysaccharide, hyaluronic acid, shows a surprising regime of insensitivity to ionic strength in the presence of trivalent ions. Using simulations and theory, we propose that this is caused by the formation of a "jacket" of ions, tightly associated with the polymer, whose charge (and thus effect on configuration) is robust against changes in solution composition.
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Affiliation(s)
- Sarah N Innes-Gold
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - Philip A Pincus
- Materials Department and Physics Department, University of California, Santa Barbara, California 93106, USA
| | - Mark J Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, Albuquerque, New Mexico 87185-1315, USA
| | - Omar A Saleh
- Materials Department and BMSE program, University of California, Santa Barbara, California 93106, USA
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5
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Abstract
We review the current understanding of the mechanics of DNA and DNA-protein complexes, from scales of base pairs up to whole chromosomes. Mechanics of the double helix as revealed by single-molecule experiments will be described, with an emphasis on the role of polymer statistical mechanics. We will then discuss how topological constraints- entanglement and supercoiling-impact physical and mechanical responses. Models for protein-DNA interactions, including effects on polymer properties of DNA of DNA-bending proteins will be described, relevant to behavior of protein-DNA complexes in vivo. We also discuss control of DNA entanglement topology by DNA-lengthwise-compaction machinery acting in concert with topoisomerases. Finally, the chapter will conclude with a discussion of relevance of several aspects of physical properties of DNA and chromatin to oncology.
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6
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Stevens MJ, Berezney JP, Saleh OA. The effect of chain stiffness and salt on the elastic response of a polyelectrolyte. J Chem Phys 2018; 149:163328. [DOI: 10.1063/1.5035340] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Mark J. Stevens
- Center for Integrated Nanotechnologies, Sandia National Laboratories, P.O. Box 5800, MS 1315, Albuquerque, New Mexico 87185-1315, USA
| | - John P. Berezney
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
| | - Omar A. Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
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7
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Engel MC, Smith DM, Jobst MA, Sajfutdinow M, Liedl T, Romano F, Rovigatti L, Louis AA, Doye JPK. Force-Induced Unravelling of DNA Origami. ACS NANO 2018; 12:6734-6747. [PMID: 29851456 DOI: 10.1021/acsnano.8b01844] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The mechanical properties of DNA nanostructures are of widespread interest as applications that exploit their stability under constant or intermittent external forces become increasingly common. We explore the force response of DNA origami in comprehensive detail by combining AFM single molecule force spectroscopy experiments with simulations using oxDNA, a coarse-grained model of DNA at the nucleotide level, to study the unravelling of an iconic origami system: the Rothemund tile. We contrast the force-induced melting of the tile with simulations of an origami 10-helix bundle. Finally, we simulate a recently proposed origami biosensor, whose function takes advantage of origami behavior under tension. We observe characteristic stick-slip unfolding dynamics in our force-extension curves for both the Rothemund tile and the helix bundle and reasonable agreement with experimentally observed rupture forces for these systems. Our results highlight the effect of design on force response: we observe regular, modular unfolding for the Rothemund tile that contrasts with strain-softening of the 10-helix bundle which leads to catastropic failure under monotonically increasing force. Further, unravelling occurs straightforwardly from the scaffold ends inward for the Rothemund tile, while the helix bundle unfolds more nonlinearly. The detailed visualization of the yielding events provided by simulation allows preferred pathways through the complex unfolding free-energy landscape to be mapped, as a key factor in determining relative barrier heights is the extensional release per base pair broken. We shed light on two important questions: how stable DNA nanostructures are under external forces and what design principles can be applied to enhance stability.
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Affiliation(s)
- Megan C Engel
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - David M Smith
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Markus A Jobst
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Martin Sajfutdinow
- Fraunhofer Institute for Cell Therapy and Immunology IZI , Perlickstraβe 1 , 04103 Leipzig , Germany
| | - Tim Liedl
- Department für Physik , Ludwig-Maximilians-Universität Amalienstrasse 54 80799 München , Germany
| | - Flavio Romano
- Dipartimento di Scienze Molecolari e Nanosistemi , Università Ca' Foscari di Venezia , Via Torino 155 , 30172 Venezia Mestre , Italy
| | - Lorenzo Rovigatti
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
- CNR-ISC , Uos Sapienza, Piazzale A. Moro 2 , 00185 Roma , Italy
- Dipartimento di Fisica , Sapienza Università di Roma , Piazzale A. Moro 2 , 00185 Roma , Italy
| | - Ard A Louis
- Rudolf Peierls Centre for Theoretical Physics , University of Oxford , 1 Keble Road , Oxford OX1 3NP , United Kingdom
| | - Jonathan P K Doye
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry , University of Oxford , South Parks Road , Oxford OX1 3QZ , United Kingdom
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8
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Chakraborty D, Hori N, Thirumalai D. Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. J Chem Theory Comput 2018; 14:3763-3779. [PMID: 29870236 PMCID: PMC6423546 DOI: 10.1021/acs.jctc.8b00091] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We develop a robust coarse-grained model for single- and double-stranded DNA by representing each nucleotide by three interaction sites (TIS) located at the centers of mass of sugar, phosphate, and base. The resulting TIS model includes base-stacking, hydrogen bond, and electrostatic interactions as well as bond-stretching and bond angle potentials that account for the polymeric nature of DNA. The choices of force constants for stretching and the bending potentials were guided by a Boltzmann inversion procedure using a large representative set of DNA structures extracted from the Protein Data Bank. Some of the parameters in the stacking interactions were calculated using a learning procedure, which ensured that the experimentally measured melting temperatures of dimers are faithfully reproduced. Without any further adjustments, the calculations based on the TIS model reproduce the experimentally measured salt and sequence-dependence of the size of single-stranded DNA (ssDNA), as well as the persistence lengths of poly(dA) and poly(dT) chains. Interestingly, upon application of mechanical force, the extension of poly(dA) exhibits a plateau, which we trace to the formation of stacked helical domains. In contrast, the force-extension curve (FEC) of poly(dT) is entropic in origin and could be described by a standard polymer model. We also show that the persistence length of double-stranded DNA, formed from two complementary ssDNAs, is consistent with the prediction based on the worm-like chain. The persistence length, which decreases with increasing salt concentration, is in accord with the Odijk-Skolnick-Fixman theory intended for stiff polyelectrolyte chains near the rod limit. Our model predicts the melting temperatures of DNA hairpins with excellent accuracy, and we are able to recover the experimentally known sequence-specific trends. The range of applications, which did not require adjusting any parameter after the initial construction based solely on PDB structures and melting profiles of dimers, attests to the transferability and robustness of the TIS model for ssDNA and dsDNA.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Naoto Hori
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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9
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Radiom M, Borkovec M. Influence of ligand-receptor interactions on force-extension behavior within the freely jointed chain model. Phys Rev E 2018; 96:062501. [PMID: 29347442 DOI: 10.1103/physreve.96.062501] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Indexed: 11/07/2022]
Abstract
We study the influence of receptor-ligand interactions on the force response of single polymer chains theoretically. The extension of the chain is modeled in terms of freely jointed chain or elastic freely jointed chain (EFJC) models. The situation involving noninteracting bonds is solved exactly, while effects of interactions are treated within a mean-field approximation. The form with shorter bonds governs the low force situation, while the form with longer bonds is relevant in the high force regime. We further discuss the accuracy of approximate relations, which were used to describe the response of the EFJC model.
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Affiliation(s)
- Milad Radiom
- School of Chemical Science and Engineering, KTH Royal Institute of Technology, Drottning Kristinas väg 51, Stockholm 10044, Sweden
| | - Michal Borkovec
- Department of Inorganic and Analytical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, 1205 Geneva, Switzerland
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10
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Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JPG, Ibarra B, Cao FJ. Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLoS One 2017; 12:e0174830. [PMID: 28380044 PMCID: PMC5381885 DOI: 10.1371/journal.pone.0174830] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Accepted: 03/15/2017] [Indexed: 01/20/2023] Open
Abstract
Ligands binding to polymers regulate polymer functions by changing their physical and chemical properties. This ligand regulation plays a key role in many biological processes. We propose here a model to explain the mechanical, thermodynamic, and kinetic properties of the process of binding of small ligands to long biopolymers. These properties can now be measured at the single molecule level using force spectroscopy techniques. Our model performs an effective decomposition of the ligand-polymer system on its covered and uncovered regions, showing that the elastic properties of the ligand-polymer depend explicitly on the ligand coverage of the polymer (i.e., the fraction of the polymer covered by the ligand). The equilibrium coverage that minimizes the free energy of the ligand-polymer system is computed as a function of the applied force. We show how ligands tune the mechanical properties of a polymer, in particular its length and stiffness, in a force dependent manner. In addition, it is shown how ligand binding can be regulated applying mechanical tension on the polymer. Moreover, the binding kinetics study shows that, in the case where the ligand binds and organizes the polymer in different modes, the binding process can present transient shortening or lengthening of the polymer, caused by changes in the relative coverage by the different ligand modes. Our model will be useful to understand ligand-binding regulation of biological processes, such as the metabolism of nucleic acid. In particular, this model allows estimating the coverage fraction and the ligand mode characteristics from the force extension curves of a ligand-polymer system.
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Affiliation(s)
- Javier Jarillo
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - José A. Morín
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Elena Beltrán-Heredia
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Juan P. G. Villaluenga
- Departamento de Física Aplicada I. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
| | - Borja Ibarra
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA Nanociencia) & CNB-CSIC-IMDEA Nanociencia Associated Unit ‘Unidad de Nanobiotecnología’, Madrid, Spain
| | - Francisco J. Cao
- Departamento de Física Atómica, Molecular y Nuclear. Facultad de Ciencias Físicas. Universidad Complutense de Madrid. Pza. de las Ciencias, 1. Madrid. Spain
- * E-mail:
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11
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Brenner MD, Zhou R, Conway DE, Lanzano L, Gratton E, Schwartz MA, Ha T. Spider Silk Peptide Is a Compact, Linear Nanospring Ideal for Intracellular Tension Sensing. NANO LETTERS 2016; 16:2096-102. [PMID: 26824190 PMCID: PMC4851340 DOI: 10.1021/acs.nanolett.6b00305] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Recent development and applications of calibrated, fluorescence resonance energy transfer (FRET)-based tension sensors have led to a new understanding of single molecule mechanotransduction in a number of biological systems. To expand the range of accessible forces, we systematically measured FRET versus force trajectories for 25, 40, and 50 amino acid peptide repeats derived from spider silk. Single molecule fluorescence-force spectroscopy showed that the peptides behaved as linear springs instead of the nonlinear behavior expected for a disordered polymer. Our data are consistent with a compact, rodlike structure that measures 0.26 nm per 5 amino acid repeat that can stretch by 500% while maintaining linearity, suggesting that the remarkable elasticity of spider silk proteins may in part derive from the properties of individual chains. We found the shortest peptide to have the widest range of force sensitivity: between 2 pN and 11 pN. Live cell imaging of the three tension sensor constructs inserted into vinculin showed similar force values around 2.4 pN. We also provide a lookup table for force versus intracellular FRET for all three constructs.
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Affiliation(s)
- Michael D. Brenner
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Ruobo Zhou
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Daniel E. Conway
- Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
| | - Luca Lanzano
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - E. Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, CA 92697, USA
| | - Martin A. Schwartz
- Cardiovascular Research Center, University of Virginia, Charlottesville, VA 22908, USA
- Yale Cardiovascular Research Center, Departments of Internal Medicine (Section of Cardiovascular Medicine) and Cell Biology, Yale University, New Haven, CT 06511, USA
| | - Taekjip Ha
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
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12
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Saleh OA. Perspective: Single polymer mechanics across the force regimes. J Chem Phys 2015; 142:194902. [DOI: 10.1063/1.4921348] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Affiliation(s)
- Omar A. Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
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13
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McIntosh DB, Duggan G, Gouil Q, Saleh OA. Sequence-dependent elasticity and electrostatics of single-stranded DNA: signatures of base-stacking. Biophys J 2014; 106:659-66. [PMID: 24507606 DOI: 10.1016/j.bpj.2013.12.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 11/17/2013] [Accepted: 12/11/2013] [Indexed: 11/19/2022] Open
Abstract
Base-stacking is a key factor in the energetics that determines nucleic acid structure. We measure the tensile response of single-stranded DNA as a function of sequence and monovalent salt concentration to examine the effects of base-stacking on the mechanical and thermodynamic properties of single-stranded DNA. By comparing the elastic response of highly stacked poly(dA) and that of a polypyrimidine sequence with minimal stacking, we find that base-stacking in poly(dA) significantly enhances the polymer's rigidity. The unstacking transition of poly(dA) at high force reveals that the intrinsic electrostatic tension on the molecule varies significantly more weakly on salt concentration than mean-field predictions. Further, we provide a model-independent estimate of the free energy difference between stacked poly(dA) and unstacked polypyrimidine, finding it to be ∼-0.25 kBT/base and nearly constant over three orders of magnitude in salt concentration.
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Affiliation(s)
- Dustin B McIntosh
- Physics Department, University of California-Santa Barbara, Santa Barbara, California
| | - Gina Duggan
- Physics Department, University of California-Santa Barbara, Santa Barbara, California
| | - Quentin Gouil
- Physics Department, École Normale Supérieure, Paris, France
| | - Omar A Saleh
- Materials Department and Biomolecular Science and Engineering Program, University of California-Santa Barbara, Santa Barbara, California.
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14
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Jacobson DR, McIntosh DB, Saleh OA. The snakelike chain character of unstructured RNA. Biophys J 2014; 105:2569-76. [PMID: 24314087 DOI: 10.1016/j.bpj.2013.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/16/2013] [Accepted: 10/23/2013] [Indexed: 01/30/2023] Open
Abstract
In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod "wormlike chain" (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a "snakelike chain," characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation.
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Affiliation(s)
- David R Jacobson
- Department of Physics, University of California, Santa Barbara, CA
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15
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Dai L, van der Maarel J, Doyle PS. Extended de Gennes Regime of DNA Confined in a Nanochannel. Macromolecules 2014. [DOI: 10.1021/ma500326w] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Liang Dai
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
| | - Johan van der Maarel
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department
of Physics, National University of Singapore, 2 Science Drive 3, Republic of Singapore 117551
| | - Patrick S. Doyle
- BioSystems
and Micromechanics (BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, Republic of Singapore 138602
- Department of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, Massachusetts 02139, United States
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16
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Bosco A, Camunas-Soler J, Ritort F. Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions. Nucleic Acids Res 2014; 42:2064-74. [PMID: 24225314 PMCID: PMC3919573 DOI: 10.1093/nar/gkt1089] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 10/16/2013] [Accepted: 10/17/2013] [Indexed: 11/16/2022] Open
Abstract
Single-stranded DNA (ssDNA) plays a major role in several biological processes. It is therefore of fundamental interest to understand how the elastic response and the formation of secondary structures are modulated by the interplay between base pairing and electrostatic interactions. Here we measure force-extension curves (FECs) of ssDNA molecules in optical tweezers set up over two orders of magnitude of monovalent and divalent salt conditions, and obtain its elastic parameters by fitting the FECs to semiflexible models of polymers. For both monovalent and divalent salts, we find that the electrostatic contribution to the persistence length is proportional to the Debye screening length, varying as the inverse of the square root of cation concentration. The intrinsic persistence length is equal to 0.7 nm for both types of salts, and the effectivity of divalent cations in screening electrostatic interactions appears to be 100-fold as compared with monovalent salt, in line with what has been recently reported for single-stranded RNA. Finally, we propose an analysis of the FECs using a model that accounts for the effective thickness of the filament at low salt condition and a simple phenomenological description that quantifies the formation of non-specific secondary structure at low forces.
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Affiliation(s)
- Alessandro Bosco
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Joan Camunas-Soler
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
| | - Felix Ritort
- SISSA - Scuola Internazionale Superiore di Studi Avanzati, via Bonomea 265, 34136 Trieste, Italy, Elettra-Sincrotrone Trieste S.C.p.A., Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza Trieste, Italy, Departament de Física Fonamental, Universitat de Barcelona, Diagonal 647, 08028 Barcelona, Spain and CIBER de Bioingeniería, Biomateriales y Nanomedicina, Instituto de Salud Carlos III, Madrid, Spain
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17
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Tree DR, Muralidhar A, Doyle PS, Dorfman KD. Is DNA a Good Model Polymer? Macromolecules 2013; 46:10.1021/ma401507f. [PMID: 24347685 PMCID: PMC3859536 DOI: 10.1021/ma401507f] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The details surrounding the cross-over from wormlike-specific to universal polymeric behavior has been the subject of debate and confusion even for the simple case of a dilute, unconfined wormlike chain. We have directly computed the polymer size, form factor, free energy and Kirkwood diffusivity for unconfined wormlike chains as a function of molecular weight, focusing on persistence lengths and effective widths that represent single-stranded and double-stranded DNA in a high ionic strength buffer. To do so, we use a chain-growth Monte Carlo algorithm, the Pruned-Enriched Rosenbluth Method (PERM), which allows us to estimate equilibrium and near-equilibrium dynamic properties of wormlike chains over an extremely large range of contour lengths. From our calculations, we find that very large DNA chains (≈ 1,000,000 base pairs depending on the choice of size metric) are required to reach flexible, swollen non-draining coils. Furthermore, our results indicate that the commonly used model polymer λ-DNA (48,500 base pairs) does not exhibit "ideal" scaling, but exists in the middle of the transition to long-chain behavior. We subsequently conclude that typical DNA used in experiments are too short to serve as an accurate model of long-chain, universal polymer behavior.
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Affiliation(s)
- Douglas R. Tree
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Abhiram Muralidhar
- Department of Chemical Engineering and Materials Science, University of Minnesota
| | - Patrick S. Doyle
- Department of Chemical Engineering, Massachusetts Institute of Technology
| | - Kevin D. Dorfman
- Department of Chemical Engineering and Materials Science, University of Minnesota
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18
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Stevens MJ, McIntosh DB, Saleh OA. Simulations of Stretching a Strong, Flexible Polyelectrolyte: Using Long Chains To Access the Pincus Scaling Regime. Macromolecules 2013. [DOI: 10.1021/ma401211w] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark J. Stevens
- Center for
Integrated Nanotechnologies, Sandia National Laboratories, P.O. Box 5800, MS 1315, Albuquerque, New Mexico 87185-1315, United
States
| | - Dustin B. McIntosh
- Physics
Department, University of California, Santa
Barbara, California
93106, United States
| | - Omar A. Saleh
- Materials
Department and BMSE Program, University of California, Santa Barbara, California 93106, United States
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19
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Affiliation(s)
- Liang Dai
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
| | - Patrick S. Doyle
- BioSystems and Micromechanics
(BioSyM) IRG, Singapore-MIT Alliance for Research and Technology (SMART) Centre, 3 Science Drive 2, Republic
of Singapore 117543
- Department
of Chemical Engineering, Massachusetts Institute of Technology (MIT), Cambridge,
Massachusetts 02139, United States
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20
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Radhakrishnan R, Underhill PT. Fluctuations in the coil-stretch transition of flexible polymers in good solvents: a peak due to nonlinear force relation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 88:012606. [PMID: 23944485 DOI: 10.1103/physreve.88.012606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Revised: 07/11/2013] [Indexed: 06/02/2023]
Abstract
Long flexible polymers undergo a coil to stretch transition (CST) in an elongational flow. Near the CST, a peak can be observed in the fluctuations of the size of a molecule (|R|). Solvent effects on the fluctuations are studied using Brownian dynamics simulations of a nonlinear spring force relation that can represent real molecules. Ignoring the influence of hydrodynamic interactions, a linear region in the spring force relation is known to cause the peak in |R| fluctuations. In contrast, we find that a peak in the fluctuations can be obtained even for the nonlinear spring force relation. We analyze the influence of hydrodynamic interactions on the fluctuations using a dumbbell model with a conformation-dependent drag coefficient.
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Affiliation(s)
- Rangarajan Radhakrishnan
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St, Troy, New York 12180, USA
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21
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Hsu HP, Paul W, Binder K. Scattering function of semiflexible polymer chains under good solvent conditions. J Chem Phys 2013; 137:174902. [PMID: 23145745 DOI: 10.1063/1.4764300] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using the pruned-enriched Rosenbluth Monte Carlo algorithm, the scattering functions of semiflexible macromolecules in dilute solution under good solvent conditions are estimated both in d = 2 and d = 3 dimensions, considering also the effect of stretching forces. Using self-avoiding walks of up to N = 25,600 steps on the square and simple cubic lattices, variable chain stiffness is modeled by introducing an energy penalty ε(b) for chain bending; varying q(b) = exp (-ε(b)∕k(B)T) from q(b) = 1 (completely flexible chains) to q(b) = 0.005, the persistence length can be varied over two orders of magnitude. For unstretched semiflexible chains, we test the applicability of the Kratky-Porod worm-like chain model to describe the scattering function and discuss methods for extracting persistence length estimates from scattering. While in d = 2 the direct crossover from rod-like chains to self-avoiding walks invalidates the Kratky-Porod description, it holds in d = 3 for stiff chains if the number of Kuhn segments n(K) does not exceed a limiting value n(K)(*) (which depends on the persistence length). For stretched chains, the Pincus blob size enters as a further characteristic length scale. The anisotropy of the scattering is well described by the modified Debye function, if the actual observed chain extension <X> (end-to-end distance in the direction of the force) as well as the corresponding longitudinal and transverse linear dimensions <X(2)> - <X>(2), <R(g,⊥)(2)> are used.
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Affiliation(s)
- Hsiao-Ping Hsu
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 7, D-55099 Mainz, Germany.
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22
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23
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Radhakrishnan R, Underhill PT. Impact of Solvent Quality on the Hysteresis in the Coil–Stretch Transition of Flexible Polymers in Good Solvents. Macromolecules 2012. [DOI: 10.1021/ma301815y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Rangarajan Radhakrishnan
- Department of Chemical
and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street,
Troy, New York 12180, United States
| | - Patrick T. Underhill
- Department of Chemical
and Biological Engineering, Rensselaer Polytechnic Institute, 110 Eighth Street,
Troy, New York 12180, United States
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24
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Landy J, McIntosh DB, Saleh OA. Quantifying screening ion excesses in single-molecule force-extension experiments. PHYSICAL REVIEW LETTERS 2012; 109:048301. [PMID: 23006113 DOI: 10.1103/physrevlett.109.048301] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Indexed: 06/01/2023]
Abstract
We derive a thermodynamic identity that allows one to infer the change in the number of screening ions that are associated with a charged macromolecule as the macromolecule is continuously stretched. Applying this identity to force-extension data on both single-stranded and double-stranded DNA, we find that the number of polymer-associated ions depends nontrivially on both the bulk salt concentration and the bare rigidity of the polymer, with single-stranded DNA exhibiting a relatively large decrease in ion excess upon stretching. We rationalize these observations using simple models for polyelectrolyte extension.
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Affiliation(s)
- Jonathan Landy
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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25
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Stevens MJ, McIntosh DB, Saleh OA. Simulations of Stretching a Strong, Flexible Polyelectrolyte. Macromolecules 2012. [DOI: 10.1021/ma300899x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mark J. Stevens
- Sandia National Laboratories, P.O. Box 5800, MS 1315, Albuquerque,
New Mexico 87185-1315, United
States
| | - Dustin B. McIntosh
- Physics Department, University of California, Santa Barbara, Santa Barbara, California 93106, United
States
| | - Omar A. Saleh
- Materials
Department and BMSE Program, University of California, Santa Barbara, Santa Barbara,
California 93106, United States
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26
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Hsu HP, Binder K. Stretching semiflexible polymer chains: evidence for the importance of excluded volume effects from Monte Carlo simulation. J Chem Phys 2012; 136:024901. [PMID: 22260610 DOI: 10.1063/1.3674303] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Semiflexible macromolecules in dilute solution under very good solvent conditions are modeled by self-avoiding walks on the simple cubic lattice (d = 3 dimensions) and square lattice (d = 2 dimensions), varying chain stiffness by an energy penalty ε(b) for chain bending. In the absence of excluded volume interactions, the persistence length l(p) of the polymers would then simply be l(p) = l(b)(2d - 2)(-1)q(b) (-1) with q(b) = exp(-ε(b)/k(B)T), the bond length l(b) being the lattice spacing, and k(B)T is the thermal energy. Using Monte Carlo simulations applying the pruned-enriched Rosenbluth method (PERM), both q(b) and the chain length N are varied over a wide range (0.005 ≤ q(b) ≤ 1, N ≤ 50,000), and also a stretching force f is applied to one chain end (fixing the other end at the origin). In the absence of this force, in d = 2 a single crossover from rod-like behavior (for contour lengths less than l(p)) to swollen coils occurs, invalidating the Kratky-Porod model, while in d = 3 a double crossover occurs, from rods to Gaussian coils (as implied by the Kratky-Porod model) and then to coils that are swollen due to the excluded volume interaction. If the stretching force is applied, excluded volume interactions matter for the force versus extension relation irrespective of chain stiffness in d = 2, while theories based on the Kratky-Porod model are found to work in d = 3 for stiff chains in an intermediate regime of chain extensions. While for q(b) ≪ 1 in this model a persistence length can be estimated from the initial decay of bond-orientational correlations, it is argued that this is not possible for more complex wormlike chains (e.g., bottle-brush polymers). Consequences for the proper interpretation of experiments are briefly discussed.
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Affiliation(s)
- Hsiao-Ping Hsu
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 7, D-55099 Mainz, Germany.
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27
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Dittmore A, McIntosh DB, Halliday S, Saleh OA. Single-molecule elasticity measurements of the onset of excluded volume in poly(ethylene glycol). PHYSICAL REVIEW LETTERS 2011; 107:148301. [PMID: 22107239 DOI: 10.1103/physrevlett.107.148301] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Indexed: 05/07/2023]
Abstract
A polymer must reach a certain size to exhibit significant excluded-volume interactions and adopt a swollen random-walk configuration. We show that single-molecule measurements can sense the onset of swelling by modulating the effective chain size with force: as the force is reduced from a large value, the polymer is first highly aligned, then a Gaussian coil, then finally a swollen chain, with each regime exhibiting a distinct elasticity. We use this approach to quantify the structural parameters of poly(ethylene glycol) and show that they vary in the expected manner with changes in solvent.
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Affiliation(s)
- Andrew Dittmore
- Materials Department, University of California, Santa Barbara, California 93106, USA
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28
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McIntosh DB, Saleh OA. Salt Species-Dependent Electrostatic Effects on ssDNA Elasticity. Macromolecules 2011. [DOI: 10.1021/ma1028196] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- D. B. McIntosh
- Physics Department, University of California, Santa Barbara, California 93106, United States
| | - O. A. Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, United States
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29
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Oliver PM, Park JS, Vezenov D. Quantitative High-Resolution Sensing of DNA Hybridization Using Magnetic Tweezers with Evanescent Illumination. NANOSCALE 2011; 3:581-91. [PMID: 21103547 PMCID: PMC3379821 DOI: 10.1039/c0nr00479k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We applied the combined approach of evanescent nanometry and force spectroscopy using magnetic tweezers to quantify the degree of hybridization of a single synthetic single-stranded DNA oligomer to a resolution approaching a single-base. In this setup, the 200 nucleotide long DNA was covalently attached to the surface of an optically transparent solid support at one end and to the surface of a superparamagnetic fluorescent microsphere (force probe) at the other end. The force was applied to the probes using an electromagnet. The end-to-end molecular distance (i.e. out-of-image-plane position of the force probe) was determined from the intensity of the probe fluorescent image observed with total-internal reflectance microscopy. An equation of state for single stranded DNA molecules under tension (extensible freely jointed chain) was used to derive the penetration depth of the evanescent field and to calibrate the magnetic properties of the force probes. The parameters of the magnetic response of the force probes obtained from the equation of state remained constant when changing the penetration depth, indicating a robust calibration procedure. The results of such a calibration were also confirmed using independently measured probe-surface distances for probes mounted onto cantilevers of an atomic force microscope. Upon hybridization of the complementary 50 nucleotide-long oligomer to the surface-bound 200-mer, the changes in the force-distance curves were consistent with the quantitative conversion of 25% of the original single-stranded DNA to its double-stranded form, which was modeled as an elastic rod. The method presented here for quantifying the hybridization state of the single DNA molecules has potential for determining the degree of hybridization of individual molecules in a single molecule array with high accuracy.
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30
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Brockman C, Kim SJ, Schroeder CM. Direct observation of single flexible polymers using single stranded DNA(). SOFT MATTER 2011; 7:8005-8012. [PMID: 22956981 PMCID: PMC3433055 DOI: 10.1039/c1sm05297g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Over the last 15 years, double stranded DNA (dsDNA) has been used as a model polymeric system for nearly all single polymer dynamics studies. However, dsDNA is a semiflexible polymer with markedly different molecular properties compared to flexible chains, including synthetic organic polymers. In this work, we report a new system for single polymer studies of flexible chains based on single stranded DNA (ssDNA). We developed a method to synthesize ssDNA for fluorescence microscopy based on rolling circle replication, which generates long strands (>65 kb) of ssDNA containing "designer" sequences, thereby preventing intramolecular base pair interactions. Polymers are synthesized to contain amine-modified bases randomly distributed along the backbone, which enables uniform labelling of polymer chains with a fluorescent dye to facilitate fluorescence microscopy and imaging. Using this approach, we synthesized ssDNA chains with long contour lengths (>30 μm) and relatively low dye loading ratios (~1 dye per 100 bases). In addition, we used epifluorescence microscopy to image single ssDNA polymer molecules stretching in flow in a microfluidic device. Overall, we anticipate that ssDNA will serve as a useful model system to probe the dynamics of polymeric materials at the molecular level.
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Affiliation(s)
- Christopher Brockman
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sun Ju Kim
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Charles M. Schroeder
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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31
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Latinwo F, Schroeder CM. Model systems for single molecule polymer dynamics. SOFT MATTER 2011; 7:7907-7913. [PMID: 22956980 PMCID: PMC3433072 DOI: 10.1039/c1sm05298e] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Double stranded DNA (dsDNA) has long served as a model system for single molecule polymer dynamics. However, dsDNA is a semiflexible polymer, and the structural rigidity of the DNA double helix gives rise to local molecular properties and chain dynamics that differ from flexible chains, including synthetic organic polymers. Recently, we developed single stranded DNA (ssDNA) as a new model system for single molecule studies of flexible polymer chains. In this work, we discuss model polymer systems in the context of "ideal" and "real" chain behavior considering thermal blobs, tension blobs, hydrodynamic drag and force-extension relations. In addition, we present monomer aspect ratio as a key parameter describing chain conformation and dynamics, and we derive dynamical scaling relations in terms of this molecular-level parameter. We show that asymmetric Kuhn segments can suppress monomer-monomer interactions, thereby altering global chain dynamics. Finally, we discuss ssDNA in the context of a new model system for single molecule polymer dynamics. Overall, we anticipate that future single polymer studies of flexible chains will reveal new insight into the dynamic behavior of "real" polymers, which will highlight the importance of molecular individualism and the prevalence of non-linear phenomena.
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Affiliation(s)
- Folarin Latinwo
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana–Champaign, UrbanaIL, 61801, USA
| | - Charles M. Schroeder
- Department of Chemical & Biomolecular Engineering, University of Illinois at Urbana–Champaign, UrbanaIL, 61801, USA
- Center for Biophysics and Computational Biology, University of Illinois at Urbana–Champaign, UrbanaIL, USA
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32
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Kosmas MK. On the Scaling Behavior of the Force/Extension Relation of a Chain. MACROMOL THEOR SIMUL 2010. [DOI: 10.1002/mats.201000037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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