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Dubrovin EV, Barinov NA, Ivanov DA, Klinov DV. Single-molecule AFM study of hyaluronic acid softening in electrolyte solutions. Carbohydr Polym 2023; 303:120472. [PMID: 36657830 DOI: 10.1016/j.carbpol.2022.120472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 11/30/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Investigation of hyaluronic acid (HA) morphology and mechanical properties at a single-molecule level is important for the development of HA based biomaterials. We have developed the atomic force microscopy (AFM) based approach for quantitative characterization of conformation of HA molecules. HA molecules adsorbed on a modified graphitic surface form oriented linear segments. Conformation of HA molecules can be considered as two-dimensional quasi-projection of a three-dimensional conformation locally straightened by a substrate. The persistence length and Young's modulus of biomolecules estimated using wormlike chain model decrease from 15.7 to 9.9 nm, and from ∼21 to ∼13 GPa, respectively, when KCl concentration increases from 0 to 100 mM. The dependence of the persistence length on ionic strength supports the Odijk-Skolnick-Fixman model of polyelectrolyte stiffening in electrolyte solution. The obtained results represent a new insight into the conformation and mechanical characteristics of HA molecules and complement the characterization of this biopolymer by bulk methods.
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Affiliation(s)
- Evgeniy V Dubrovin
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Nikolay A Barinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France.
| | - Dmitry V Klinov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation.
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2
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Zhang CY, Zhang NH. Mechanical Constraint Effect on DNA Persistence Length. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27227769. [PMID: 36431871 PMCID: PMC9696218 DOI: 10.3390/molecules27227769] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 10/31/2022] [Accepted: 11/04/2022] [Indexed: 11/16/2022]
Abstract
Persistence length is a significant criterion to characterize the semi-flexibility of DNA molecules. The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. In this work, the classical buckling theory of Euler beam and Manning's statistical theories of electrostatic force and thermal fluctuation force are combined for an isolated DNA fragment to formulate a quantitative model, which interprets the relationship between DNA persistence length and critical buckling length. Moreover, this relationship is further applied to identify the mechanical constraints in different DNA experiments by fitting the effective length factors of buckled fragments. Then, the mechanical constraint effects on DNA persistence lengths are explored. A good agreement among the results by theoretical models, previous experiments, and present molecular dynamics simulations demonstrates that the new superposition relationship including three constraint-dependent terms can effectively characterize changes in DNA persistence lengths with environmental conditions, and the strong constraint-environment coupling term dominates the significant changes of persistence lengths; via fitting effective length factors, the weakest mechanical constraints on DNAs in bulk experiments and stronger constraints on DNAs in single-molecule experiments are identified, respectively. Moreover, the consideration of DNA buckling provides a new perspective to examine the bendability of short-length DNA.
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Affiliation(s)
- Cheng-Yin Zhang
- Department of Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200444, China
| | - Neng-Hui Zhang
- Department of Mechanics, School of Mechanics and Engineering Science, Shanghai University, Shanghai 200444, China
- Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai Institute of Applied Mathematics and Mechanics, Shanghai University, Shanghai 200072, China
- Correspondence:
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3
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Fuladi S, McGuinness S, Shen L, Weber CR, Khalili-Araghi F. Molecular mechanism of claudin-15 strand flexibility: A computational study. J Gen Physiol 2022; 154:213632. [PMID: 36318156 PMCID: PMC9629798 DOI: 10.1085/jgp.202213116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 07/30/2022] [Accepted: 10/05/2022] [Indexed: 11/09/2022] Open
Abstract
Claudins are one of the major components of tight junctions that play a key role in the formation and maintenance of the epithelial barrier function. Tight junction strands are dynamic and capable of adapting their structure in response to large-scale tissue rearrangement and cellular movement. Here, we present molecular dynamics simulations of claudin-15 strands of up to 225 nm in length in two parallel lipid membranes and characterize their mechanical properties. The persistence length of claudin-15 strands is comparable with those obtained from analyses of freeze-fracture electron microscopy. Our results indicate that lateral flexibility of claudin strands is due to an interplay of three sets of interfacial interaction networks between two antiparallel double rows of claudins in the membranes. In this model, claudins are assembled into interlocking tetrameric ion channels along the strand that slide with respect to each other as the strands curve over submicrometer-length scales. These results suggest a novel molecular mechanism underlying claudin-15 strand flexibility. It also sheds light on intermolecular interactions and their role in maintaining epithelial barrier function.
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Affiliation(s)
- Shadi Fuladi
- Department of Physics, University of Illinois, Chicago, IL
| | - Sarah McGuinness
- Department of Bioengineering, University of Illinois, Chicago, IL
| | - Le Shen
- Department of Surgery, The University of Chicago, Chicago, IL
| | | | - Fatemeh Khalili-Araghi
- Department of Physics, University of Illinois, Chicago, IL,Correspondence to Fatemeh Khalili-Araghi:
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4
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Dubrovin EV, Klinov DV. Atomic Force Microscopy of Biopolymers on Graphite Surfaces. POLYMER SCIENCE SERIES A 2021. [DOI: 10.1134/s0965545x2106002x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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5
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Freedman SL, Banerjee S, Hocky GM, Dinner AR. A Versatile Framework for Simulating the Dynamic Mechanical Structure of Cytoskeletal Networks. Biophys J 2017; 113:448-460. [PMID: 28746855 DOI: 10.1016/j.bpj.2017.06.003] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 05/26/2017] [Accepted: 06/02/2017] [Indexed: 01/07/2023] Open
Abstract
Computer simulations can aid in understanding how collective materials properties emerge from interactions between simple constituents. Here, we introduce a coarse-grained model that enables simulation of networks of actin filaments, myosin motors, and cross-linking proteins at biologically relevant time and length scales. We demonstrate that the model qualitatively and quantitatively captures a suite of trends observed experimentally, including the statistics of filament fluctuations, and mechanical responses to shear, motor motilities, and network rearrangements. We use the simulation to predict the viscoelastic scaling behavior of cross-linked actin networks, characterize the trajectories of actin in a myosin motility assay, and develop order parameters to measure contractility of a simulated actin network. The model can thus serve as a platform for interpretation and design of cytoskeletal materials experiments, as well as for further development of simulations incorporating active elements.
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Affiliation(s)
- Simon L Freedman
- Department of Physics, University of Chicago, Chicago, Illinois; James Franck Institute, University of Chicago, Chicago, Illinois
| | - Shiladitya Banerjee
- Department of Physics and Astronomy, University College London, London, United Kingdom; Institute for Physics of Living Systems, University College London, London, United Kingdom
| | - Glen M Hocky
- James Franck Institute, University of Chicago, Chicago, Illinois; Department of Chemistry, University of Chicago, Chicago, Illinois
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, Illinois; Department of Chemistry, University of Chicago, Chicago, Illinois; Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois.
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6
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Paci JT, Chapman CT, Lee WK, Odom TW, Schatz GC. Wrinkles in Polytetrafluoroethylene on Polystyrene: Persistence Lengths and the Effect of Nanoinclusions. ACS APPLIED MATERIALS & INTERFACES 2017; 9:9079-9088. [PMID: 28252927 DOI: 10.1021/acsami.6b14789] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We characterize wrinkling on the surfaces of prestrained polystyrene sheets coated with thin polytetrafluoroethylene skins using a combination of mechanical strain measurements and 3D finite element simulations. The simulations show that wrinkle wavelength increases with skin thickness, in agreement with a well-known continuum model and recent experiments. The wrinkle amplitudes also increase with strain. Nanoinclusions, such as holes and patterned lines, influence wrinkle patterns over limited distances, and these distances are shown to scale with the wrinkle wavelengths. Good agreement between experimental and simulated influence distances is observed. The inclusions provide strain relief, and they behave as if they are attracting adjacent material when the sheets are under strain. The wrinkles have stiffnesses in much the same way as do polymers (but at different length scales), a property that is quantified for polymers using persistence lengths. We show that the concept of persistence length can be useful in characterizing the wrinkle properties that we have observed. However, the calculated persistence lengths do not vary systematically with thickness and strain, as interactions between neighboring wrinkles produce confinement that is analogous to the kinetic confinement of polymers.
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Affiliation(s)
- Jeffrey T Paci
- Department of Chemistry, University of Victoria , P.O. Box 3065, Victoria, British Columbia, Canada V8W 3V6
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7
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Pseudomonas aeruginosa AmrZ Binds to Four Sites in the algD Promoter, Inducing DNA-AmrZ Complex Formation and Transcriptional Activation. J Bacteriol 2016; 198:2673-81. [PMID: 27185826 DOI: 10.1128/jb.00259-16] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 05/09/2016] [Indexed: 11/20/2022] Open
Abstract
During late stages of cystic fibrosis pulmonary infections, Pseudomonas aeruginosa often overproduces the exopolysaccharide alginate, protecting the bacterial community from host immunity and antimicrobials. The transcription of the alginate biosynthesis operon is under tight control by a number of factors, including AmrZ, the focus of this study. Interestingly, multiple transcription factors interact with the far-upstream region of this promoter (PalgD), in which one AmrZ binding site has been identified previously. The mechanisms of AmrZ binding and subsequent activation remain unclear and require more-detailed investigation. In this study, in-depth examinations elucidated four AmrZ binding sites, and their disruption eliminated AmrZ binding and promoter activation. Furthermore, our in vitro fluorescence resonance energy transfer experiments suggest that AmrZ holds together multiple binding sites in PalgD and thereafter induces the formation of higher-order DNA-AmrZ complexes. To determine the importance of interactions between those AmrZ oligomers in the cell, a DNA phasing experiment was performed. PalgD transcription was significantly impaired when the relative phase between AmrZ binding sites was reversed (5 bp), while a full-DNA-turn insertion (10 bp) restored promoter activity. Taken together, the investigations presented here provide a deeper mechanistic understanding of AmrZ-mediated binding to PalgD IMPORTANCE: Overproduction of the exopolysaccharide alginate provides protection to Pseudomonas aeruginosa against antimicrobial treatments and is associated with chronic P. aeruginosa infections in the lungs of cystic fibrosis patients. In this study, we combined a variety of microbiological, genetic, biochemical, and biophysical approaches to investigate the activation of the alginate biosynthesis operon promoter by a key transcription factor named AmrZ. This study has provided important new information on the mechanism of activation of this extremely complex promoter.
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8
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Koroleva ON, Dubrovin EV, Tolstova AP, Kuzmina NV, Laptinskaya TV, Yaminsky IV, Drutsa VL. A hypothetical hierarchical mechanism of the self-assembly of the Escherichia coli RNA polymerase σ(70) subunit. SOFT MATTER 2016; 12:1974-1982. [PMID: 26758573 DOI: 10.1039/c5sm02934a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Diverse morphology of aggregates of amyloidogenic proteins has been attracting much attention in the last few years, and there is still no complete understanding of the relationships between various types of aggregates. In this work, we propose the model, which universally explains the formation of morphologically different (wormlike and rodlike) aggregates on the example of a σ(70) subunit of RNA polymerase, which has been recently shown to form amyloid fibrils. Aggregates were studied using AFM in solution and depolarized dynamic light scattering. The obtained results demonstrate comparably low Young's moduli of the wormlike structures (7.8-12.3 MPa) indicating less structured aggregation of monomeric proteins than that typical for β-sheet formation. To shed light on the molecular interaction of the protein during the aggregation, early stages of fibrillization of the σ(70) subunit were modeled using all-atom molecular dynamics. Simulations have shown that the σ(70) subunit is able to form quasi-symmetric extended dimers, which may further interact with each other and grow linearly. The proposed general model explains different pathways of σ(70) subunit aggregation and may be valid for other amyloid proteins.
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Affiliation(s)
- O N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Leninskie gory, 1/3, Moscow, 119991 Russian Federation
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9
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Dubrovin EV, Schächtele M, Schäffer TE. Nanotemplate-directed DNA segmental thermal motion. RSC Adv 2016. [DOI: 10.1039/c6ra14383k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Nanotemplate directed DNA segmental thermal motion on molecular nanotemplates on graphite was directly observed and characterized using AFM in a liquid.
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Affiliation(s)
- E. V. Dubrovin
- Lomonosov Moscow State University
- Faculty of Physics
- 119991 Moscow
- Russian Federation
- University of Tübingen
| | - M. Schächtele
- University of Tübingen
- Institute of Applied Physics
- 72076 Tübingen
- Germany
| | - T. E. Schäffer
- University of Tübingen
- Institute of Applied Physics
- 72076 Tübingen
- Germany
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10
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Yuan B, Brandt JA, Shaw S, Mohapatra P, Cademartiri L. Towards bulk syntheses of nanomaterials: a homeostatically supersaturated synthesis of polymer-like Bi 2S 3 nanowires with nearly 100% yield and no injection. RSC Adv 2016. [DOI: 10.1039/c6ra20772c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
This paper reports the implementation of a one-pot strategy for the synthesis of polymer-like Bi2S3 nanowires from supersaturated precursors.
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Affiliation(s)
- Bin Yuan
- Department of Materials Science & Engineering
- Iowa State University of Science and Technology
- Ames
- USA
- Department of Chemical & Biological Engineering
| | - Jordan Aaron Brandt
- Department of Materials Science & Engineering
- Iowa State University of Science and Technology
- Ames
- USA
| | - Santosh Shaw
- Department of Materials Science & Engineering
- Iowa State University of Science and Technology
- Ames
- USA
| | - Pratyasha Mohapatra
- Department of Materials Science & Engineering
- Iowa State University of Science and Technology
- Ames
- USA
| | - Ludovico Cademartiri
- Department of Materials Science & Engineering
- Iowa State University of Science and Technology
- Ames
- USA
- Department of Chemical & Biological Engineering
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11
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Lilledahl MB, Stokke BT. Novel imaging technologies for characterization of microbial extracellular polysaccharides. Front Microbiol 2015; 6:525. [PMID: 26074906 PMCID: PMC4446548 DOI: 10.3389/fmicb.2015.00525] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/12/2015] [Indexed: 12/20/2022] Open
Abstract
Understanding of biology is underpinned by the ability to observe structures at various length scales. This is so in a historical context and is also valid today. Evolution of novel insight often emerges from technological advancement. Recent developments in imaging technologies that is relevant for characterization of extraceullar microbiological polysaccharides are summarized. Emphasis is on scanning probe and optical based techniques since these tools offers imaging capabilities under aqueous conditions more closely resembling the physiological state than other ultramicroscopy imaging techniques. Following the demonstration of the scanning probe microscopy principle, novel operation modes to increase data capture speed toward video rate, exploitation of several cantilever frequencies, and advancement of utilization of specimen mechanical properties as contrast, also including their mode of operation in liquid, have been developed on this platform. Combined with steps in advancing light microscopy with resolution beyond the far field diffraction limit, non-linear methods, and combinations of the various imaging modalities, the potential ultramicroscopy toolbox available for characterization of exopolysaccharides (EPS) are richer than ever. Examples of application of such ultramicroscopy strategies range from imaging of isolated microbial polysaccharides, structures being observed when they are involved in polyelectrolyte complexes, aspects of their enzymatic degradation, and cell surface localization of secreted polysaccharides. These, and other examples, illustrate that the advancement in imaging technologies relevant for EPS characterization supports characterization of structural aspects.
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Affiliation(s)
| | - Bjørn T. Stokke
- Biophysics and Medical Technology, Department of Physics, The Norwegian University of Science and TechnologyTrondheim, Norway
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12
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Dubrovin EV, Speller S, Yaminsky IV. Statistical analysis of molecular nanotemplate driven DNA adsorption on graphite. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15423-15432. [PMID: 25470069 DOI: 10.1021/la5041773] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, we have studied the conformation of DNA molecules aligned on the nanotemplates of octadecylamine, stearyl alcohol, and stearic acid on highly oriented pyrolytic graphite (HOPG). For this purpose, fluctuations of contours of adsorbed biopolymers obtained from atomic force microscopy (AFM) images were analyzed using the wormlike chain model. Moreover, the conformations of adsorbed biopolymer molecules were characterized by the analysis of the scaling exponent ν, which relates the mean squared end-to-end distance and contour length of the polymer. During adsorption on octadecylamine and stearyl alcohol nanotemplates, DNA forms straight segments, which order along crystallographic axes of graphite. In this case, the conformation of DNA molecules can be described using two different length scales. On a large length scale (at contour lengths l > 200-400 nm), aligned DNA molecules have either 2D compact globule or partially relaxed 2D conformation, whereas on a short length scale (at l ≤ 200-400 nm) their conformation is close to that of rigid rods. The latter type of conformation can be also assigned to DNA adsorbed on a stearic acid nanotemplate. The different conformation of DNA molecules observed on the studied monolayers is connected with the different DNA-nanotemplate interactions associated with the nature of the functional group of the alkane derivative in the nanotemplate (amine, alcohol, or acid). The persistence length of λ-DNA adsorbed on octadecylamine nanotemplates is 31 ± 2 nm indicating the loss of DNA rigidity in comparison with its native state. Similar values of the persistence length (34 ± 2 nm) obtained for 24-times shorter DNA molecules adsorbed on an octadecylamine nanotemplate demonstrate that this rigidity change does not depend on biopolymer length. Possible reasons for the reduction of DNA persistence length are discussed in view of the internal DNA structure and DNA-surface interaction.
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Affiliation(s)
- E V Dubrovin
- Chair of Physics of Polymers and Crystals, Faculty of Physics, M. V. Lomonosov Moscow State University , Leninskie gory, 1/2, Moscow 119991, Russia
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13
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Di Pasquale N, Marchisio DL, Barresi AA, Carbone P. Solvent Structuring and Its Effect on the Polymer Structure and Processability: The Case of Water–Acetone Poly-ε-caprolactone Mixtures. J Phys Chem B 2014; 118:13258-67. [DOI: 10.1021/jp505348t] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nicodemo Di Pasquale
- Istituto
di Ingegneria Chimica, Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Daniele Luca Marchisio
- Istituto
di Ingegneria Chimica, Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Antonello Alessandro Barresi
- Istituto
di Ingegneria Chimica, Dipartimento di Scienza Applicata e Tecnologia, Politecnico di Torino, C.so Duca degli Abruzzi 24, 10129 Torino, Italy
| | - Paola Carbone
- School
of Chemical Engineering and Analytical Science, The University of Manchester, Oxford Road, Manchester, M13 9PL, United Kingdom
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14
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Rao AN, Grainger DW. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE. Biomater Sci 2014; 2:436-471. [PMID: 24765522 PMCID: PMC3992954 DOI: 10.1039/c3bm60181a] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools.
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Affiliation(s)
- Archana N. Rao
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
| | - David W. Grainger
- Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah, Salt Lake City, UT 84112 USA
- Department of Bioengineering, University of Utah, Salt Lake City, UT 84112 USA
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15
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Boroudjerdi H, Naji A, Naji A, Netz R. Global analysis of the ground-state wrapping conformation of a charged polymer on an oppositely charged nano-sphere. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2014; 37:21. [PMID: 24676863 DOI: 10.1140/epje/i2014-14021-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 02/28/2014] [Accepted: 03/03/2014] [Indexed: 06/03/2023]
Abstract
We investigate the wrapping conformations of a single, strongly adsorbed polymer chain on an oppositely charged nano-sphere by employing a reduced (dimensionless) representation of a primitive chain-sphere model. This enables us to determine the global behavior of the chain conformation in a wide range of values for the system parameters including the chain contour length, its linear charge density and persistence length as well as the nano-sphere charge and radius, and also the salt concentration in the bathing solution. The structural behavior of a charged chain-sphere complex can be described in terms of a few distinct conformational symmetry classes separated by continuous or discontinuous transition lines which are determined by means of appropriately defined (order) parameters. Our results can be applied to a wide class of strongly coupled polymer-sphere complexes including, for instance, complexes that comprise a mechanically flexible or semiflexible polymer chain or an extremely short or long chain and, as a special case, include the biologically relevant example of DNA-histone complexes.
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Affiliation(s)
- Hoda Boroudjerdi
- Fachbereich Physik, Freie Universität Berlin, Arnimalle 14, 14195, Berlin, Germany
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16
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Thomasson MS, Macnaughtan MA. Microscopy basics and the study of actin-actin-binding protein interactions. Anal Biochem 2013; 443:156-65. [PMID: 24044992 DOI: 10.1016/j.ab.2013.09.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Revised: 09/05/2013] [Accepted: 09/06/2013] [Indexed: 12/20/2022]
Abstract
Actin is a multifunctional eukaryotic protein with a globular monomer form that polymerizes into a thin, linear microfilament in cells. Through interactions with various actin-binding proteins (ABPs), actin plays an active role in many cellular processes, such as cell motility and structure. Microscopy techniques are powerful tools for determining the role and mechanism of actin-ABP interactions in these processes. In this article, we describe the basic concepts of fluorescent speckle microscopy, total internal reflection fluorescence microscopy, atomic force microscopy, and cryoelectron microscopy and review recent studies that utilize these techniques to visualize the binding of actin with ABPs.
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Affiliation(s)
- Maggie S Thomasson
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70803, USA
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17
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Sharma S, Zhu H, Grintsevich EE, Reisler E, Gimzewski JK. Correlative nanoscale imaging of actin filaments and their complexes. NANOSCALE 2013; 5:5692-702. [PMID: 23727693 PMCID: PMC4030708 DOI: 10.1039/c3nr01039b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Actin remodeling is an area of interest in biology in which correlative microscopy can bring a new way to analyze protein complexes at the nanoscale. Advances in EM, X-ray diffraction, fluorescence, and single molecule techniques have provided a wealth of information about the modulation of the F-actin structure and its regulation by actin binding proteins (ABPs). Yet, there are technological limitations of these approaches to achieving quantitative molecular level information on the structural and biophysical changes resulting from ABPs interaction with F-actin. Fundamental questions about the actin structure and dynamics and how these determine the function of ABPs remain unanswered. Specifically, how local and long-range structural and conformational changes result in ABPs induced remodeling of F-actin needs to be addressed at the single filament level. Advanced, sensitive and accurate experimental tools for detailed understanding of ABP-actin interactions are much needed. This article discusses the current understanding of nanoscale structural and mechanical modulation of F-actin by ABPs at the single filament level using several correlative microscopic techniques, focusing mainly on results obtained by Atomic Force Microscopy (AFM) analysis of ABP-actin complexes.
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Affiliation(s)
- Shivani Sharma
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
| | - Huanqi Zhu
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Elena E. Grintsevich
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
| | - Emil Reisler
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- Molecular Biology Institute, University of California, Los Angeles, California, USA
| | - James K. Gimzewski
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California, USA. Fax: +1 310 206 4038; +1 310 206 4038; Tel: +1 310 794 7514; +1 310 983 1027
- California NanoSystems Institute, University of California, Los Angeles, California, USA
- International Center for Materials Nanoarchitectonics Satellite (MANA), National Institute for Materials Science (NIMS), Tsukuba, Japan
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18
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Mendez MA, Szalai VA. Synapsable quadruplex-mediated fibers. NANOSCALE RESEARCH LETTERS 2013; 8:210. [PMID: 23641903 PMCID: PMC3655031 DOI: 10.1186/1556-276x-8-210] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/20/2013] [Indexed: 06/02/2023]
Abstract
We have fabricated a DNA-based nanofiber created by self-assembly of guanine quadruplex (Hoogsteen base pairing) and double-stranded DNA (Watson-Crick base pairing). When duplexes containing a long stretch of contiguous guanines and single-stranded overhangs are incubated in potassium-containing buffer, the preformed duplexes create high molecular weight species that contain quadruplexes. In addition to observation of these larger species by gel electrophoresis, solutions were analyzed by atomic force microscopy to reveal nanofibers. Analysis of the atomic force microscopy images indicates that fibers form with lengths ranging from 250 to 2,000 nm and heights from 0.45 to 4.0 nm. This work is a first step toward the creation of new structurally heterogeneous (quadruplex/duplex), yet controllable, DNA-based materials exhibiting novel properties suitable for a diverse array of nanotechnology applications.
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Affiliation(s)
- Miguel Angel Mendez
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD, 21250, USA
- Universidad San Francisco de Quito, Vía Interoceánica Km 2 1/2, Cumbayá, Quito, 17-1200-84, Ecuador
| | - Veronika A Szalai
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Drive, Baltimore, MD, 21250, USA
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899-6204, USA
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19
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Loong CKP, Zhou HX, Chase PB. Familial hypertrophic cardiomyopathy related E180G mutation increases flexibility of human cardiac α-tropomyosin. FEBS Lett 2012; 586:3503-7. [PMID: 22958892 DOI: 10.1016/j.febslet.2012.08.005] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Revised: 08/02/2012] [Accepted: 08/03/2012] [Indexed: 01/10/2023]
Abstract
α-Tropomyosin (αTm) is central to Ca(2+)-regulation of cardiac muscle contraction. The familial hypertrophic cardiomyopathy mutation αTm E180G enhances Ca(2+)-sensitivity in functional assays. To investigate the molecular basis, we imaged single molecules of human cardiac αTm E180G by direct probe atomic force microscopy. Analyses of tangent angles along molecular contours yielded persistence length corresponding to ~35% increase in flexibility compared to wild-type. Increased flexibility of the mutant was confirmed by fitting end-to-end length distributions to the worm-like chain model. This marked increase in flexibility can significantly impact systolic and possibly diastolic phases of cardiac contraction, ultimately leading to hypertrophy.
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Affiliation(s)
- Campion K P Loong
- Department of Biological Science, The Florida State University, Tallahassee, FL 32306-4370, USA
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20
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Li XE, Suphamungmee W, Janco M, Geeves MA, Marston SB, Fischer S, Lehman W. The flexibility of two tropomyosin mutants, D175N and E180G, that cause hypertrophic cardiomyopathy. Biochem Biophys Res Commun 2012; 424:493-6. [PMID: 22789852 DOI: 10.1016/j.bbrc.2012.06.141] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 06/26/2012] [Indexed: 01/19/2023]
Abstract
Point mutations targeting muscle thin filament proteins are the cause of a number of cardiomyopathies. In many cases, biological effects of the mutations are well-documented, whereas their structural and mechanical impact on filament assembly and regulatory function is lacking. In order to elucidate molecular defects leading to cardiac dysfunction, we have examined the structural mechanics of two tropomyosin mutants, E180G and D175N, which are associated with hypertrophic cardiomyopathy (HCM). Tropomyosin is an α-helical coiled-coil dimer which polymerizes end-to-end to create an elongated superhelix that wraps around F-actin filaments of muscle and non-muscle cells, thus modulating the binding of other actin-binding proteins. Here, we study how flexibility changes in the E180G and D175N mutants might affect tropomyosin binding and regulatory motion on F-actin. Electron microscopy and Molecular Dynamics simulations show that E180G and D175N mutations cause an increase in bending flexibility of tropomyosin both locally and globally. This excess flexibility is likely to increase accessibility of the myosin-binding sites on F-actin, thus destabilizing the low-Ca(2+) relaxed-state of cardiac muscle. The resulting imbalance in the on-off switching mechanism of the mutants will shift the regulatory equilibrium towards Ca(2+)-activation of cardiac muscle, as is observed in affected muscle, accompanied by enhanced systolic activity, diastolic dysfunction, and cardiac compensations associated with HCM and heart failure.
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Affiliation(s)
- Xiaochuan Edward Li
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA 02118, USA
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21
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Loong CKP, Zhou HX, Chase PB. Persistence length of human cardiac α-tropomyosin measured by single molecule direct probe microscopy. PLoS One 2012; 7:e39676. [PMID: 22737252 PMCID: PMC3380901 DOI: 10.1371/journal.pone.0039676] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 05/29/2012] [Indexed: 12/20/2022] Open
Abstract
α-Tropomyosin (αTm) is the predominant tropomyosin isoform in adult human heart and constitutes a major component in Ca²+-regulated systolic contraction of cardiac muscle. We present here the first direct probe images of WT human cardiac αTm by atomic force microscopy, and quantify its mechanical flexibility with three independent analysis methods. Single molecules of bacterially-expressed human cardiac αTm were imaged on poly-lysine coated mica and their contours were analyzed. Analysis of tangent-angle (θ(s)) correlation along molecular contours, second moment of tangent angles (<θ²(s)>), and end-to-end length (L(e-e)) distributions respectively yielded values of persistence length (L(p)) of 41-46 nm, 40-45 nm, and 42-52 nm, corresponding to 1-1.3 molecular contour lengths (L(c)). We also demonstrate that a sufficiently large population, with at least 100 molecules, is required for a reliable L(p) measurement of αTm in single molecule studies. Our estimate that L(p) for αTm is only slightly longer than L(c) is consistent with a previous study showing there is little spread of cooperative activation into near-neighbor regulatory units of cardiac thin filaments. The L(p) determined here for human cardiac αTm perhaps represents an evolutionarily tuned optimum between Ca²+ sensitivity and cooperativity in cardiac thin filaments and likely constitutes an essential parameter for normal function in the human heart.
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Affiliation(s)
- Campion K. P. Loong
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- Department of Physics, Florida State University, Tallahassee, Florida, United States of America
- * E-mail: (PBC) (CKPL)
| | - Huan-Xiang Zhou
- Department of Physics, Florida State University, Tallahassee, Florida, United States of America
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - P. Bryant Chase
- Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America
- * E-mail: (PBC) (CKPL)
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22
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Abstract
The advent of new technologies allowing the study of single biological molecules continues to have a major impact on studies of interacting systems as well as enzyme reactions. These approaches (fluorescence, optical, and magnetic tweezers), in combination with ensemble methods, have been particularly useful for mechanistic studies of protein-nucleic acid interactions and enzymes that function on nucleic acids. We review progress in the use of single-molecule methods to observe and perturb the activities of proteins and enzymes that function on flexible single-stranded DNA. These include single-stranded DNA binding proteins, recombinases (RecA/Rad51), and helicases/translocases that operate as motor proteins and play central roles in genome maintenance. We emphasize methods that have been used to detect and study the movement of these proteins (both ATP-dependent directional and random movement) along the single-stranded DNA and the mechanistic and functional information that can result from detailed analysis of such movement.
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Affiliation(s)
- Taekjip Ha
- Department of Physics and the Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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23
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Vafabakhsh R, Lee KS, Ha T. Recent Advances in Studying Mechanical Properties of DNA. ADVANCES IN CHEMICAL PHYSICS 2012. [DOI: 10.1002/9781118197714.ch4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
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24
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Govedarica B, Sovány T, Pintye-Hódi K, Škarabot M, Baumgartner S, Muševič I, Srčič S. Addressing potent single molecule AFM study in prediction of swelling and dissolution rate in polymer matrix tablets. Eur J Pharm Biopharm 2012; 80:217-25. [DOI: 10.1016/j.ejpb.2011.09.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2011] [Accepted: 09/12/2011] [Indexed: 10/17/2022]
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25
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Boroudjerdi H, Naji A, Netz RR. Salt-modulated structure of polyelectrolyte-macroion complex fibers. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011; 34:72. [PMID: 21792745 DOI: 10.1140/epje/i2011-11072-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2011] [Accepted: 06/21/2011] [Indexed: 05/31/2023]
Abstract
The structure and stability of strongly charged complex fibers, formed by complexation of a single long semi-flexible polyelectrolyte chain and many oppositely charged spherical macroions, are investigated numerically at the ground-state level using a chain-sphere cell model. The model takes into account chain elasticity as well as electrostatic interactions between charged spheres and chain segments. Using a numerical optimization method based on a periodically repeated unit cell, we obtain fiber configurations that minimize the total energy. The optimal fiber configurations exhibit a variety of helical structures for the arrangement of macroions including zig-zag, solenoidal and beads-on-a-string patterns. These structures result from the competition between attraction between spheres and the polyelectrolyte chain (which favors chain wrapping around the spheres), chain bending rigidity and electrostatic repulsion between chain segments (which favor unwrapping of the chain), and the interactions between neighboring sphere-chain complexes which can be attractive or repulsive depending on the system parameters such as salt concentration, macroion charge and chain length per macroion (linker size). At about physiological salt concentration, dense zig-zag patterns are found to be energetically most stable when parameters appropriate for the DNA-histone system in the chromatin fiber are adopted. In fact, the predicted fiber diameter in this regime is found to be around 30 nanometers, which roughly agrees with the thickness observed in in vitro experiments on chromatin. We also find a macroion (histone) density of 5-6 per 11nm which agrees with results from the zig-zag or cross-linker models of chromatin. Since our study deals primarily with a generic chain-sphere model, these findings suggest that structures similar to those found for chromatin should also be observable for polyelectrolyte-macroion complexes formed in solutions of DNA and synthetic nano-colloids of opposite charge. In the ensemble where the mean linear density of spheres on the chain is fixed, the present model predicts a phase separation at intermediate salt concentrations into a densely packed complex phase and a dilute phase.
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Affiliation(s)
- Hoda Boroudjerdi
- Department of Physics, Technical University of Munich, 85748 Garching, Germany
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26
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Machado JAT, Costa AC, Quelhas MD. Wavelet analysis of human DNA. Genomics 2011; 98:155-63. [PMID: 21672622 DOI: 10.1016/j.ygeno.2011.05.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2011] [Revised: 05/21/2011] [Accepted: 05/27/2011] [Indexed: 10/18/2022]
Abstract
This paper studies the human DNA in the perspective of signal processing. Six wavelets are tested for analyzing the information content of the human DNA. By adopting real Shannon wavelet several fundamental properties of the code are revealed. A quantitative comparison of the chromosomes and visualization through multidimensional and dendograms is developed.
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Affiliation(s)
- J A Tenreiro Machado
- Institute of Engineering of Porto, Dept. of Electrical Engineering, Rua Dr. António Bernardino de Almeida, 431, 4200-072 Porto, Portugal.
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27
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Gallyamov MO. Scanning Force Microscopy as Applied to Conformational Studies in Macromolecular Research. Macromol Rapid Commun 2011; 32:1210-46. [DOI: 10.1002/marc.201100150] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 04/06/2011] [Indexed: 01/17/2023]
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28
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Uemura H, Ichikawa M, Kimura Y. Crossover behavior in static and dynamic properties of a single DNA molecule from three to quasi-two dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 81:051801. [PMID: 20866253 DOI: 10.1103/physreve.81.051801] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Indexed: 05/29/2023]
Abstract
We studied the conformation and dynamics of a single DNA molecule in a thin slit by a fluorescent microscope. In a slit thinner than the Flory radius in three dimensions, the length of the major axis, the translational self-diffusion coefficient and the rotational relaxation time in a dilute solution show the apparent dependence on the thickness of the slit. The observed dependence is in agreement with that predicted by blob theory, despite the number of blobs is very small. The radial distribution of the segments around the center of mass of a single molecule was also studied and compared with that calculated for a Gaussian and an excluded volume chain. The influence of the polymer concentration on the geometrical confinement by slits was also studied in a semidilute solution near the overlap concentration c∗. The confinement effect is found to be not so serious near c∗ and is only significant in the so-called "two-dimensional pancake" region.
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Affiliation(s)
- Hitoshi Uemura
- Department of Physics, School of Sciences, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan
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29
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Sivakumar L, Agarwal G. The influence of discoidin domain receptor 2 on the persistence length of collagen type I fibers. Biomaterials 2010; 31:4802-8. [PMID: 20346496 DOI: 10.1016/j.biomaterials.2010.02.070] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 02/26/2010] [Indexed: 10/19/2022]
Abstract
Collagen fibers in the vertebrate tissue are responsible for its tensile strength. A disruption in the morphological or mechanical properties of collagen fibers is bound to impact tensile strength and contractility of tissues and affect several cellular processes. We had recently established that binding of discoidin domain receptor (DDR2) with collagen type I results in disruption of the native structure and morphology of collagen fibers. In this study we investigate if DDR2 affects the mechanical properties of collagen fibers. We used an analytical approach to determine the persistence length (P(L)) of collagen fibers from transmission electron microscope images of immobilized collagen. Fluctuations in the curvature of collagen fibers formed in-vitro (with or without recombinant DDR2) were analyzed to ascertain their P(L). The P(L) values and fiber-diameter measurements were utilized to estimate Young's Modulus (E) of collagen fibers. Our results show that DDR2 significantly reduced P(L) and E of collagen fibers. We further found that P(L) for native collagen fibers increases as a function of collagen concentration with little dependence on fiber diameter. These results signify a physiological role of DDR2 in modulating extracellular matrix stiffness, which may be of relevance for tissue engineering and medical implants especially in diseases where DDR2 is upregulated.
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Affiliation(s)
- Lalitha Sivakumar
- Department of Biomedical Engineering, The Ohio State University, 270 Bevis Hall, 1080 Carmack Road, Columbus, OH 43210, USA
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30
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The effect of underlying octadecylamine monolayer on the DNA conformation on the graphite surface. Colloids Surf B Biointerfaces 2010; 76:63-9. [DOI: 10.1016/j.colsurfb.2009.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2009] [Revised: 09/25/2009] [Accepted: 10/08/2009] [Indexed: 11/19/2022]
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31
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The relationship between curvature, flexibility and persistence length in the tropomyosin coiled-coil. J Struct Biol 2010; 170:313-8. [PMID: 20117217 DOI: 10.1016/j.jsb.2010.01.016] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 01/25/2010] [Accepted: 01/25/2010] [Indexed: 01/29/2023]
Abstract
The inherent flexibility of rod-like tropomyosin coiled-coils is a significant factor that constrains tropomyosin's complex positional dynamics on actin filaments. Flexibility of elongated straight molecules typically is assessed by persistence length, a measure of lengthwise thermal bending fluctuations. However, if a molecule's equilibrium conformation is curved, this formulation yields an "apparent" persistence length ( approximately 100nm for tropomyosin), measuring deviations from idealized straight conformations which then overestimate actual dynamic flexibility. To obtain the "dynamic" persistence length, a true measurement of flexural stiffness, the average curvature of the molecule must be taken into account. Different methods used in our studies for measuring the dynamic persistence length directly from Molecular Dynamics (MD) simulations of tropomyosin are described here in detail. The dynamic persistence length found, 460+/-40nm, is approximately 12-times longer than tropomyosin and 5-times the apparent persistence length, showing that tropomyosin is considerably stiffer than previously thought. The longitudinal twisting behavior of tropomyosin during MD shows that the amplitude of end-to-end twisting fluctuation is approximately 30 degrees when tropomyosin adopts its near-average conformation. The measured bending and twisting flexibilities are used to evaluate different models of tropomyosin motion on F-actin.
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32
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Abstract
The determination of the contour length of DNA imaged by either electron microscopy or atomic force microscopy is frequently required for investigating the physical properties of nucleic acids. Nevertheless, these measurements are often carried out with methods that are not optimized for the curvilinear shape of DNA or are too complex to be of practical use. The aim of this study is to provide a method for the contour length measurements of DNA that is accurate, practical, and computationally simple. Computer simulated DNA fragments were used as experimental benchmarks in order to compute the coefficients a and b of the (n(e), n(o))-characterization [L(n(e),n(o)) = an(e) + bn(o)] so as to minimize the error of the measurements. The data show that, at variance with straight lines, a DNA length estimator depends on both the DNA flexibility and the image resolution, but it is independent of the DNA contour length. A table with DNA estimators to be used for length measurements of digitized contours obtained under commonly used imaging conditions is provided. Although the method has been developed using DNA as a benchmark, its applicability can be extended to other polymers as well as to other imaging techniques.
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Affiliation(s)
- Claudio Rivetti
- Department of Biochemistry and Molecular Biology, University of Parma, Parma 43100, Italy.
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33
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WU J, DENG X, ZHANG Y, WANG L, TIAN BQ, XIE BJ. Application of Atomic Force Microscopy in the Study of Polysaccharide. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/s1671-2927(08)60359-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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34
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Mücke N, Klenin K, Kirmse R, Bussiek M, Herrmann H, Hafner M, Langowski J. Filamentous biopolymers on surfaces: atomic force microscopy images compared with Brownian dynamics simulation of filament deposition. PLoS One 2009; 4:e7756. [PMID: 19888472 PMCID: PMC2768466 DOI: 10.1371/journal.pone.0007756] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Accepted: 09/30/2009] [Indexed: 11/19/2022] Open
Abstract
Nanomechanical properties of filamentous biopolymers, such as the persistence length, may be determined from two-dimensional images of molecules immobilized on surfaces. For a single filament in solution, two principal adsorption scenarios are possible. Both scenarios depend primarly on the interaction strength between the filament and the support: i) For interactions in the range of the thermal energy, the filament can freely equilibrate on the surface during adsorption; ii) For interactions much stronger than the thermal energy, the filament will be captured by the surface without having equilibrated. Such a ‘trapping’ mechanism leads to more condensed filament images and hence to a smaller value for the apparent persistence length. To understand the capture mechanism in more detail we have performed Brownian dynamics simulations of relatively short filaments by taking the two extreme scenarios into account. We then compared these ‘ideal’ adsorption scenarios with observed images of immobilized vimentin intermediate filaments on different surfaces. We found a good agreement between the contours of the deposited vimentin filaments on mica (‘ideal’ trapping) and on glass (‘ideal’ equilibrated) with our simulations. Based on these data, we have developed a strategy to reliably extract the persistence length of short worm-like chain fragments or network forming filaments with unknown polymer-surface interactions.
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Affiliation(s)
- Norbert Mücke
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Konstantin Klenin
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Robert Kirmse
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Malte Bussiek
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
| | - Harald Herrmann
- Department of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany
| | - Mathias Hafner
- Institute of Molecular and Cell Biology, University of Applied Sciences Mannheim, Mannheim, Germany
| | - Jörg Langowski
- Division Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, Germany
- * E-mail:
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35
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Faas FGA, Rieger B, van Vliet LJ, Cherny DI. DNA deformations near charged surfaces: electron and atomic force microscopy views. Biophys J 2009; 97:1148-57. [PMID: 19686663 DOI: 10.1016/j.bpj.2009.06.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2009] [Revised: 06/03/2009] [Accepted: 06/11/2009] [Indexed: 10/20/2022] Open
Abstract
DNA is a very important cell structural element, which determines the level of expression of genes by virtue of its interaction with regulatory proteins. We use electron (EM) and atomic force microscopy (AFM) to characterize the flexibility of double-stranded DNA ( approximately 150-950 nm long) close to a charged surface. Automated procedures for the extraction of DNA contours ( approximately 10-120 nm for EM data and approximately 10-300 nm for AFM data) combined with new statistical chain descriptors indicate a uniquely two-dimensional equilibration of the molecules on the substrate surface regardless of the procedure of molecule mounting. However, in contrast to AFM, the EM mounting leads to a noticeable decrease in DNA persistence length together with decreased kurtosis. Analysis of local bending on short length scales (down to 6 nm in the EM study) shows that DNA flexibility behaves as predicted by the wormlike chain model. We therefore argue that adhesion of DNA to a charged surface may lead to additional static bending (kinking) of approximately 5 degrees per dinucleotide step without impairing the dynamic behavior of the DNA backbone. Implications of this finding are discussed.
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Affiliation(s)
- F G A Faas
- Department of Imaging Science and Technology Delft University of Technology, Delft, The Netherlands
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36
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Ge H, Jin F, Li J, Wu C. How Much Force Is Needed To Stretch a Coiled Chain in Solution? Macromolecules 2009. [DOI: 10.1021/ma9005523] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui Ge
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Fan Jin
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
| | - Junfang Li
- The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, The University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Chi Wu
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong
- The Hefei National Laboratory of Physical Science at Microscale, Department of Chemical Physics, The University of Science and Technology of China, Hefei, Anhui 230026, China
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37
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Sbrana F, Fanelli D, Vassalli M, Carresi L, Scala A, Pazzagli L, Cappugi G, Tiribilli B. Progressive pearl necklace collapse mechanism for cerato-ulmin aggregation film. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2009; 39:971-7. [DOI: 10.1007/s00249-009-0465-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2009] [Revised: 04/21/2009] [Accepted: 04/29/2009] [Indexed: 12/01/2022]
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38
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Rittman M, Gilroy E, Koohy H, Rodger A, Richards A. Is DNA a worm-like chain in Couette flow? In search of persistence length, a critical review. Sci Prog 2009; 92:163-204. [PMID: 19697713 PMCID: PMC10361128 DOI: 10.3184/003685009x462205] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Persistence length is the foremost measure of DNA flexibility. Its origins lie in polymer theory which was adapted for DNA following the determination of BDNA structure in 1953. There is no single definition of persistence length used, and the links between published definitions are based on assumptions which may, or may not be, clearly stated. DNA flexibility is affected by local ionic strength, solvent environment, bound ligands and intrinsic sequence-dependent flexibility. This article is a review of persistence length providing a mathematical treatment of the relationships between four definitions of persistence length, including: correlation, Kuhn length, bending, and curvature. Persistence length has been measured using various microscopy, force extension and solution methods such as linear dichroism and transient electric birefringence. For each experimental method a model of DNA is required to interpret the data. The importance of understanding the underlying models, along with the assumptions required by each definition to determine a value of persistence length, is highlighted for linear dichroism data, where it transpires that no model is currently available for long DNA or medium to high shear rate experiments.
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Affiliation(s)
- Martyn Rittman
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Emma Gilroy
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Hashem Koohy
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
| | - Alison Rodger
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Adair Richards
- Molecular Organisation and Assembly in Cells Doctoral Training Centre
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Griffin J, Singh A, Senapati D, Rhodes P, Mitchell K, Robinson B, Yu E, Ray P. Size- and Distance-Dependent Nanoparticle Surface-Energy Transfer (NSET) Method for Selective Sensing of Hepatitis C Virus RNA. Chemistry 2008; 15:342-51. [DOI: 10.1002/chem.200801812] [Citation(s) in RCA: 179] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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40
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Douarche C, Cortès R, Roser SJ, Sikorav JL, Braslau A. DNA Adsorption at Liquid/Solid Interfaces. J Phys Chem B 2008; 112:13676-9. [DOI: 10.1021/jp807759d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Carine Douarche
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Robert Cortès
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Steven J. Roser
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Jean-Louis Sikorav
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
| | - Alan Braslau
- Physique de la Matière Condensée École Polytechnique, CNRS, 91128 Palaiseau, France, Institut de Recherche Interdisciplinaire, Cité Scientifique, Avenue Poincaré BP 60069, 59652 Villeneuve d’Ascq Cedex, France, Department of Chemistry, University of Bath, Bath, Avon, U.K. BA2 7AY, Service de Biologie Intégrative et de Génétique Moléculaire, Institut de Physique Théorique, CNRS URA 2306, and Service de Physique de l′État Condensé, CNRS URA 2464, CEA/Saclay, 91191 Gif-sur-Yvette Cedex, France
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41
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Griffin J, Ray PC. Gold nanoparticle based NSET for monitoring Mg2+ dependent RNA folding. J Phys Chem B 2008; 112:11198-201. [PMID: 18702540 DOI: 10.1021/jp8059322] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the mechanism of how RNA molecules fold into their native structures are vital to their functional properties. Here we report for the first time that gold nanoparticle based NSET can be used for probing the transition states of an RNA unfolding reaction. Our result shows that time-dependent NSET can clearly distinguish structural transitions between unfolded to folded states. Our experimental observation point out that NSET can be used for the design of an optical based molecular ruler to track RNA folding transition states at distances more than double the distances achievable using traditional dipole-dipole Coulombic energy transfer based methods.
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Affiliation(s)
- Jelani Griffin
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217-0510, USA
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42
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Douarche C, Cortès R, Henry de Villeneuve C, Roser SJ, Braslau A. DNA adsorption at functionalized Si/buffer interfaces studied by x-ray reflectivity. J Chem Phys 2008; 128:225108. [DOI: 10.1063/1.2927256] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Nanopore-based DNA analysis is a single-molecule technique with revolutionary potential. It promises to carry out a range of analyses, orders of magnitude faster than current methods, including length measurement, specific sequence detection, single-molecule dynamics and even de novo sequencing. The concept involves using an applied voltage to drive DNA molecules through a narrow pore that separates chambers of electrolyte solution. This voltage also drives a flow of electrolyte ions through the pore, measured as an electric current. When molecules pass through the pore, they block the flow of ions and, thus, their structure and length can be determined based on the degree and duration of the resulting current reductions. In this review, I explain the nanopore-based DNA analysis concept and briefly explore its historical foundations, before discussing and summarizing all experimental results reported to date. I conclude with a summary of the obstacles that must be overcome for it to realize its promised potential.
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Affiliation(s)
- Ken Healy
- University College Cork, Department of Electrical and Electronic Engineering, Ireland.
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Manning GS. The persistence length of DNA is reached from the persistence length of its null isomer through an internal electrostatic stretching force. Biophys J 2006; 91:3607-16. [PMID: 16935960 PMCID: PMC1630458 DOI: 10.1529/biophysj.106.089029] [Citation(s) in RCA: 163] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2006] [Accepted: 08/09/2006] [Indexed: 11/18/2022] Open
Abstract
To understand better the effect of electrostatics on the rigidity of the DNA double helix, we define DNA*, the null isomer of DNA, as the hypothetical structure that would result from DNA if its phosphate groups were not ionized. For the purposes of theoretical analysis, we model DNA* as identical to ordinary DNA but supplemented by a longitudinal compression force equal in magnitude but oppositely directed to the stretching (tension) force on DNA caused by phosphate-phosphate repulsions. The null isomer DNA* then becomes an elastically buckled form of fully ionized DNA. On this basis, we derive a nonadditive relationship between the persistence length P of DNA and the persistence length P* of its null isomer. From the formula obtained we can predict the value of P* if P is known, and we can predict the ionic strength dependence of P under the assumption that P* does not depend on ionic strength. We predict a value of P* for null DNA drastically lower than the value of P for DNA in its ordinary state of fully ionized phosphates. The predicted dependence of P on salt concentration is log-c over most of the concentration range, with no tendency toward a salt-independent value in the range of validity of the theory. The predictions are consistent with much of the persistence-length data available for DNA. Alternate theories of the Odijk-Skolnik-Fixman type, including one by the author, are considered skeptically on the grounds that the underlying model may not be realistic. Specifically, we doubt the accuracy for real polyelectrolytes of the Odijk-Skolnik-Fixman assumption that the polymer structure is invariant to changes in electrostatic forces.
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Affiliation(s)
- Gerald S Manning
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, USA.
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Ray PC, Fortner A, Darbha GK. Gold Nanoparticle Based FRET Asssay for the Detection of DNA Cleavage. J Phys Chem B 2006; 110:20745-8. [PMID: 17048879 DOI: 10.1021/jp065121l] [Citation(s) in RCA: 112] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report gold nanoparticle based FRET assay to monitor the cleavage of DNA by nucleases. Fluorescence signal enhancement is observed by a factor of 120 after the cleavage reaction in the presence of S1 nuclease. The mechanism of distant dependent fluorescence quenching has been discussed. Our experimental results on distance dependent fluorescence quenching match quite well with theoretical findings obtained from the fluorescence quenching model by Gersten and Nitzan (Surf. Sci. 1985, 158, 165). Our experimental observation paradigm for the design of optical based molecular ruler strategies at distances more than double the distances achievable using traditional dipole-dipole Columbic energy transfer based methods.
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Zhao Y, Mahajan N, Fang J. Bending and Radial Deformation of Lipid Tubules on Self-Assembled Thiol Monolayers. J Phys Chem B 2006; 110:22060-3. [PMID: 17078640 DOI: 10.1021/jp0550199] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Lipid tubules represent a hollow, cylindrical supramolecular structure formed by rolled-up lipid bilayers. We find that the lipid tubules of 1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine can be bent into a loopike shape by the shrinking contact line of droplets on self-assembled monolayers (SAMs) of 1-dodecanethiol. The persistence length of individual lipid tubules is estimated to be approximately 41 microm. The radial deformation of the lipid tubules on SAMs is studied under applied load using atomic force microscope. The stiffness of the tubules in the radial direction is found to increase when the number of the lipid bilayers in the tubule wall increases.
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Affiliation(s)
- Yue Zhao
- Advanced Materials Processing and Analysis Center and Department of Mechanical, Materials, and Aerospace Engineering, University of Central Florida, Orlando, Florida 32816, USA
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Samorì P, Surin M, Palermo V, Lazzaroni R, Leclère P. Functional polymers: scanning force microscopy insights. Phys Chem Chem Phys 2006; 8:3927-38. [PMID: 17028683 DOI: 10.1039/b607502a] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Scanning force microscopy (SFM) and related techniques make it possible to visualize polymer systems with a molecular resolution. Beyond imaging, they also enable the unveiling of a variety of (dynamic) physico-chemical properties of both isolated polymer chains and their supramolecular architectures, including structural, mechanical and electronic properties. This article reviews recent progress in the use of SFM on polymers, with a particular emphasis on the mechanical properties of copolymers and single polymer chains, as well as on the bottom-up fabrication of supramolecular polymeric (helical) nanostructures in particular based upon pi-conjugated macromolecules as building blocks for nanoelectronics. Through a detailed understanding of the polymer behavior, we propose solutions for the generation of organic functional (nano)systems.
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Affiliation(s)
- Paolo Samorì
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, via Gobetti, 101, I-40129 Bologna, Italy.
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Pastré D, Piétrement O, Landousy F, Hamon L, Sorel I, David MO, Delain E, Zozime A, Le Cam E. A new approach to DNA bending by polyamines and its implication in DNA condensation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 35:214-23. [PMID: 16247626 DOI: 10.1007/s00249-005-0025-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2005] [Revised: 07/28/2005] [Accepted: 08/02/2005] [Indexed: 11/30/2022]
Abstract
Polyamines are known to induce dynamical bending of DNA molecules. This mechanism is very important since many DNA binding proteins (DNAse, transcription factor, etc.) exert their action by their ability to bend DNA. We propose an analytical model which describes the dynamical bending of DNA by polyamine ions in highly diluted DNA solutions. The bending probability depends on the entropy loss of polyamines due to their localization. This localization is facilitated by the electrostatic repulsion between multivalent counterions condensed on DNA, which reduces the entropy loss in counterion localization. Therefore DNA bending by polyamines depends on the competition between monovalent counterions and polyamines. We find that the bending probability is weak for a low binding ratio of polyamines (i.e. number of bound polyamines per base pair), whereas a high bending probability can be reached at large polyamine binding ratio. In addition, we describe a new mechanism of DNA bending. It occurs with the help of thermal agitation, which initiates the bending and favours the polyamine localization. This model provides further insights into DNA bending by polyamines and its implication in DNA condensation. A qualitative estimation of the DNA bending probability is obtained by measuring the cleavage efficiency of DNA by bleomycin versus spermidine concentration. Indeed, a local helix distortion by polyamines results in an amplification of the double-strand cleavage by bleomycin. The measurement of the bleomycin amplification is performed by analysing images of DNA molecules with atomic force microscope. Some features of the dynamical bending indicate that condensation and bending are interrelated.
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Affiliation(s)
- David Pastré
- Laboratoire d'Etude des Milieux Nanométriques, Université d'Evry, Rue du Père Jarlan, 91025 Evry Cedex, France.
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Guérin G, Raez J, Manners I, Winnik MA. Light Scattering Study of Rigid, Rodlike Organometallic Block Copolymer Micelles in Dilute Solution. Macromolecules 2005. [DOI: 10.1021/ma0498870] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gérald Guérin
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Jose Raez
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Ian Manners
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
| | - Mitchell A. Winnik
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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Podestà A, Indrieri M, Brogioli D, Manning GS, Milani P, Guerra R, Finzi L, Dunlap D. Positively charged surfaces increase the flexibility of DNA. Biophys J 2005; 89:2558-63. [PMID: 16040760 PMCID: PMC1366755 DOI: 10.1529/biophysj.105.064667] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Many proteins "bind" DNA through positively charged amino acids on their surfaces. However, to overcome significant energetic and topological obstacles, proteins that bend or package DNA might also modulate the stiffness that is generated by repulsions between phosphates within DNA. Much previous work describes how ions change the flexibility of DNA in solution, but when considering macromolecules such as chromatin in which the DNA contacts the nucleosome core each turn of the double helix, it may be more appropriate to assess the flexibility of DNA on charged surfaces. Mica coated with positively charged molecules is a convenient substrate upon which the flexibility of DNA may be directly measured with a scanning force microscope. In the experiments described below, the flexibility of DNA increased as much as fivefold depending on the concentration and type of polyamine used to coat mica. Using theory that relates charge neutralization to flexibility, we predict that phosphate repulsions were attenuated by approximately 50% in the most flexible DNA observed. This simple method is an important tool for investigating the physiochemical causes and molecular biological effects of DNA flexibility, which affects DNA biochemistry ranging from chromatin stability to viral encapsulation.
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Affiliation(s)
- Alessandro Podestà
- Department of Physics, INFM and CIMAINA, and Department of Biology and CIMAINA, University of Milan, Milan, Italy
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