1
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Tafech B, Rokhforouz MR, Leung J, Sung MM, Lin PJ, Sin DD, Lauster D, Block S, Quon BS, Tam Y, Cullis P, Feng JJ, Hedtrich S. Exploring Mechanisms of Lipid Nanoparticle-Mucus Interactions in Healthy and Cystic Fibrosis Conditions. Adv Healthc Mater 2024; 13:e2304525. [PMID: 38563726 DOI: 10.1002/adhm.202304525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 03/05/2024] [Indexed: 04/04/2024]
Abstract
Mucus forms the first defense line of human lungs, and as such hampers the efficient delivery of therapeutics to the underlying epithelium. This holds particularly true for genetic cargo such as CRISPR-based gene editing tools which cannot readily surmount the mucosal barrier. While lipid nanoparticles (LNPs) emerge as versatile non-viral gene delivery systems that can help overcome the delivery challenge, many knowledge gaps remain, especially for diseased states such as cystic fibrosis (CF). This study provides fundamental insights into Cas9 mRNA or ribonucleoprotein-loaded LNP-mucus interactions in healthy and diseased states by assessing the impact of the genetic cargo, mucin sialylation, mucin concentration, ionic strength, pH, and polyethylene glycol (PEG) concentration and nature on LNP diffusivity leveraging experimental approaches and Brownian dynamics (BD) simulations. Taken together, this study identifies key mucus and LNP characteristics that are critical to enabling a rational LNP design for transmucosal delivery.
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Affiliation(s)
- Belal Tafech
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Mohammad-Reza Rokhforouz
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Jerry Leung
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Molly Mh Sung
- Acuitas Therapeutics, Vancouver, BC, V6T 1Z3, Canada
| | - Paulo Jc Lin
- Acuitas Therapeutics, Vancouver, BC, V6T 1Z3, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Daniel Lauster
- Institute of Pharmacy, Biopharmaceuticals, Freie Universität Berlin, 12169, Berlin, Germany
| | - Stephan Block
- Institute of Organic Chemistry, Freie Universität Berlin, 14195, Berlin, Germany
| | - Bradley S Quon
- Centre for Heart Lung Innovation, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Faculty of Medicine, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Adult Cystic Fibrosis Clinic, St Paul's Hospital, Vancouver, BC, V6Z 1Y6, Canada
| | - Ying Tam
- Acuitas Therapeutics, Vancouver, BC, V6T 1Z3, Canada
| | - Pieter Cullis
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - James J Feng
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- Department of Mathematics, University of British Columbia, Vancouver, BC, V6T 1Z2, Canada
| | - Sarah Hedtrich
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
- Center of Biological Design, Berlin Institute of Health at Charité, Universitätsmedizin Berlin, Berlin, Germany
- Department of Infectious Diseases and Respiratory Medicine, Charité, Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt Universität zu Berlin, Berlin, Germany
- Max-Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
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2
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G Lopez C, Matsumoto A, Shen AQ. Dilute polyelectrolyte solutions: recent progress and open questions. SOFT MATTER 2024; 20:2635-2687. [PMID: 38427030 DOI: 10.1039/d3sm00468f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Polyelectrolytes are a class of polymers possessing ionic groups on their repeating units. Since counterions can dissociate from the polymer backbone, polyelectrolyte chains are strongly influenced by electrostatic interactions. As a result, the physical properties of polyelectrolyte solutions are significantly different from those of electrically neutral polymers. The aim of this article is to highlight key results and some outstanding questions in the polyelectrolyte research from recent literature. We focus on the influence of electrostatics on conformational and hydrodynamic properties of polyelectrolyte chains. A compilation of experimental results from the literature reveals significant disparities with theoretical predictions. We also discuss a new class of polyelectrolytes called poly(ionic liquid)s that exhibit unique physical properties in comparison to ordinary polyelectrolytes. We conclude this review by listing some key research challenges in order to fully understand the conformation and dynamics of polyelectrolytes in solutions.
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Affiliation(s)
- Carlos G Lopez
- Institute of Physical Chemistry, RWTH Aachen University, Aachen, 52056, Germany
| | - Atsushi Matsumoto
- Department of Applied Chemistry and Biotechnology, Graduate School of Engineering, University of Fukui, 3-9-1 Bunkyo, Fukui City, Fukui 910-8507, Japan.
| | - Amy Q Shen
- Micro/Bio/Nanofluidics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan.
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3
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Wang T, Coshic K, Badiee M, Aksimentiev A, Pollack L, Leung AKL. Length-dependent Intramolecular Coil-to-Globule Transition in Poly(ADP-ribose) Induced by Cations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.25.564012. [PMID: 37961637 PMCID: PMC10634823 DOI: 10.1101/2023.10.25.564012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Poly(ADP-ribose) (PAR), as part of a post-translational modification, serves as a flexible scaffold for noncovalent protein binding. Such binding is influenced by PAR chain length through a mechanism yet to be elucidated. Structural insights have been elusive, partly due to the difficulties associated with synthesizing PAR chains of defined lengths. Here, we employ an integrated approach combining molecular dynamics (MD) simulations with small-angle X-ray scattering (SAXS) experiments, enabling us to identify highly heterogeneous ensembles of PAR conformers at two different, physiologically relevant lengths: PAR 15 and PAR 22 . Our findings reveal that numerous factors including backbone conformation, base stacking, and chain length contribute to determining the structural ensembles. We also observe length-dependent compaction of PAR upon the addition of small amounts of Mg 2+ ions, with the 22-mer exhibiting ADP-ribose bundles formed through local intramolecular coil-to-globule transitions. This study illuminates how such bundling could be instrumental in deciphering the length-dependent action of PAR. GRAPHICAL ABSTRACT
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4
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Sampl C, Schaubeder J, Hirn U, Spirk S. Interplay of electrolyte concentration and molecular weight of polyDADMAC on cellulose surface adsorption. Int J Biol Macromol 2023; 239:124286. [PMID: 37011749 DOI: 10.1016/j.ijbiomac.2023.124286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/13/2023] [Accepted: 03/28/2023] [Indexed: 04/04/2023]
Abstract
Cationic polyelectrolytes (PEs) are commonly used additives in manufacturing of cellulose based products such as regenerated fibers and paper to tailor their product properties. Here we are studying the adsorption of poly(diallyldimethylammonium chloride), PD, on cellulose, using in situ surface plasmon resonance spectroscopy (SPR) measurements. We employ model surfaces from regenerated cellulose xanthate (CX) and trimethylsilyl cellulose (TMSC), mimicking industrially relevant regenerated cellulose substrates. The effects of the PDs molecular weight were strongly depending on the ionic strength and type of electrolyte (NaCl vs CaCl2). Without electrolytes, the adsorption was monolayer-type, i.e. independent of molecular weight. At moderate ionic strength, adsorption increased due to more pronounced PE coiling, while at high ionic strength electrostatic shielding strongly reduced adsorption of PDs. Results exhibited pronounced differences for the chosen substrates (cellulose regenerated from xanthate (CXreg) vs. regenerated from trimethylsilyl cellulose, TMSCreg). Consistently higher adsorbed amounts of the PD were determined on CXreg surfaces compared TMSC. This can be attributed to a more negative zeta potential, a higher AFM roughness and a higher degree of swelling (investigated by QCM-D) of the CXreg substrates.
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5
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Sun LZ, Qian JL, Cai P, Hu HX, Xu X, Luo MB. Mg2+ effects on the single-stranded DNA conformations and nanopore translocation dynamics. POLYMER 2022. [DOI: 10.1016/j.polymer.2022.124895] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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6
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Si DQ, Liu XY, Wu JB, Hu GH. Modulation of DNA conformation in electrolytic nanodroplets. Phys Chem Chem Phys 2022; 24:6002-6010. [PMID: 35199810 DOI: 10.1039/d1cp05329a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The behavior of deoxyribonucleic acid (DNA) molecules in confinement is of profound importance in various bioengineering and medical applications. In the present study, all-atom molecular dynamics simulation is utilized to investigate the transition of the double-strand DNA (dsDNA) conformation in the electrolytic nanodroplet. Three typical conformations, i.e., C-shaped, folded S-shaped, and double C-shaped, are observed for different droplet sizes and ionic concentrations. To reveal the physics underlying this phenomenon, the characteristics of the dsDNA molecules, such as the overcharging intensity, the end-to-end distance, the radius of gyration, etc. are analyzed in detail based on the numerical results. It is found that the transition can be ascribed to the buckling of the polymer molecules under the compression due to the confinement of the nanodroplet, and it can be modulated by the ionic concentration in the electrolyte. Generally, nanoscale confinement dominates dsDNA behavior over the electrostatic effects in smaller nanodroplets, while the latter becomes more important for larger nanodroplets. This competition results in the persistence length increasing with the nanodroplet radii. Based on these discussions, a non-dimensional elasto-capillary number μ is proposed to classify the dsDNA conformations into three regions.
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Affiliation(s)
- Dong-Qing Si
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Xin-Yue Liu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
| | - Jin-Bo Wu
- Materials Genome Institute, Shanghai University, Shanghai 200444, China
| | - Guo-Hui Hu
- Shanghai Institute of Applied Mathematics and Mechanics, School of Mechanics and Engineering Science, Shanghai Key Laboratory of Mechanics in Energy Engineering, Shanghai University, Shanghai 200072, China.
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7
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Yang Q, Li W, Stober ST, Burns AB, Gopinadhan M, Martini A. Molecular Dynamics Simulation of the Stress–Strain Behavior of Polyamide Crystals. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00974] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Quanpeng Yang
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
| | - Wenjun Li
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, New Jersey 08801, United States
| | - Spencer T. Stober
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, New Jersey 08801, United States
| | - Adam B. Burns
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, New Jersey 08801, United States
| | - Manesh Gopinadhan
- ExxonMobil Research and Engineering Company, 1545 Route 22 East, Annandale, New Jersey 08801, United States
| | - Ashlie Martini
- Department of Mechanical Engineering, University of California-Merced, 5200 N. Lake Road, Merced, California 95343, United States
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8
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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021. [PMID: 34584211 DOI: 10.1101/2020.10.03.322354v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA
- The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.
- Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA.
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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9
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Bashirzadeh Y, Redford SA, Lorpaiboon C, Groaz A, Moghimianavval H, Litschel T, Schwille P, Hocky GM, Dinner AR, Liu AP. Actin crosslinker competition and sorting drive emergent GUV size-dependent actin network architecture. Commun Biol 2021; 4:1136. [PMID: 34584211 PMCID: PMC8478941 DOI: 10.1038/s42003-021-02653-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
The proteins that make up the actin cytoskeleton can self-assemble into a variety of structures. In vitro experiments and coarse-grained simulations have shown that the actin crosslinking proteins α-actinin and fascin segregate into distinct domains in single actin bundles with a molecular size-dependent competition-based mechanism. Here, by encapsulating actin, α-actinin, and fascin in giant unilamellar vesicles (GUVs), we show that physical confinement can cause these proteins to form much more complex structures, including rings and asters at GUV peripheries and centers; the prevalence of different structures depends on GUV size. Strikingly, we found that α-actinin and fascin self-sort into separate domains in the aster structures with actin bundles whose apparent stiffness depends on the ratio of the relative concentrations of α-actinin and fascin. The observed boundary-imposed effect on protein sorting may be a general mechanism for creating emergent structures in biopolymer networks with multiple crosslinkers. By encapsulating proteins in giant unilamellar vesicles, Bashirzadeh et al find that actin crosslinkers, α-actinin and fascin, can self-assemble with actin into complex structures that depend on the degree of confinement. Further analysis and modeling show that α-actinin and fascin sort to separate domains of these structures. These insights may be generalizable to other biopolymer networks containing crosslinkers.
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Affiliation(s)
- Yashar Bashirzadeh
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Steven A Redford
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.,The graduate program in Biophysical Sciences, University of Chicago, Chicago, IL, 60637, USA
| | | | - Alessandro Groaz
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA.,Department of Neuroscience, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Thomas Litschel
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.,John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, 02138, USA
| | - Petra Schwille
- Department of Cellular and Molecular Biophysics, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Glen M Hocky
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Aaron R Dinner
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA. .,Department of Chemistry, University of Chicago, Chicago, IL, 60637, USA.
| | - Allen P Liu
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI, 48109, USA. .,Department of Biophysics, University of Michigan, Ann Arbor, MI, 48109, USA. .,Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, 48109, USA.
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10
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Plumridge A, Andresen K, Pollack L. Visualizing Disordered Single-Stranded RNA: Connecting Sequence, Structure, and Electrostatics. J Am Chem Soc 2019; 142:109-119. [PMID: 31804813 DOI: 10.1021/jacs.9b04461] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Disordered homopolymeric regions of single-stranded RNA, such as U or A tracts, are found within functional RNAs where they play distinct roles in defining molecular structure and facilitating recognition by partners. Despite this prominence, details of conformational and biophysical properties of these regions have not yet been resolved. We apply a number of experimental techniques to investigate the conformations of these biologically important motifs and provide quantitative measurements of their ion atmospheres. Single strands of RNA display pronounced sequence-dependent conformations that relate to the unique ion atmospheres each attracts. Chains of rU bases are relatively unstructured under all conditions, while chains of rA bases display distinct ordering through stacking or clustering motifs, depending on the composition of the surrounding solution. These dramatic structural differences are consistent with the measured disparity in ion composition and atmospheres around each homopolymer, revealing a complex interplay of base, ion, and single-strand ordering. The unique structural and ionic signatures of homopolymer ssRNAs explains their role(s) in folding structured RNAs and may explain their distinct recognition by protein partners.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
| | - Kurt Andresen
- Department of Physics , Gettysburg College , Gettysburg , Pennsylvania 17325 , United States
| | - Lois Pollack
- School of Applied and Engineering Physics , Cornell University , Ithaca , New York 14853 , United States
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11
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Pavlov GM, Dommes OA, Okatova OV, Gavrilova II, Panarin EF. Influence of Electrostatic Long-Range and Short-Range Effects on the Conformations of Flexible-Chain Linear Polyelectrolyte Macromolecules with Different Charge Density in Salt-Free Aqueous Solutions. POLYMER SCIENCE SERIES A 2019. [DOI: 10.1134/s0965545x19060087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Fong KD, Self J, Diederichsen KM, Wood BM, McCloskey BD, Persson KA. Ion Transport and the True Transference Number in Nonaqueous Polyelectrolyte Solutions for Lithium Ion Batteries. ACS CENTRAL SCIENCE 2019; 5:1250-1260. [PMID: 31403073 PMCID: PMC6661974 DOI: 10.1021/acscentsci.9b00406] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Indexed: 05/14/2023]
Abstract
Nonaqueous polyelectrolyte solutions have been recently proposed as high Li+ transference number electrolytes for lithium ion batteries. However, the atomistic phenomena governing ion diffusion and migration in polyelectrolytes are poorly understood, particularly in nonaqueous solvents. Here, the structural and transport properties of a model polyelectrolyte solution, poly(allyl glycidyl ether-lithium sulfonate) in dimethyl sulfoxide, are studied using all-atom molecular dynamics simulations. We find that the static structural analysis of Li+ ion pairing is insufficient to fully explain the overall conductivity trend, necessitating a dynamic analysis of the diffusion mechanism, in which we observe a shift from largely vehicular transport to more structural diffusion as the Li+ concentration increases. Furthermore, we demonstrate that despite the significantly higher diffusion coefficient of the lithium ion, the negatively charged polyion is responsible for the majority of the solution conductivity at all concentrations, corresponding to Li+ transference numbers much lower than previously estimated experimentally. We quantify the ion-ion correlations unique to polyelectrolyte systems that are responsible for this surprising behavior. These results highlight the need to reconsider the approximations typically made for transport in polyelectrolyte solutions.
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Affiliation(s)
- Kara D. Fong
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Julian Self
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Kyle M. Diederichsen
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Brandon M. Wood
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Bryan D. McCloskey
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
| | - Kristin A. Persson
- Department
of Chemical and Biomolecular Engineering, Department of Materials Science and Engineering, and Department of Applied
Science and Technology, University of California, Berkeley, California 94720, United States
- Energy
Technologies Area, Lawrence Berkeley National
Laboratory, Berkeley, California 94720, United States
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13
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Kim YC, Shin TJ, Hur SM, Kwon SJ, Kim SY. Shear-solvo defect annihilation of diblock copolymer thin films over a large area. SCIENCE ADVANCES 2019; 5:eaaw3974. [PMID: 31214653 PMCID: PMC6570509 DOI: 10.1126/sciadv.aaw3974] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 05/03/2019] [Indexed: 05/21/2023]
Abstract
Achieving defect-free block copolymer (BCP) nanopatterns with a long-ranged orientation over a large area remains a persistent challenge, impeding the successful and widespread application of BCP self-assembly. Here, we demonstrate a new experimental strategy for defect annihilation while conserving structural order and enhancing uniformity of nanopatterns. Sequential shear alignment and solvent vapor annealing generate perfectly aligned nanopatterns with a low defect density over centimeter-scale areas, outperforming previous single or sequential combinations of annealing. The enhanced order quality and pattern uniformity were characterized in unprecedented detail via scattering analysis and incorporating new mathematical indices using elaborate image processing algorithms. In addition, using an advanced sampling method combined with a coarse-grained molecular simulation, we found that domain swelling is the driving force for enhanced defect annihilation. The superior quality of large-scale nanopatterns was further confirmed with diffraction and optical properties after metallized patterns, suggesting strong potential for application in optoelectrical devices.
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Affiliation(s)
- Ye Chan Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
| | - Tae Joo Shin
- UNIST Central Research Facilities and School of Natural Science, UNIST, Ulsan 44919, Republic of Korea
| | - Su-Mi Hur
- School of Polymer Science and Engineering, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seok Joon Kwon
- Nanophotonics Research Center, Korea Institute of Science and Technology, Seongbuk-Gu, Seoul 02792, Republic of Korea
| | - So Youn Kim
- School of Energy and Chemical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Republic of Korea
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14
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Emamyari S, Fazli H. Single-Chain Conformational Characteristics of Comb-Like Polyelectrolytes: Molecular Dynamics Simulation Study. Macromol Res 2018. [DOI: 10.1007/s13233-019-7010-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Jin L, Shi YZ, Feng CJ, Tan YL, Tan ZJ. Modeling Structure, Stability, and Flexibility of Double-Stranded RNAs in Salt Solutions. Biophys J 2018; 115:1403-1416. [PMID: 30236782 DOI: 10.1016/j.bpj.2018.08.030] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/10/2018] [Accepted: 08/24/2018] [Indexed: 11/16/2022] Open
Abstract
Double-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability, and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability, and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions for 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions for thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that the thermally unfolding pathway of dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix, and the calculated salt-dependent persistence lengths are in good accordance with experiments.
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Affiliation(s)
- Lei Jin
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Zhou Shi
- Research Center of Nonlinear Science, School of Mathematics and Computer Science, Wuhan Textile University, Wuhan, China
| | - Chen-Jie Feng
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Ya-Lan Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China
| | - Zhi-Jie Tan
- Center for Theoretical Physics and Key Laboratory of Artificial Micro- & Nanostructures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, China.
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16
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Bleha T, Cifra P. Correlation anisotropy and stiffness of DNA molecules confined in nanochannels. J Chem Phys 2018; 149:054903. [PMID: 30089382 DOI: 10.1063/1.5034219] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The anisotropy of orientational correlations in DNA molecules confined in cylindrical channels is explored by Monte Carlo simulations using a coarse-grained model of double-stranded (ds) DNA. We find that the correlation function ⟨C(s)⟩⊥ in the transverse (confined) dimension exhibits a region of negative values in the whole range of channel sizes. Such a clear-cut sign of the opposite orientation of chain segments represents a microscopic validation of the Odijk deflection mechanism in narrow channels. At moderate-to-weak confinement, the negative ⟨C(s)⟩⊥ correlations imply a preference of DNA segments for transverse looping. The inclination for looping can explain a reduction of stiffness as well as the enhanced knotting of confined DNA relative to that detected earlier in bulk at some channel sizes. Furthermore, it is shown that the orientational persistence length Por fails to convey the apparent stiffness of DNA molecules in channels. Instead, correlation lengths P∥ and P⊥ in the axial and transverse directions, respectively, encompass the channel-induced modifications of DNA stiffness.
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Affiliation(s)
- Tomáš Bleha
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
| | - Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, 84541 Bratislava, Slovakia
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17
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Huang J, Liu X, Thormann E. Surface Forces between Highly Charged Cationic Polyelectrolytes Adsorbed to Silica: How Control of pH and the Adsorbed Amount Determines the Net Surface Charge. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:7264-7271. [PMID: 29864283 DOI: 10.1021/acs.langmuir.8b00909] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Atomic force microscopy (AFM) and quartz crystal microbalance with dissipation (QCM-D) were employed to investigate the pH-dependent adsorption of poly(diallyldimethylammonium chloride) (polyDADMAC) to silica surfaces as well as the surface forces between these layers. It was found that polyDADMAC adopted a relatively flat conformation when adsorbed to a silica surface and that the adsorbed amount increased with increasing pH. From the surface force measurements it is evident that the surface undergoes a charge reversal upon saturation with polyDADMAC, at the three different investigated pH values, and that some degree of charge regulation of the silica surface takes place during the adsorption process. Finally, the overcharging phenomenon is discussed in terms of a geometrical mismatch due to the different average spacing between the surface charges on the silica surface and the size of the DADMAC monomer.
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18
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Berezney JP, Marciel AB, Schroeder CM, Saleh OA. Scale-Dependent Stiffness and Internal Tension of a Model Brush Polymer. PHYSICAL REVIEW LETTERS 2017; 119:127801. [PMID: 29341644 DOI: 10.1103/physrevlett.119.127801] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Indexed: 06/07/2023]
Abstract
Bottle-brush polymers exhibit closely grafted side chains that interact by steric repulsion, thereby causing stiffening of the main polymer chain. We use single-molecule elasticity measurements of model brush polymers to quantify this effect. We find that stiffening is only significant on long length scales, with the main chain retaining flexibility on short scales. From the elasticity data, we extract an estimate of the internal tension generated by side-chain repulsion; this estimate is consistent with the predictions of blob-based scaling theories.
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Affiliation(s)
- John P Berezney
- Materials Department, University of California, Santa Barbara, California 93106, USA
| | - Amanda B Marciel
- Institute for Molecular Engineering, The University of Chicago, Chicago, Illinois 60637, USA
| | - Charles M Schroeder
- Department of Chemical and Biomolecular Engineering, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Champaign, Illinois 61801, USA
| | - Omar A Saleh
- Materials Department and BMSE Program, University of California, Santa Barbara, California 93106, USA
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19
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Plumridge A, Meisburger SP, Pollack L. Visualizing single-stranded nucleic acids in solution. Nucleic Acids Res 2017; 45:e66. [PMID: 28034955 PMCID: PMC5435967 DOI: 10.1093/nar/gkw1297] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 12/09/2016] [Accepted: 12/13/2016] [Indexed: 02/06/2023] Open
Abstract
Single-stranded nucleic acids (ssNAs) are ubiquitous in many key cellular functions. Their flexibility limits both the number of high-resolution structures available, leaving only a small number of protein-ssNA crystal structures, while forcing solution investigations to report ensemble averages. A description of the conformational distributions of ssNAs is essential to more fully characterize biologically relevant interactions. We combine small angle X-ray scattering (SAXS) with ensemble-optimization methods (EOM) to dynamically build and refine sets of ssNA structures. By constructing candidate chains in representative dinucleotide steps and refining the models against SAXS data, a broad array of structures can be obtained to match varying solution conditions and strand sequences. In addition to the distribution of large scale structural parameters, this approach reveals, for the first time, intricate details of the phosphate backbone and underlying strand conformations. Such information on unperturbed strands will critically inform a detailed understanding of an array of problems including protein-ssNA binding, RNA folding and the polymer nature of NAs. In addition, this scheme, which couples EOM selection with an iteratively refining pool to give confidence in the underlying structures, is likely extendable to the study of other flexible systems.
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Affiliation(s)
- Alex Plumridge
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | | | - Lois Pollack
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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20
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Luzhbin DA, Chen YL. Shifting the Isotropic–Nematic Transition in Very Strongly Confined Semiflexible Polymer Solutions. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00986] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Dmytro A. Luzhbin
- Institute of Physics, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan, R.O.C
- Department of Physics, National Taiwan University, Taipei, Taiwan, R.O.C
| | - Yeng-Long Chen
- Institute of Physics, Academia Sinica, Taipei, Taiwan, R.O.C
- Department of Chemical Engineering, National Tsing-Hua University, Hsinchu, Taiwan, R.O.C
- Department of Physics, National Taiwan University, Taipei, Taiwan, R.O.C
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21
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Granzotti CRF, Martinez AS, da Silva MAA. Scaling analysis of random walks with persistence lengths: Application to self-avoiding walks. Phys Rev E 2016; 93:052116. [PMID: 27300839 DOI: 10.1103/physreve.93.052116] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Indexed: 11/07/2022]
Abstract
We develop an approach for performing scaling analysis of N-step random walks (RWs). The mean square end-to-end distance, 〈R[over ⃗]_{N}^{2}〉, is written in terms of inner persistence lengths (IPLs), which we define by the ensemble averages of dot products between the walker's position and displacement vectors, at the jth step. For RW models statistically invariant under orthogonal transformations, we analytically introduce a relation between 〈R[over ⃗]_{N}^{2}〉 and the persistence length, λ_{N}, which is defined as the mean end-to-end vector projection in the first step direction. For self-avoiding walks (SAWs) on 2D and 3D lattices we introduce a series expansion for λ_{N}, and by Monte Carlo simulations we find that λ_{∞} is equal to a constant; the scaling corrections for λ_{N} can be second- and higher-order corrections to scaling for 〈R[over ⃗]_{N}^{2}〉. Building SAWs with typically 100 steps, we estimate the exponents ν_{0} and Δ_{1} from the IPL behavior as function of j. The obtained results are in excellent agreement with those in the literature. This shows that only an ensemble of paths with the same length is sufficient for determining the scaling behavior of 〈R[over ⃗]_{N}^{2}〉, being that the whole information needed is contained in the inner part of the paths.
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Affiliation(s)
- C R F Granzotti
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Avenida Bandeirantes 3900, CEP 14040-901, Ribeirão Preto, São Paulo, Brazil
| | - A S Martinez
- Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP), Universidade de São Paulo (USP), Avenida Bandeirantes 3900, CEP 14040-901, Ribeirão Preto, São Paulo, Brazil
| | - M A A da Silva
- Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP), Universidade de São Paulo (USP), Avenida Bandeirantes 3900, CEP 14040-901, Ribeirão Preto, São Paulo, Brazil
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22
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Wang FH, Wu YY, Tan ZJ. Salt contribution to the flexibility of single-stranded nucleic acid offinite length. Biopolymers 2016; 99:370-81. [PMID: 23529689 DOI: 10.1002/bip.22189] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 11/18/2012] [Indexed: 12/15/2022]
Abstract
Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this article, the salt effects on the flexibility of single-stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse-grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual-bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and both trivalent/small divalent ions can induce more compact state than a random relaxation state. We found that monovalent, divalent, and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion-exclusion-volume effect to ion Coulomb correlations. In addition, the predicted Na(+) and Mg(2+)-dependent persistence length l(p)'s of ss nucleic acid are in accordance with the available experimental data, and through systematic calculations, we obtained the empirical formulas for l(p) as a function of [Na(+)], [Mg(2+)] and chain length.
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Affiliation(s)
- Feng-Hua Wang
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-structures of Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan, 430072, China
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23
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Chremos A, Douglas JF. Counter-ion distribution around flexible polyelectrolytes having different molecular architecture. SOFT MATTER 2016; 12:2932-2941. [PMID: 26864861 DOI: 10.1039/c5sm02873f] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We explore the monovalent counter-ion distribution around flexible highly-charged polyelectrolytes with different molecular architectures (linear chains, stars, and unknotted and trefoil rings) using molecular dynamics simulations that include an explicit solvent that interacts with the polyelectrolyte. In particular, we find that the molecular topology influences the fraction of counter-ions transiently associating with the polyelectrolyte on a scale of the order of the chain segments, forming a "condensed" counter-ion interfacial layer. As with the hydrogen bonding of water to proteins and other polymers, the persistence time of these interfacial "bound" counter-ions is relatively short, O(1 ps), and we characterize the fluctuations in the number of the counter-ions populating the interfacial layer. We also find that the counter-ions are distributed in a non-uniform fashion on the polyelectrolyte backbone, forming dynamical clusters whose form and average size is sensitive to molecular architecture. In addition, we find that the residual bound counter-ions, not located in either the interfacial layer or the bulk solution, form a diffuse ionic cloud around the polyelectrolyte due to the uncompensated polyelectrolyte charge along the backbone. Generally charge valence strongly influences the extent of the diffuse counter-ion cloud, but in the case of monovalent counter-ions, we find that the size of the diffuse counter-ion cloud nearly coincides with the polyelectrolyte radius of gyration, independent of molecular topology.
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Affiliation(s)
- Alexandros Chremos
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
| | - Jack F Douglas
- Materials Science and Engineering Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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24
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Henke PS, Mak CH. An implicit divalent counterion force field for RNA molecular dynamics. J Chem Phys 2016; 144:105104. [DOI: 10.1063/1.4943387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Affiliation(s)
- Paul S. Henke
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
| | - Chi H. Mak
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
- Center of Applied Mathematical Sciences, University of Southern California, Los Angeles, California 90089, USA
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25
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Chremos A, Douglas JF. Impact of Monovalent Counter-ions on the Conformation of Flexible Polyelectrolytes Having Different Molecular Architectures. ACTA ACUST UNITED AC 2016. [DOI: 10.1557/adv.2016.122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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26
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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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27
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Markegard CB, Fu IW, Reddy KA, Nguyen HD. Coarse-grained simulation study of sequence effects on DNA hybridization in a concentrated environment. J Phys Chem B 2015; 119:1823-34. [PMID: 25581253 DOI: 10.1021/jp509857k] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A novel coarse-grained model is developed to elucidate thermodynamics and kinetic mechanisms of DNA self-assembly. It accounts for sequence and solvent conditions to capture key experimental results such as sequence-dependent thermal property and salt-dependent persistence length of ssDNA and dsDNA. Moreover, constant-temperature simulations on two single strands of a homogeneous sequence show two main mechanisms of hybridization: a slow slithering mechanism and a one-order faster zippering mechanism. Furthermore, large-scale simulations at a high DNA strand concentration demonstrate that DNA self-assembly is a robust and enthalpically driven process in which the formation of double helices is deciphered to occur via multiple self-assembly pathways including the strand displacement mechanism. However, sequence plays an important role in shifting the majority of one pathway over the others and controlling size distribution of self-assembled aggregates. This study yields a complex picture on the role of sequence on programmable self-assembly and demonstrates a promising simulation tool that is suitable for studies in DNA nanotechnology.
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Affiliation(s)
- Cade B Markegard
- Department of Chemical Engineering and Materials Science, University of California-Irvine , Irvine, California 92697-2575, United States
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28
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Jacobson DR, Saleh OA. Measuring the differential stoichiometry and energetics of ligand binding to macromolecules by single-molecule force spectroscopy: an extended theory. J Phys Chem B 2015; 119:1930-8. [PMID: 25621932 DOI: 10.1021/jp511555g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Many chemical techniques exist for measuring the stoichiometry of ligand binding to a macromolecule; however, these techniques are often specific to certain ligands or require the presumption of specific binding models. Here, we further develop a previously reported, general, thermodynamic method for extracting the change in number of ligands bound to a macromolecule as that macromolecule undergoes a conformational transition driven by mechanical stretching, for example, by magnetic tweezers or optical trapping. We extend the theory of this method to consider systems with many ligands, experiments conducted in different thermodynamic ensembles (e.g., constant-force, constant-extension), and experiments in which the system is not at equilibrium. Further, we show that analysis of the same single-molecule mechanical manipulation data yields a measure of the differential free energy of stabilization due to ligand binding, that is, the free energy contribution by which ligand binding favors one conformation of the macromolecule over another. We interpret an existing data set measuring ion binding to RNA and DNA in terms of this free energy.
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Affiliation(s)
- David R Jacobson
- Department of Physics, and ‡Materials Department and BMSE Program, University of California , Santa Barbara, California 93106, United States
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29
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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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30
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Angelescu DG, Linse P. Branched-linear polyion complexes investigated by Monte Carlo simulations. SOFT MATTER 2014; 10:6047-6058. [PMID: 24999910 DOI: 10.1039/c4sm01055h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Complexes formed by one charged and branched copolymer with an oppositely charged and linear polyion have been investigated by Monte Carlo simulations. A coarse-grained description has been used, in which the main chain of the branched polyion and the linear polyion possess the same absolute charge and charge density. The spatial extension and other structural properties, such as bond-angle orientational correlation function, asphericity, and scaling analysis of formed complexes, at varying branching density and side-chain length of the branched polyion, have been explored. In particular, the balance between cohesive Coulomb attraction and side-chain repulsions resulted in two main structures of a polyion complex. These structures are (i) a globular polyion core surrounded by side chains appearing at low branching density and (ii) an extended polyion core with side chains still being expelled at high branching density. The globule-to-extended transition occurred at a crossover branching density being practically independent of the side chain length.
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Affiliation(s)
- Daniel G Angelescu
- Romanian Academy, "Ilie Murgulescu" Institute of Physical Chemistry, Splaiul Independentei 202, 060021 Bucharest, Romania.
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31
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Dias R, Rosa M, Pais AC, Miguel M, Lindman B. DNA-Surfactant Interactions. Compaction, Condensation, Decompaction and Phase Separation. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200400069] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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32
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Strong and Weak Polyelectrolyte Adsorption onto Oppositely Charged Curved Surfaces. POLYELECTROLYTE COMPLEXES IN THE DISPERSED AND SOLID STATE I 2013. [DOI: 10.1007/12_2012_183] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Cranford SW, Buehler MJ. Variation of Weak Polyelectrolyte Persistence Length through an Electrostatic Contour Length. Macromolecules 2012. [DOI: 10.1021/ma3008465] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Steven W. Cranford
- Center for Materials Science
and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-235A&B, Cambridge, Massachusetts 02139, United States
| | - Markus J. Buehler
- Center for Materials Science
and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United
States
- Laboratory for Atomistic and Molecular Mechanics, Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-235A&B, Cambridge, Massachusetts 02139, United States
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34
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Elder RM, Jayaraman A. Coarse-Grained Simulation Studies of Effects of Polycation Architecture on Structure of the Polycation and Polycation–Polyanion Complexes. Macromolecules 2012. [DOI: 10.1021/ma3011944] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Robert M. Elder
- Department of Chemical and Biological
Engineering, University of Colorado, 3415
Colorado Avenue, UCB 596,
Boulder, Colorado 80303, United States
| | - Arthi Jayaraman
- Department of Chemical and Biological
Engineering, University of Colorado, 3415
Colorado Avenue, UCB 596,
Boulder, Colorado 80303, United States
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35
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Bačová P, Košovan P, Uhlík F, Kuldová J, Limpouchová Z, Procházka K. Double-exponential decay of orientational correlations in semiflexible polyelectrolytes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2012; 35:53. [PMID: 22733112 DOI: 10.1140/epje/i2012-12053-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Accepted: 05/31/2012] [Indexed: 06/01/2023]
Abstract
In this paper we revisited the problem of persistence length of polyelectrolytes. We performed a series of Molecular Dynamics simulations using the Debye-Hückel approximation for electrostatics to test several equations which go beyond the classical description of Odijk, Skolnick and Fixman (OSF). The data confirm earlier observations that in the limit of large contour separations the decay of orientational correlations can be described by a single-exponential function and the decay length can be described by the OSF relation. However, at short countour separations the behaviour is more complex. Recent equations which introduce more complicated expressions and an additional length scale could describe the results very well on both the short and the long length scale. The equation of Manghi and Netz when used without adjustable parameters could capture the qualitative trend but deviated in a quantitative comparison. Better quantitative agreement within the estimated error could be obtained using three equations with one adjustable parameter: 1) the equation of Manghi and Netz; 2) the equation proposed by us in this paper; 3) the equation proposed by Cannavacciuolo and Pedersen. Two characteristic length scales can be identified in the data: the intrinsic or bare persistence length and the electrostatic persistence length. All three equations use a single parameter to describe a smooth crossover from the short-range behaviour dominated by the intrinsic stiffness of the chain to the long-range OSF-like behaviour.
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Affiliation(s)
- P Bačová
- Materials Physics Center CSIC-UPV/EHU, University of the Basque Country, San Sebastián, Spain.
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36
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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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37
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Campbell RA, Yanez Arteta M, Angus-Smyth A, Nylander T, Varga I. Effects of Bulk Colloidal Stability on Adsorption Layers of Poly(diallyldimethylammonium Chloride)/Sodium Dodecyl Sulfate at the Air–Water Interface Studied by Neutron Reflectometry. J Phys Chem B 2011; 115:15202-13. [DOI: 10.1021/jp2088803] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Richard A. Campbell
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
| | - Marianna Yanez Arteta
- Department of Physical Chemistry, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Anna Angus-Smyth
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
- Department of Chemistry, Durham University, South Road, DH1 3LE, United Kingdom
| | - Tommy Nylander
- Department of Physical Chemistry, Lund University, P.O. Box 124, S-221 00 Lund, Sweden
| | - Imre Varga
- Institute of Chemistry, Eötvös Loránd University, Budapest 112, P.O. Box 32, H-1518 Hungary
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39
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Liu X, Vesterinen AH, Genzer J, Seppälä JV, Rojas OJ. Adsorption of PEO-PPO-PEO triblock copolymers with end-capped cationic chains of poly(2-dimethylaminoethyl methacrylate). LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:9769-9780. [PMID: 21721578 DOI: 10.1021/la201596x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We study the adsorption of a symmetric triblock copolymer of ethylene oxide, EO, and propylene oxide, PO, end-capped with quarternized poly(2-dimethylaminoethyl methacrylate), DMAEMA (DMAEMA(24)-EO(132)PO(50)EO(132)-DMAEMA(24)). Light scattering and tensiometry are used to measure the relative size of the associated structures and surface excess at the air-liquid interface. The adsorbed amount, the amount of coupled water, and the viscoelasticity of the adsorbed polymer layer are measured on hydrophobic and hydrophilic surfaces (polypropylene, cellulose, and silica) by using quartz crystal microgravimetry (QCM) and surface plasmon resonance (SPR) at different ionic strengths and temperatures. The results of the experiments are compared with those obtained after adsorption of the uncharged precursor copolymer, without the cationic end-caps (EO(132)PO(50)EO(132)). DMAEMA(24)-EO(132)PO(50)EO(132)-DMAEMA(24) possesses higher affinity with the negatively charged silica and cellulose surfaces while the uncharged copolymer adsorbs to a larger extent on polypropylene surfaces. In this latter case, adsorption increases with increasing solution ionic strength and temperature. Adsorption of EO(132)PO(50)EO(132) on silica surfaces has little effect on the water contact angle (WCA), while adsorption of DMAEMA(24)-EO(132)PO(50)EO(132)-DMAEMA(24) increases the WCA of silica to 32°, indicating a large density of exposed PPO blocks upon adsorption. After adsorption of EO(132)PO(50)EO(132) and DMAEMA(24)-EO(132)PO(50)EO(132)-DMAEMA(24) on PP, the WCA is reduced by ≈14° and ≈28°, respectively, due to the exposed hydrophilic EO and highly water-soluble DMAEMA segments on the surfaces. The extent of surface coverage at saturation at the polypropylene/liquid interfaces (≈31 and 40 nm(2)/molecule obtained by QCM and SPR, respectively) is much lower, as expected, when compared with results obtained at the air/liquid interface, where a tighter packing is observed. The percentage of water coupled to the adsorbed cationic polymer decreases with solution ionic strength. Overall, these observations are ascribed to the effects of electrostatic screening, polymer hydrodynamic size, and solvency.
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Affiliation(s)
- Xiaomeng Liu
- Department of Forest Biomaterials, North Carolina State University, Raleigh, North Carolina 27695, United States
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40
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Saywell A, Sprafke JK, Esdaile LJ, Britton AJ, Rienzo A, Anderson HL, O'Shea JN, Beton PH. Conformation and Packing of Porphyrin Polymer Chains Deposited Using Electrospray on a Gold Surface. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201004896] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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41
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Saywell A, Sprafke JK, Esdaile LJ, Britton AJ, Rienzo A, Anderson HL, O'Shea JN, Beton PH. Conformation and Packing of Porphyrin Polymer Chains Deposited Using Electrospray on a Gold Surface. Angew Chem Int Ed Engl 2010; 49:9136-9. [DOI: 10.1002/anie.201004896] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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42
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Cifra P, Benková Z, Bleha T. Persistence length of DNA molecules confined in nanochannels. Phys Chem Chem Phys 2010; 12:8934-42. [PMID: 20589298 DOI: 10.1039/b923598a] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The influence of confinement on the persistence length of dsDNA molecules under a high ionic strength environment was explored by coarse-grained Monte Carlo simulations in channels of different profiles. It was found that under confinement three definitions of the persistence length of DNA molecules were not equivalent and represented different properties. In case of the global quantities, the projection and the WLC persistence lengths, the apparent values up to several hundred nanometres are observed for DNA confined in narrow channels. The orientational correlation function cos theta(s) of confined DNA shows a complex pattern, distinctive for semiflexible polymers. At weak and moderate confinements the function cos theta(s) suggests an unexpected increase in the apparent DNA flexibility. The orientational persistence length computed from the initial slope of the function cos theta(s) mirrors only short-scale correlations and gives the value close to the intrinsic persistence length of DNA. The simulation data of direct relevance to experimental studies of DNA in microfluidic devices are compared with analytical theories for stiff chains.
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Affiliation(s)
- Peter Cifra
- Polymer Institute, Slovak Academy of Sciences, Dúbravská cesta 9, 842 36 Bratislava, Slovakia
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43
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Jesudason CG, Lyubartsev AP, Laaksonen A. Conformational characteristics of single flexible polyelectrolyte chain. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2009; 30:341-350. [PMID: 19946724 DOI: 10.1140/epje/i2009-10532-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Revised: 07/13/2009] [Accepted: 10/08/2009] [Indexed: 05/28/2023]
Abstract
The behaviour of a flexible anionic chain of 150 univalent and negatively charged beads connected by a harmonic-like potential with each other in the presence of an equal number of positive and free counterions, is studied in molecular dynamics simulations with Langevin thermostat in a wide range of temperatures. Simulations were carried out for several values of the bending parameter, corresponding to fully flexible polyion, moderately and strongly stiff polyion as well as for the case when bend conformation is preferable to the straight one. We have found that in all cases three regimes can be distinguished, which can be characterized as "random coil", observed at high temperatures; "extended conformation" observed at moderate temperatures (of the order of 1 in reduced units), and compact "globular conformation" attained at low temperatures. While the transition between high-temperature random and extended conformations is gradual, the transition from the extended coil to the globular state, taking place at a temperature of about 0.2 in reduced units, is of abrupt character resembling a phase transition.
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Affiliation(s)
- C G Jesudason
- Department of Chemistry, University of Malaya, 50603, Kuala Lumpur, West Malaysia, Malaysia.
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44
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Dobrynin AV, Carrillo JMY. Swelling of biological and semiflexible polyelectrolytes. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:424112. [PMID: 21715847 DOI: 10.1088/0953-8984/21/42/424112] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
We have developed a theoretical model of swelling of semiflexible (biological) polyelectrolytes in salt solutions. Our approach is based on separation of length scales which allowed us to split a chain's electrostatic energy into two parts that describe local and remote electrostatic interactions along the polymer backbone. The local part takes into account interactions between charged monomers that are separated by distances along the polymer backbone shorter than the chain's persistence length. These electrostatic interactions renormalize chain persistence length. The second part includes electrostatic interactions between remote charged pairs along the polymer backbone located at distances larger than the chain persistence length. These interactions are responsible for chain swelling. In the framework of this approach we calculated effective chain persistence length and chain size as a function of the Debye screening length, chain degree of ionization, bare persistence length and chain degree of polymerization. Our crossover expression for the effective chain's persistence length is in good quantitative agreement with the experimental data on DNA. We have been able to fit experimental datasets by using two adjustable parameters: DNA ionization degree (α = 0.15-0.17) and a bare persistence length (l(p) = 40-44 nm).
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Affiliation(s)
- Andrey V Dobrynin
- Polymer Program, Institute of Materials Science and Department of Physics, University of Connecticut, Storrs, CT 06269-3136, USA
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45
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Grass K, Holm C, Slater GW. Optimizing End-Labeled Free-Solution Electrophoresis by Increasing the Hydrodynamic Friction of the Drag Tag. Macromolecules 2009. [DOI: 10.1021/ma9003067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kai Grass
- Frankfurt Institute for Advanced Studies, Goethe University, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main, Germany
| | - Christian Holm
- Frankfurt Institute for Advanced Studies, Goethe University, Ruth-Moufang-Strasse 1, D-60438 Frankfurt am Main, Germany
- Institute for Computational Physics, University of Stuttgart, Pfaffenwaldring 27, D-70569 Stuttgart, Germany
| | - Gary W. Slater
- Department of Physics, University of Ottawa, 150 Louis-Pasteur, Ottawa, Ontario K1N 6N5, Canada
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Calò A, Stoliar P, Bystrenova E, Valle F, Biscarini F. Measurement of DNA Morphological Parameters at Highly Entangled Regime on Surfaces. J Phys Chem B 2009; 113:4987-90. [DOI: 10.1021/jp8097318] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Annalisa Calò
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via Gobetti 101 - 40129 Bologna, Italy
| | - Pablo Stoliar
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via Gobetti 101 - 40129 Bologna, Italy
| | - Eva Bystrenova
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via Gobetti 101 - 40129 Bologna, Italy
| | - Francesco Valle
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via Gobetti 101 - 40129 Bologna, Italy
| | - Fabio Biscarini
- CNR-Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), Via Gobetti 101 - 40129 Bologna, Italy
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Sambriski E, Schwartz D, de Pablo J. A mesoscale model of DNA and its renaturation. Biophys J 2009; 96:1675-90. [PMID: 19254530 PMCID: PMC2717267 DOI: 10.1016/j.bpj.2008.09.061] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2008] [Accepted: 09/30/2008] [Indexed: 11/26/2022] Open
Abstract
A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.
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Affiliation(s)
- E.J. Sambriski
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
| | - D.C. Schwartz
- Laboratory for Molecular and Computational Genomics, Department of Chemistry, Laboratory for Genetics, University of Wisconsin-Madison, Madison, Wisconsin
| | - J.J. de Pablo
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, Wisconsin
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48
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Angelescu DG, Linse P, Nguyen TT, Bruinsma RF. Structural transitions of encapsidated polyelectrolytes. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2008; 25:323-334. [PMID: 18385931 DOI: 10.1140/epje/i2007-10301-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2007] [Accepted: 02/18/2008] [Indexed: 05/26/2023]
Abstract
Conformations and structural transitions of polyelectrolytes strictly confined onto a spherical 2D surface have been investigated by scaling descriptions based on physical arguments concerning polyelectrolyte adsorption onto planar surface and liquid crystals as well as by Monte Carlo simulations using a bead-spring model with short-range and electrostatic repulsions. In case of the electrostatic screened regime, a disordered-ordered (spiral) transition at increasing persistence length of the chain was found. It was predicted that the transition occurred when the persistence length is comparable with the mean spacing between adjacent strands of the ordered chain. The presence of a non-screened electrostatic repulsion led to a more complex behavior with i) a re-entrant order-disorder transition and ii) a tennis ball texture as an additional smectic/nematic structure. The various competing structures given by the theory were recovered by the Monte Carlo simulations, which also indicated that the tennis ball texture was favored over the spiral structure by the long-range interactions for semi-flexible chains.
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Affiliation(s)
- D G Angelescu
- Physical Chemistry 1, Lund University, Box 124, SE-221 00 Lund, Sweden.
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49
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Doose S, Barsch H, Sauer M. Polymer properties of polythymine as revealed by translational diffusion. Biophys J 2007; 93:1224-34. [PMID: 17513377 PMCID: PMC1929036 DOI: 10.1529/biophysj.107.107342] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Biopolymers, such as single-stranded DNA (ssDNA), are often described as semiflexible polymers or wormlike chains. We investigated the length dependence of diffusional properties of homogeneous ssDNA (polythymine) with up to 100 nucleotides using fluorescence correlation spectroscopy. We found that the hydrodynamic radius Rh scales according to a power law, with an exponent between 0.5 and 0.7 depending on ionic strength I. With Rh being proportional to the square root of the persistence length Lp, we found that Lp approximately Im, with m=-0.22+/-0.01 for polythymine with 100 residues. For comparison, we performed molecular dynamics (MD) simulations with a force field that accounts for short-range interactions in vacuum, and determined the characteristic polymer properties end-to-end distance R, radius of gyration S, and persistence length Lp of various labeled and nonlabeled polythymine derivatives. We found excellent agreement for the length dependence of simulated S and experimental Rh measured at 100 mM NaCl, revealing that electrostatic interactions are completely shielded in aqueous solution at such ionic strength. MD simulations further showed that polythymine with >approximately 30 residues can be described as a semiflexible polymer with negligible influence of the fluorescent label; and that static flexibility is limited by geometrical and steric constraints as expressed by an intrinsic persistence length of approximately 1.7 nm. These results provide a benchmark for theories and MD simulations describing the influence of electrostatic interactions on polyelectrolyte properties, and thus help to develop a complete and accurate description of ssDNA.
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Affiliation(s)
- Sören Doose
- Applied Laser Physics and Laser Spectroscopy, University of Bielefeld, Bielefeld, Germany.
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50
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Akinchina A, Linse P. Diblock polyampholytes grafted onto spherical particles: effect of stiffness, charge density, and grafting density. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:1465-72. [PMID: 17241074 DOI: 10.1021/la062481r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The structure of spherical brushes formed by symmetric diblock polyampholytes end-grafted onto small spherical particles in aqueous solution is examined within the framework of the so-called primitive model using Monte Carlo simulations. The properties of the two blocks are identical except for the sign of their charges. Three different chain flexibilities corresponding to flexible, semiflexible, and stiff blocks are considered at various polyampholyte linear charge densities and grafting densities. The link between the two blocks is flexible at all conditions, and the grafted segments are laterally mobile. Radial and lateral spatial distribution functions of different types and single-chain properties are analyzed. The brush structure strongly depends on the chain flexibility. With flexible chains, a disordered polyelectrolyte complex is formed at the surface of the particle, the complex becoming more compact at increasing linear charge density. With stiff blocks, the inner blocks are radially oriented. At low linear charged density, the outer blocks are orientationally disordered, whereas at increasing electrostatic interaction the two blocks of a polyampholyte are parallel and close to each other, leading to an ordered structure referred to as a polyampholyte star. As the grafting density is increased, the brush thickness responds differently for flexible and nonflexible chains, depending on a different balance between electrostatic interactions and excluded volume effects.
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Affiliation(s)
- Anna Akinchina
- Physical Chemistry 1, Center for Chemistry and Chemical Engineering, Lund University, Box 124, SE-221 00 Lund, Sweden
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