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Singh TV, Shagolsem LS. Universality and Identity Ordering in Heteropolymer Coil–Globule Transition. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c01559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Thoudam Vilip Singh
- Department of Physics, National Institute of Technology Manipur, Imphal795004, India
| | - Lenin S. Shagolsem
- Department of Physics, National Institute of Technology Manipur, Imphal795004, India
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2
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Vasiliu T, Mocci F, Laaksonen A, Engelbrecht LDV, Perepelytsya S. Caging Polycations: Effect of Increasing Confinement on the Modes of Interaction of Spermidine3+ With DNA Double Helices. Front Chem 2022; 10:836994. [PMID: 35281557 PMCID: PMC8915389 DOI: 10.3389/fchem.2022.836994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/04/2022] [Indexed: 11/23/2022] Open
Abstract
Polyamines have important roles in the modulation of the cellular function and are ubiquitous in cells. The polyamines putrescine2+, spermidine3+, and spermine4+ represent the most abundant organic counterions of the negatively charged DNA in the cellular nucleus. These polyamines are known to stabilize the DNA structure and, depending on their concentration and additional salt composition, to induce DNA aggregation, which is often referred to as condensation. However, the modes of interactions of these elongated polycations with DNA and how they promote condensation are still not clear. In the present work, atomistic molecular dynamics (MD) computer simulations of two DNA fragments surrounded by spermidine3+ (Spd3+) cations were performed to study the structuring of Spd3+ “caged” between DNA molecules. Microsecond time scale simulations, in which the parallel DNA fragments were constrained at three different separations, but allowed to rotate axially and move naturally, provided information on the conformations and relative orientations of surrounding Spm3+ cations as a function of DNA-DNA separation. Novel geometric criteria allowed for the classification of DNA-Spd3+ interaction modes, with special attention given to Spd3+ conformational changes in the space between the two DNA molecules (caged Spd3+). This work shows how changes in the accessible space, or confinement, around DNA affect DNA-Spd3+ interactions, information fundamental to understanding the interactions between DNA and its counterions in environments where DNA is compacted, e.g. in the cellular nucleus.
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Affiliation(s)
- Tudor Vasiliu
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
| | - Francesca Mocci
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | - Aatto Laaksonen
- Centre of Advanced Research in Bionanoconjugates and Biopolymers “Petru Poni” Institute of Macromolecular Chemistry, Iasi, Romania
- Dipartimento di Scienze Chimiche e Geologiche, Cagliari University, Cagliari, Italy
- Division of Energy Science, Energy Engineering, Luleå University of Technology, Luleå, Sweden
- Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Materials-Oriented and Chemical Engineering, Nanjing Tech University, Nanjing, China
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
| | | | - Sergiy Perepelytsya
- Bogolyubov Institute for Theoretical Physics of the NAS of Ukraine, Kyiv, Ukraine
- *Correspondence: Francesca Mocci, ; Aatto Laaksonen, ; Sergiy Perepelytsya,
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3
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Intrinsically disordered protein regions and phase separation: sequence determinants of assembly or lack thereof. Emerg Top Life Sci 2021; 4:307-329. [PMID: 33078839 DOI: 10.1042/etls20190164] [Citation(s) in RCA: 130] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 09/23/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023]
Abstract
Intrinsically disordered protein regions (IDRs) - regions that do not fold into a fixed three-dimensional structure but instead exist in a heterogeneous ensemble of conformations - have recently entered mainstream cell biology in the context of liquid-liquid phase separation (LLPS). IDRs are frequently found to be enriched in phase-separated compartments. Due to this observation, the presence of an IDR in a protein is frequently assumed to be diagnostic of its ability to phase separate. In this review, we clarify the role of IDRs in biological assembly and explore the physical principles through which amino acids can confer the attractive molecular interactions that underlie phase separation. While some disordered regions will robustly drive phase separation, many others will not. We emphasize that rather than 'disorder' driving phase separation, multivalency drives phase separation. As such, whether or not a disordered region is capable of driving phase separation will depend on the physical chemistry encoded within its amino acid sequence. Consequently, an in-depth understanding of that physical chemistry is a prerequisite to make informed inferences on how and why an IDR may be involved in phase separation or, more generally, in protein-mediated intermolecular interactions.
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4
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nat Commun 2021; 12:1936. [PMID: 33782395 PMCID: PMC8007728 DOI: 10.1038/s41467-021-21953-3] [Citation(s) in RCA: 286] [Impact Index Per Article: 95.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 02/18/2021] [Indexed: 12/15/2022] Open
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA-binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA-binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Sukrit Singh
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Michael D Ward
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Maxwell I Zimmerman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Neha Vithani
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Daniel Griffith
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Jason A Wagoner
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, USA.
- Center for Science and Engineering of Living Systems (CSELS), Washington University in St. Louis, St. Louis, MO, USA.
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5
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Muzzopappa F, Hertzog M, Erdel F. DNA length tunes the fluidity of DNA-based condensates. Biophys J 2021; 120:1288-1300. [PMID: 33640380 PMCID: PMC8059207 DOI: 10.1016/j.bpj.2021.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/31/2021] [Accepted: 02/15/2021] [Indexed: 02/09/2023] Open
Abstract
Living organisms typically store their genomic DNA in a condensed form. Mechanistically, DNA condensation can be driven by macromolecular crowding, multivalent cations, or positively charged proteins. At low DNA concentration, condensation triggers the conformational change of individual DNA molecules into a compacted state, with distinct morphologies. Above a critical DNA concentration, condensation goes along with phase separation into a DNA-dilute and a DNA-dense phase. The latter DNA-dense phase can have different material properties and has been reported to be rather liquid-like or solid-like depending on the characteristics of the DNA and the solvent composition. Here, we systematically assess the influence of DNA length on the properties of the resulting condensates. We show that short DNA molecules with sizes below 1 kb can form dynamic liquid-like assemblies when condensation is triggered by polyethylene glycol and magnesium ions, binding of linker histone H1, or nucleosome reconstitution in combination with linker histone H1. With increasing DNA length, molecules preferentially condense into less dynamic more solid-like assemblies, with phage λ-DNA with 48.5 kb forming mostly solid-like assemblies under the conditions assessed here. The transition from liquid-like to solid-like condensates appears to be gradual, with DNA molecules of roughly 1–10 kb forming condensates with intermediate properties. Titration experiments with linker histone H1 suggest that the fluidity of condensates depends on the net number of attractive interactions established by each DNA molecule. We conclude that DNA molecules that are much shorter than a typical human gene are able to undergo liquid-liquid phase separation, whereas longer DNA molecules phase separate by default into rather solid-like condensates. We speculate that the local distribution of condensing factors can modulate the effective length of chromosomal domains in the cell. We anticipate that the link between DNA length and fluidity established here will improve our understanding of biomolecular condensates involving DNA.
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Affiliation(s)
- Fernando Muzzopappa
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Maud Hertzog
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France
| | - Fabian Erdel
- MCD, Center for Integrative Biology (CBI), University of Toulouse, CNRS, Toulouse, France.
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6
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Cubuk J, Alston JJ, Incicco JJ, Singh S, Stuchell-Brereton MD, Ward MD, Zimmerman MI, Vithani N, Griffith D, Wagoner JA, Bowman GR, Hall KB, Soranno A, Holehouse AS. The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.17.158121. [PMID: 32587966 PMCID: PMC7310622 DOI: 10.1101/2020.06.17.158121] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2023]
Abstract
The SARS-CoV-2 nucleocapsid (N) protein is an abundant RNA binding protein critical for viral genome packaging, yet the molecular details that underlie this process are poorly understood. Here we combine single-molecule spectroscopy with all-atom simulations to uncover the molecular details that contribute to N protein function. N protein contains three dynamic disordered regions that house putative transiently-helical binding motifs. The two folded domains interact minimally such that full-length N protein is a flexible and multivalent RNA binding protein. N protein also undergoes liquid-liquid phase separation when mixed with RNA, and polymer theory predicts that the same multivalent interactions that drive phase separation also engender RNA compaction. We offer a simple symmetry-breaking model that provides a plausible route through which single-genome condensation preferentially occurs over phase separation, suggesting that phase separation offers a convenient macroscopic readout of a key nanoscopic interaction.
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7
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Nishio T, Sugino K, Yoshikawa Y, Matsumoto M, Oe Y, Sadakane K, Yoshikawa K. K+ promotes the favorable effect of polyamine on gene expression better than Na. PLoS One 2020; 15:e0238447. [PMID: 32881909 PMCID: PMC7470421 DOI: 10.1371/journal.pone.0238447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+. PRINCIPAL FINDINGS It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge. CONCLUSION AND SIGNIFICANCE We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kaito Sugino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | | | - Yohei Oe
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan
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8
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Birshtein TM. Conformations of Macromolecules and Intramolecular Conformational Transitions. POLYMER SCIENCE SERIES A 2019. [DOI: 10.1134/s0965545x19060014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Zinchenko A, Hiramatsu H, Yamaguchi H, Kubo K, Murata S, Kanbe T, Hazemoto N, Yoshikawa K, Akitaya T. Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription. Biophys J 2019; 116:1836-1844. [PMID: 31076102 PMCID: PMC6531782 DOI: 10.1016/j.bpj.2019.04.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 03/04/2019] [Accepted: 04/12/2019] [Indexed: 02/04/2023] Open
Abstract
Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan.
| | - Hiroyuki Hiramatsu
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | | | - Koji Kubo
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Shizuaki Murata
- Graduate School of Environmental Studies, Nagoya University, Furocho, Chikusa-ku, Nagoya, Japan
| | - Toshio Kanbe
- Laboratory of Medical Mycology, Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Norio Hazemoto
- Faculty of Pharmaceutical Science, Nagoya City University, Mizuho-ku, Nagoya, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyotanabe, Japan
| | - Tatsuo Akitaya
- Department of Chemistry, Asahikawa Medical University, Asahikawa, Hokkaido, Japan.
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Mardoum WM, Gorczyca SM, Regan KE, Wu TC, Robertson-Anderson RM. Crowding Induces Entropically-Driven Changes to DNA Dynamics That Depend on Crowder Structure and Ionic Conditions. FRONTIERS IN PHYSICS 2018; 6:53. [PMID: 31667164 PMCID: PMC6820857 DOI: 10.3389/fphy.2018.00053] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Macromolecular crowding plays a principal role in a wide range of biological processes including gene expression, chromosomal compaction, and viral infection. However, the impact that crowding has on the dynamics of nucleic acids remains a topic of debate. To address this problem, we use single-molecule fluorescence microscopy and custom particle-tracking algorithms to investigate the impact of varying macromolecular crowding conditions on the transport and conformational dynamics of large DNA molecules. Specifically, we measure the mean-squared center-of-mass displacements, as well as the conformational size, shape, and fluctuations, of individual 115 kbp DNA molecules diffusing through various in vitro solutions of crowding polymers. We determine the role of crowder structure and concentration, as well as ionic conditions, on the diffusion and configurational dynamics of DNA. We find that branched, compact crowders (10 kDa PEG, 420 kDa Ficoll) drive DNA to compact, whereas linear, flexible crowders (10, 500 kDa dextran) cause DNA to elongate. Interestingly, the extent to which DNA mobility is reduced by increasing crowder concentrations appears largely insensitive to crowder structure (branched vs. linear), despite the highly different configurations DNA assumes in each case. We also characterize the role of ionic conditions on crowding-induced DNA dynamics. We show that both DNA diffusion and conformational size exhibit an emergent non-monotonic dependence on salt concentration that is not seen in the absence of crowders.
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Affiliation(s)
- Warren M. Mardoum
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
| | - Stephanie M. Gorczyca
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
| | - Kathryn E. Regan
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
| | - Tsai-Chin Wu
- Department of Physics and Biophysics, University of San Diego, San Diego, CA, United States
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11
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Zinchenko A, Berezhnoy NV, Chen Q, Nordenskiöld L. Compaction of Single-Molecule Megabase-Long Chromatin under the Influence of Macromolecular Crowding. Biophys J 2018; 114:2326-2335. [PMID: 29729833 PMCID: PMC6129467 DOI: 10.1016/j.bpj.2018.04.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/05/2018] [Accepted: 04/02/2018] [Indexed: 12/21/2022] Open
Abstract
The megabase-sized length of chromatin is highly relevant to the state of chromatin in vivo, where it is subject to a highly crowded environment and is organized in topologically associating domains of similar dimension. We developed an in vitro experimental chromatin model system reconstituted from T4 DNA (approximately 166 kbp) and histone octamers and studied the monomolecular compaction of this megabase-sized chromatin fiber under the influence of macromolecular crowding. We used single-molecule fluorescence microscopy and observed compaction in aqueous solutions containing poly(ethylene glycol) in the presence of monovalent (Na+ and K+) and divalent (Mg2+) cations. Both DNA and chromatin demonstrated compaction under comparable conditions in the presence of poly(ethylene glycol) and Na+ or Mg2+ salt. However, the mechanism of the compaction changed from a first-order phase transition for DNA to a continuous folding for megabase-sized chromatin fibers. A more efficient and pronounced chromatin compaction was observed in the presence of Na+ compared to K+. A flow-stretching technique to unfold DNA and chromatin coils was used to gain further insight into the morphology of partially folded chromatin fibers. The results revealed a distribution of partially folded chromatin fibers. This variability is likely the result of the heterogeneous distribution of nucleosomes on the DNA chain. The packaging of DNA in the form of chromatin in the crowded nuclear environment appears essential to ensure gradual conformational changes of DNA.
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Affiliation(s)
- Anatoly Zinchenko
- Graduate School of Environmental Studies, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan; School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Nikolay V Berezhnoy
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Qinming Chen
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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Yevdokimov YM, Sonin AS. DNA nanoscience: from prebiotic origins to emerging nanotechnology, by Kenneth Douglas, Boca Raton, CRC Press, 2016, 424 p., £45 ($58, 52 Euro) (Paperback), ISBN-10:1498750125. LIQUID CRYSTALS TODAY 2016. [DOI: 10.1080/1358314x.2016.1242255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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13
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D'Adamo G, Dietler G, Micheletti C. Tuning knot abundance in semiflexible chains with crowders of different sizes: a Monte Carlo study of DNA chains. SOFT MATTER 2016; 12:6708-6715. [PMID: 27443238 DOI: 10.1039/c6sm01327a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We use stochastic simulation techniques to sample the conformational space of linear semiflexible polymers in a crowded medium and study how the knotting properties depend on the crowder size and concentration. The abundance of physical knots in the chains, which for definiteness we model on 10 kb long DNA filaments, is shown to have a non-monotonic, unimodal dependence on the colloid diameter, dc. The maximum incidence of knots occurs when dc is about equal to half of the gyration radius of the isolated chain. The degree of enhancement of knots grows rapidly with the solution density and can be very conspicuous relative to the case of isolated chains with no crowders. For instance, at 30% volume fraction the relative increase is more than fourfold. This dramatic enhancement is shown to originate from the depletion-induced chain compaction over multiple and concurring length scales. The same effect accounts for the variations of the knot length that accompany the changes in knotting probability. The findings suggest that crowded media could be viably used as a passive physical means for controlling and modulating the incidence and length of knots in DNA and other types of semiflexible polymers.
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Affiliation(s)
- Giuseppe D'Adamo
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy.
| | - Giovanni Dietler
- Institut de Physique des Systèmes Biologiques, Ecole Polytechnique Fédérale de Lausanne, BSP, CH-1015 Lausanne, Switzerland
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136 Trieste, Italy.
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14
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Odagiri K, Seki K. Coil–globule transition of a polymer involved in excluded-volume interactions with macromolecules. J Chem Phys 2015; 143:134903. [DOI: 10.1063/1.4932344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Kenta Odagiri
- School of Network and Information, Senshu University, Kawasaki 214-8580, Japan
| | - Kazuhiko Seki
- National Institute of Advanced Industrial Science and Technology (AIST), AIST Tsukuba Central 5, Tsukuba, Ibaraki 305-8565, Japan
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15
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Joyeux M. Compaction of bacterial genomic DNA: clarifying the concepts. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2015; 27:383001. [PMID: 26345139 DOI: 10.1088/0953-8984/27/38/383001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The unconstrained genomic DNA of bacteria forms a coil, whose volume exceeds 1000 times the volume of the cell. Since prokaryotes lack a membrane-bound nucleus, in sharp contrast with eukaryotes, the DNA may consequently be expected to occupy the whole available volume when constrained to fit in the cell. Still, it has been known for more than half a century that the DNA is localized in a well-defined region of the cell, called the nucleoid, which occupies only 15% to 25% of the total volume. Although this problem has focused the attention of many scientists in recent decades, there is still no certainty concerning the mechanism that enables such a dramatic compaction. The goal of this Topical Review is to take stock of our knowledge on this question by listing all possible compaction mechanisms with the proclaimed desire to clarify the physical principles they are based upon and discuss them in the light of experimental results and the results of simulations based on coarse-grained models. In particular, the fundamental differences between ψ-condensation and segregative phase separation and between the condensation by small and long polycations are highlighted. This review suggests that the importance of certain mechanisms, like supercoiling and the architectural properties of DNA-bridging and DNA-bending nucleoid proteins, may have been overestimated, whereas other mechanisms, like segregative phase separation and the self-association of nucleoid proteins, as well as the possible role of the synergy of two or more mechanisms, may conversely deserve more attention.
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Affiliation(s)
- Marc Joyeux
- Laboratoire Interdisciplinaire de Physique (CNRS UMR5588), Université Joseph Fourier Grenoble 1, BP 87, 38402 St Martin d'Hères, France
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16
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Kang H, Toan NM, Hyeon C, Thirumalai D. Unexpected Swelling of Stiff DNA in a Polydisperse Crowded Environment. J Am Chem Soc 2015; 137:10970-8. [PMID: 26267166 DOI: 10.1021/jacs.5b04531] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We investigate the conformations of DNA-like stiff chains, characterized by contour length (L) and persistence length (lp), in a variety of crowded environments containing monodisperse soft spherical (SS) and spherocylindrical (SC) particles, a mixture of SS and SC, and a milieu mimicking the composition of proteins in the Escherichia coli cytoplasm. The stiff chain, whose size modestly increases in SS crowders up to ϕ ≈ 0.1, is considerably more compact at low volume fractions (ϕ ≤ 0.2) in monodisperse SC particles than in a medium containing SS particles. A 1:1 mixture of SS and SC crowders induces greater chain compaction than the pure SS or SC crowders at the same ϕ, with the effect being highly nonadditive. We also discover a counterintuitive result that the polydisperse crowding environment, mimicking the composition of a cell lysate, swells the DNA-like polymer, which is in stark contrast to the size reduction of flexible polymers in the same milieu. Trapping of the stiff chain in a fluctuating tube-like environment created by large-sized crowders explains the dramatic increase in size and persistence length of the stiff chain. In the polydisperse medium, mimicking the cellular environment, the size of the DNA (or related RNA) is determined by L/lp. At low L/lp, the size of the polymer is unaffected, whereas there is a dramatic swelling at an intermediate value of L/lp. We use these results to provide insights into recent experiments on crowding effects on RNA and also make testable predictions.
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Affiliation(s)
| | | | | | - D Thirumalai
- Korea Institute for Advanced Study , Seoul 130-722, Korea
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17
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Goryachkovskaya TN, Kozlov AS, Popik VM, Kolchanov NA, Peltek SE. Dependence of a DNA globule size in a gas phase on the chain length. ACTA ACUST UNITED AC 2015. [DOI: 10.1134/s2079059715040061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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18
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Cheng C, Jia JL, Ran SY. Polyethylene glycol and divalent salt-induced DNA reentrant condensation revealed by single molecule measurements. SOFT MATTER 2015; 11:3927-35. [PMID: 25871460 DOI: 10.1039/c5sm00619h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In this study, we investigated the DNA condensation induced by polyethylene glycol (PEG) with different molecular weights (PEG 600 and PEG 6000) in the presence of NaCl or MgCl2 by using magnetic tweezers (MT) and atomic force microscopy (AFM). The MT measurements show that with increasing NaCl concentration, the critical condensation force in the PEG 600-DNA or PEG 6000-DNA system increased approximately linearly. PEG 6000 solution has a larger critical force than PEG 600 solution at a given NaCl concentration. In comparison, a parabolic trend of the critical condensation force was observed with increasing MgCl2 concentration, indicating that DNA undergoes a reentrant condensation. The AFM results show that the morphologies of the compacted DNA-PEG complexes depended on the salt concentration and were consistent with the MT results.
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Affiliation(s)
- Chao Cheng
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
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19
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Shendruk TN, Bertrand M, de Haan HW, Harden JL, Slater GW. Simulating the entropic collapse of coarse-grained chromosomes. Biophys J 2015; 108:810-820. [PMID: 25692586 PMCID: PMC4336370 DOI: 10.1016/j.bpj.2014.11.3487] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 10/31/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022] Open
Abstract
Depletion forces play a role in the compaction and decompaction of chromosomal material in simple cells, but it has remained debatable whether they are sufficient to account for chromosomal collapse. We present coarse-grained molecular dynamics simulations, which reveal that depletion-induced attraction is sufficient to cause the collapse of a flexible chain of large structural monomers immersed in a bath of smaller depletants. These simulations use an explicit coarse-grained computational model that treats both the supercoiled DNA structural monomers and the smaller protein crowding agents as combinatorial, truncated Lennard-Jones spheres. By presenting a simple theoretical model, we quantitatively cast the action of depletants on supercoiled bacterial DNA as an effective solvent quality. The rapid collapse of the simulated flexible chromosome at the predicted volume fraction of depletants is a continuous phase transition. Additional physical effects to such simple chromosome models, such as enthalpic interactions between structural monomers or chain rigidity, are required if the collapse is to be a first-order phase transition.
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Affiliation(s)
- Tyler N Shendruk
- The Rudolf Peierls Centre for Theoretical Physics, Department of Physics, Theoretical Physics, University of Oxford, Oxford, United Kingdom.
| | - Martin Bertrand
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Hendrick W de Haan
- Faculty of Science, University of Ontario Institute of Technology, Oshawa, Ontario, Canada
| | - James L Harden
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada
| | - Gary W Slater
- Department of Physics, University of Ottawa, Ottawa, Ontario, Canada.
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20
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Yang D, Wang Q. Structural and phase transitions of one and two polymer mushrooms in poor solvent. J Chem Phys 2014; 140:194902. [PMID: 24852558 DOI: 10.1063/1.4875475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using the recently proposed fast lattice Monte Carlo (FLMC) simulations and the corresponding lattice self-consistent field (LSCF) calculations based on the same model system, where multiple occupancy of lattice sites is allowed [Q. Wang, Soft Matter 5, 4564 (2009); Q. Wang, Soft Matter 5, 6206 (2010)], we studied the coil-globule transition (CGT) of one-mushroom systems and the fused-separated transition (FST) of two-mushroom systems, where a polymer mushroom is formed by a group of n homopolymer chains each of N segments end-grafted at the same point onto a flat substrate and immersed in a poor solvent. With our soft potential that allows complete particle overlapping, LSCF theory neglecting the system fluctuations/correlations becomes exact in the limit of n → ∞, and FLMC results approach LSCF predictions with increasing n. Using LSCF calculations, we systematically constructed the phase diagrams of one- and two-mushroom systems. A second-order symmetric-asymmetric transition (SAT) was found in the globule state of one-mushroom systems, where the rotational symmetry around the substrate normal passing through the grafting point is broken in each individual configuration but preserved by the degeneracy of different orientations of these asymmetric configurations. Three different states were also found in two-mushroom systems: separated coils, separated globules, and fused globule. We further studied the coupling between FST in two-mushroom systems and CGT and SAT of each mushroom. Finally, direct comparisons between our simulation and theoretical results, without any parameter-fitting, unambiguously and quantitatively revealed the fluctuation/correlation effects on these phase transitions.
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Affiliation(s)
- Delian Yang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
| | - Qiang Wang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, USA
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21
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Zinchenko A, Tsumoto K, Murata S, Yoshikawa K. Crowding by Anionic Nanoparticles Causes DNA Double-Strand Instability and Compaction. J Phys Chem B 2014; 118:1256-62. [DOI: 10.1021/jp4107712] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Anatoly Zinchenko
- Graduate
School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Kanta Tsumoto
- Graduate
School of Engineering, Mie University, Mie, 514-8507, Japan
| | - Shizuaki Murata
- Graduate
School of Environmental Studies, Nagoya University, Nagoya, 464-8601, Japan
| | - Kenichi Yoshikawa
- Faculty
of Life and Medical Sciences, Doshisha University, Kyotanabe, 610-0394, Japan
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22
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Yang D, Wang Q. Unified View on the Mean-Field Order of Coil-Globule Transition. ACS Macro Lett 2013; 2:952-954. [PMID: 35581858 DOI: 10.1021/mz400457h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is concluded that the mean-field coil-globule transition of a polymer chain of finite length N immersed in a small-molecule solvent exhibits the type-I behavior; that is, it is either a first-order phase transition, a critical point, or a crossover depending on the location of the critical point. It becomes a second-order phase transition with respect to the solvent equality characterized by the Flory-Huggins parameter χ (or equivalently the second virial coefficient υ or the temperature T) only in the limit of N → ∞. Even in this limit, it still has the type-I behavior with respect to υN1/2 (or equivalently (1 - 2χ)N1/2).
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Affiliation(s)
- Delian Yang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, United States
| | - Qiang Wang
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado 80523-1370, United States
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23
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Li C, Ma C, Xu P, Gao Y, Zhang J, Qiao R, Zhao Y. Effective and reversible DNA condensation induced by a simple cyclic/rigid polyamine containing carbonyl moiety. J Phys Chem B 2013; 117:7857-67. [PMID: 23734659 DOI: 10.1021/jp312766u] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The transfection of DNA in gene therapy largely depends on the possibility of obtaining its condensation. The details of nanoparticle formation are essential for functioning, as mediated by the diverse elements containing molecular structure, ionic strength in mediums, and condensing motivator. Here, we report two kinds of DNA condensing agents based on simple cyclic/rigid polyamine molecules, having evaluated their structural effect on nanoparticle formation. The reversible condensation-dissociation process was achieved by ion-switching, attributing to a possible condensing mechanism-competitive building of external hydrogen bonds. Using poly[(dA-dT)2] and poly[(dG-dC)2] as substrates, respectively, circular dichroism (CD) signals clearly presented dissimilar interactions between polyamines and both rich sequences, implying potential preference for G-C sequence. The presence of divalent ion Zn(2+) as an efficient motivator accelerated the achievement of DNA condensation, and an accessible schematic model was depicted to explain the promotion in detail. In addition, by comparison with the behaviors of linear polyamines, differences between condensation and aggregation were explicitly elucidated in aspects of morphology and surface charges, as well as induced condition. The present work may have the potential to reveal the precise mechanism of DNA nanoparticle formation and, in particular, be applied to gene delivery as an efficient nonviral vector.
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Affiliation(s)
- Chao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing, 100029, PR China
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24
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Effects of long DNA folding and small RNA stem-loop in thermophoresis. Proc Natl Acad Sci U S A 2012; 109:17972-7. [PMID: 23071341 DOI: 10.1073/pnas.1215764109] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In thermophoresis, with the fluid at rest, suspensions move along a gradient of temperature. In an aqueous solution, a PEG polymer suspension is depleted from the hot region and builds a concentration gradient. In this gradient, DNA polymers of different sizes can be separated. In this work the effect of the polymer structure for genomic DNA and small RNA is studied. For genome-size DNA, individual single T4 DNA is visualized and tracked in a PEG solution under a temperature gradient built by infrared laser focusing. We find that T4 DNA follows steps of depletion, ring-like localization, and accumulation patterns as the PEG volume fraction is increased. Furthermore, a coil-globule transition for DNA is observed for a large enough PEG volume fraction. This drastically affects the localization position of T4 DNA. In a similar experiment, with small RNA such as ribozymes we find that the stem-loop folding of such polymers has important consequences. The RNA polymers having a long and rigid stem accumulate, whereas a polymer with stem length less than 4 base pairs shows depletion. Such measurements emphasize the crucial contribution of the double-stranded parts of RNA for thermal separation and selection under a temperature gradient. Because huge temperature gradients are present around hydrothermal vents in the deep ocean seafloor, this process might be relevant, at the origin of life, in an RNA world hypothesis. Ribozymes could be selected from a pool of random sequences depending on the length of their stems.
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25
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Kasyanenko NA, Lysyakova LA, Dribinskii BA, Zolotova YI, Nazarova OV, Panarin EF. DNA-polymer complexes for gene therapy. POLYMER SCIENCE SERIES C 2012. [DOI: 10.1134/s181123821207003x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Krotova MK, Vasilevskaya VV, Khokhlov AR. Compaction of DNA in solutions of highly charged proteins carrying the same charge as DNA. POLYMER SCIENCE SERIES C 2012. [DOI: 10.1134/s1811238212020014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Fechner M, Koetz J. Potentiometric Behavior of Polyampholytes Based on N
,N
′-diallyl-N
,N
′-dimethylammonium Chloride and Maleamic Acid Derivatives. MACROMOL CHEM PHYS 2011. [DOI: 10.1002/macp.201100532] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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28
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Condensed DNA: condensing the concepts. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2010; 105:208-22. [PMID: 20638406 DOI: 10.1016/j.pbiomolbio.2010.07.002] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 07/11/2010] [Indexed: 01/09/2023]
Abstract
DNA is stored in vivo in a highly compact, so-called condensed phase, where gene regulatory processes are governed by the intricate interplay between different states of DNA compaction. These systems often have surprising properties, which one would not predict from classical concepts of dilute solutions. The mechanistic details of DNA packing are essential for its functioning, as revealed by the recent developments coming from biochemistry, electrostatics, statistical mechanics, and molecular and cell biology. Different aspects of condensed DNA behavior are linked to each other, but the links are often hidden in the bulk of experimental and theoretical details. Here we try to condense some of these concepts and provide interconnections between the different fields. After a brief description of main experimental features of DNA condensation inside viruses, bacteria, eukaryotes and the test tube, main theoretical approaches for the description of these systems are presented. We end up with an extended discussion of the role of DNA condensation in the context of gene regulation and mention potential applications of DNA condensation in gene therapy and biotechnology.
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29
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Holthauzen LMF, Rösgen J, Bolen DW. Hydrogen bonding progressively strengthens upon transfer of the protein urea-denatured state to water and protecting osmolytes. Biochemistry 2010; 49:1310-8. [PMID: 20073511 PMCID: PMC2817916 DOI: 10.1021/bi9015499] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using osmolyte cosolvents, we show that hydrogen-bonding contributions can be separated from hydrophobic interactions in the denatured state ensemble (DSE). Specifically, the effects of urea and the protecting osmolytes sarcosine and TMAO are reported on the thermally unfolded DSE of Nank4-7*, a truncated notch ankyrin protein. The high thermal energy of this state in the presence and absence of 6 M urea or 1 M sarcosine solution is sufficient to allow large changes in the hydrodynamic radius (R(h)) and secondary structure accretion without populating the native state. The CD change at 228 nm is proportional to the inverse of the volume of the DSE, giving a compact species equivalent to a premolten globule in 1 M sarcosine. The same general effects portraying hierarchical folding observed in the DSE at 55 degrees C are also often seen at room temperature. Analysis of Nank4-7* DSE structural energetics at room temperature as a function of solvent provides rationale for understanding the structural and dimensional effects in terms of how modulation of the solvent alters solvent quality for the peptide backbone. Results show that while the strength of hydrophobic interactions changes little on transferring the DSE from 6 M urea to water and then to 1 M TMAO, backbone-backbone (hydrogen-bonding) interactions are greatly enhanced due to progressively poorer solvent quality for the peptide backbone. Thus, increased intrachain hydrogen bonding guides secondary structure accretion and DSE contraction as solvent quality is decreased. This process is accompanied by increasing hydrophobic contacts as chain contraction gathers hydrophobes into proximity and the declining urea-backbone free energy gradient reaches urea concentrations that are energetically insufficient to keep hydrophobes apart in the DSE.
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Affiliation(s)
- Luis Marcelo F Holthauzen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas 77555-1052, USA
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30
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You S, Van Winkle DH. Single Molecule Observation of DNA Electrophoresis in Pluronic F127. J Phys Chem B 2010; 114:4171-7. [DOI: 10.1021/jp911183m] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Seungyong You
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
| | - David H. Van Winkle
- Department of Physics and Martech, The Florida State University, Tallahassee, Florida, 32306-4351
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31
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Zhou K, Lu Y, Li J, Shen L, Zhang G, Xie Z, Wu C. The Coil-to-Globule-to-Coil Transition of Linear Polymer Chains in Dilute Aqueous Solutions: Effect of Intrachain Hydrogen Bonding. Macromolecules 2008. [DOI: 10.1021/ma8019128] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kejin Zhou
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Yijie Lu
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Junfang Li
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Lei Shen
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Guangzhao Zhang
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Zuowei Xie
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
| | - Chi Wu
- Shanghai-Hong Kong Joint Laboratory in Chemical Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, China; The Hefei National Laboratory for Physical Sciences at Microscale, Department of Chemical Physics, University of Science and Technology of China, Hefei, China; and Department of Chemistry, The Chinese University of Hong Kong,Shatin, N.T., Hong Kong, China
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33
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Skolnick J, Kolinski A. Monte Carlo Approaches to the Protein Folding Problem. ADVANCES IN CHEMICAL PHYSICS 2007. [DOI: 10.1002/9780470141649.ch7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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34
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Sarraguça JMG, Dias RS, Pais AACC. Coil-globule coexistence and compaction of DNA chains. J Biol Phys 2006; 32:421-34. [PMID: 19669448 DOI: 10.1007/s10867-006-9026-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2006] [Accepted: 09/27/2006] [Indexed: 10/23/2022] Open
Abstract
In this work we discuss different factors governing coil-globule coexistence in the compaction process of DNA. We initially analyse the role played by fluctuations in the degree of binding of an external compacting agent in the conformational behavior of the chain backbone. The analysis relies both on Monte Carlo simulation results and simple statistical approaches. Compacting agents of various binding characteristics are taken into consideration and the degree of charge neutralization upon the chain is related to conformational indicators. Selected model systems comprising stiff chains in the presence of multivalent ions are employed to assess intrinsic single-chain conformational fluctuation, in the presence of external agents but not resulting from differences in binding. It is shown that trends found for a variety of compacting agents, including the extension of the coil-globule coexistence regions, can be rationalised on the basis of this analysis.
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Affiliation(s)
- J M G Sarraguça
- Departamento de Química, Universidade de Coimbra, 3004-535 Coimbra, Portugal
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35
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de Vries R. Depletion-induced instability in protein-DNA mixtures: Influence of protein charge and size. J Chem Phys 2006; 125:014905. [PMID: 16863331 DOI: 10.1063/1.2209683] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
While there is abundant experimental and theoretical work on polymer-induced DNA condensation, it is still unclear whether globular proteins can condense linear DNA or not. We develop a simple analytical approximation for the depletion attraction between rodlike segments of semiflexible polyelectrolytes such as DNA, induced by nonbinding globular proteins. Monte Carlo simulations show that the approximation works well up to protein volume fractions of at least 20%. From the expression for the depletion attraction we estimate instability thresholds by computing the effective virial coefficient of DNA segments in protein solutions. While globular proteins are found to be much poorer depletion agents than flexible polymers, it should be possible to condense linear DNA with small highly charged globular proteins, at relatively low ionic strengths.
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Affiliation(s)
- Renko de Vries
- Laboratory of Physical Chemistry and Colloid Science, Wageningen University, P.O. Box 8038, 6700 EK Wageningen, The Netherlands
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36
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Kombrabail MH, Krishnamoorthy G. Fluorescence dynamics of DNA condensed by the molecular crowding agent poly(ethylene glycol). J Fluoresc 2006; 15:741-7. [PMID: 16341792 DOI: 10.1007/s10895-005-2982-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 07/26/2005] [Indexed: 10/25/2022]
Abstract
Condensation of extended DNA into compact structures is encountered in a variety of situations, both natural and artificial. While condensation of DNA has been routinely carried out by the use of multivalent cations, cationic lipids, detergents, and polyvalent cationic polymers, the use of molecular crowding agents in condensing DNA is rather striking. In this work, we have studied the dynamics of plasmid DNA condensed in the presence of a molecular crowding agent, polyethylene glycol (PEG). Steady-state and time-resolved fluorescence of the recently established condensation-indicating DNA binder, YOYO-1 [G. Krishnamoorthy, G. Duportail, and Y. Mely (2002), Biochemistry 41, 15277-15287] was used in inferring the dynamic aspects of DNA condensates. It is shown that DNA condensed by PEG is more flexible and less compact when compared to DNA condensed by binding agents such as polyethyleneimine. The relevance of such differences in dynamics toward functional aspects of condensed DNA is discussed.
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Affiliation(s)
- Mamata H Kombrabail
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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37
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Folding and Formation of Mesoglobules in Dilute Copolymer Solutions. CONFORMATION-DEPENDENT DESIGN OF SEQUENCES IN COPOLYMERS I 2006. [DOI: 10.1007/12_050] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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38
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Barsegov V, Thirumalai D. Influence of surface interactions on folding and forced unbinding of semiflexible chains. J Phys Chem B 2005; 109:21979-88. [PMID: 16853856 DOI: 10.1021/jp053803n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have investigated the folding and forced unbinding transitions of adsorbed semiflexible polymer chains using theory and simulations. These processes describe, at an elementary level, a number of biologically relevant phenomena that include adhesive interactions between proteins and tethering of receptors to cell walls. The binding interface is modeled as a solid surface, and the wormlike chain (WLC) is used for the semiflexible chain (SC). Using Langevin simulations, in the overdamped limit we examine the ordering kinetics of racquet-like and toroidal structures in the presence of an attractive interaction between the surface and the polymer chain. For a range of interactions, temperature, and the persistence length, l(p), we obtained the monomer density distribution, n(x), (x is the perpendicular distance of a tagged chain end from the surface) for all of the relevant morphologies. There is a single peak in n(x) inside the range of attractive forces, b, for chains in the extended conformations, whereas in racquet and toroidal structures there is an additional peak at x approximately b. The simulated results for n(x) are in good agreement with theory. The formation of toroids on the surface appears to be a first-order transition as evidenced by the bimodal distribution in n(x). The theoretical result underestimates the simulated n(x) for x << b and follows n(x) closely for x >/= b; the calculated density agrees exactly with n(x) in the range x << b. The chain-surface interaction is probed by subjecting the surface structures to a pulling force, f. The average extension, x( f), as a function of f exhibits a sigmoidal profile with sharp all-or-none transition at the unfolding force threshold f = f(c) which increases for more structured states. Simulated x(f) compare well with the theoretical predictions. The critical force, f(c), is a function of l(s)/l(c) for a fixed temperature, where l(c) and l(s) are the length scales that express the strength of the intramolecular and SC-surface attraction, respectively. For a fixed l(s), f(c) increases as l(p) decreases.
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Affiliation(s)
- V Barsegov
- Biophysics Program, Institute for Physical Science and Technology, and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, USA
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39
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Teif VB. Ligand-induced DNA condensation: choosing the model. Biophys J 2005; 89:2574-87. [PMID: 16085765 PMCID: PMC1366757 DOI: 10.1529/biophysj.105.063909] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 07/18/2005] [Indexed: 11/18/2022] Open
Abstract
We test and compare different models for ligand-induced DNA condensation. Using 14C-labeled spermidine3+, we measure the binding to condensed DNA at micromolar to molar polyamine concentrations. DNA aggregates at a critical polyamine concentration. Spermidine3+ binding becomes highly cooperative at the onset of aggregation. At higher concentrations, spermidine3+ binding to condensed DNA reaches a plateau with the degree of binding equal to 0.7 (NH(4+)/PO3-). Condensed DNA exists in a wide range of spermidine concentrations with the roughly constant degree of ligand binding. At greater concentrations, the degree of binding increases again. Further spermidine penetration between the double helices causes DNA resolubilization. We show that a simple two-state model without ligand-ligand interactions qualitatively predicts the reentrant aggregation-resolubilization behavior and the dependence on the ligand, Na+, and DNA concentrations. However, such models are inconsistent with the cooperative ligand binding to condensed DNA. Including the contact or long-range ligand-ligand interactions improves the coincidence with the experiments, if binding to condensed DNA is slightly more cooperative than to the starting DNA. For example, in the contact interaction model it is equivalent to an additional McGhee-von Hippel cooperativity parameter of approximately 2. Possible physical mechanisms for the observed cooperativity of ligand binding are discussed.
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Affiliation(s)
- Vladimir B Teif
- Laboratory of Nucleoprotein Biophysics and Biochemistry, Institute of Bioorganic Chemistry, Belarus National Academy of Sciences, Minsk, Belarus
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40
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Grosberg AY, Khokhlov AR. Statistical theory of polymeric lyotropic liquid crystals. ADVANCES IN POLYMER SCIENCE 2005. [DOI: 10.1007/3-540-10554-9_10] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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41
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Zinchenko AA, Yoshikawa K. Na+ shows a markedly higher potential than K+ in DNA compaction in a crowded environment. Biophys J 2005; 88:4118-23. [PMID: 15778438 PMCID: PMC1305642 DOI: 10.1529/biophysj.104.057323] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2004] [Accepted: 03/08/2005] [Indexed: 11/18/2022] Open
Abstract
Whereas many physicochemical investigations have shown that among monovalent cations Na(+) ion possesses minimal potential for DNA binding, biological assays have shown that Na(+) ion (in contrast to K(+) ion) plays a primary role in chromatin compaction and related processes. It is difficult to explain this inverse relationship between the compaction potentials of Na(+) and K(+) and their binding abilities. In this study we sought to resolve this contradiction and emphasize the phenomenological distinction between DNA compaction and DNA binding processes in the case of DNA compaction by monocations. Using polyethylene glycol solutions as a model of a crowded cell environment, we studied DNA compaction by alkali metal salts LiCl, NaCl, KCl, RbCl, and CsCl, and found that all of these monocations promote DNA compaction. Among these monovalent cations Na(+) produces the greatest compaction and the ratio of K(+) cand Na(+) oncentrations for DNA compaction is approximately 1.5-2. A comparative analysis of recent experimental results indicates that a higher binding activity of monocation generally corresponds to a low compaction potential of the corresponding monovalent ion. This inverse relation is explained as a result of partial dehydration of monocations in the compact state.
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Affiliation(s)
- Anatoly A Zinchenko
- Department of Physics, Graduate School of Science, Kyoto University, Sakyo, Japan.
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42
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Cheng R, Yang H. Application of time-temperature superposition principle to polymer transition kinetics. J Appl Polym Sci 2005. [DOI: 10.1002/app.22706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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43
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Maki Y, Sasaki N, Nakata M. Coil−Globule Transition of Poly(methyl methacrylate) in Acetonitrile. Macromolecules 2004. [DOI: 10.1021/ma049208l] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yasuyuki Maki
- Department of Polymer Science, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Sasaki
- Department of Polymer Science, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Mitsuo Nakata
- Department of Polymer Science, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
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44
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Sakaue T. Emergence of multiple tori structures in a single polyelectrolyte chain. J Chem Phys 2004; 120:6299-305. [PMID: 15267517 DOI: 10.1063/1.1652433] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We investigated the collapsed structure of a weakly charged wormlike chain under a moderate concentration of 1:1 electrolyte solution. By assuming a torus as a grand state, we found that the size of a torus is determined by the balance between surface energy and electrostatic energy, which leads to a finite torus thickness almost independent of the chain contour length. Owing to this unique characteristic, a long charged wormlike chain forms multiple tori structure as a collapsed product, which is never seen with a neutral wormlike chain. These features were confirmed by a Monte Carlo simulation.
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Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Graduate School of Science, Kyoto University and CREST, Kyoto 606-8504, Japan.
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Cao H, Ihm Y, Wang CZ, Morris JR, Su M, Dobbs D, Ho KM. Three-dimensional threading approach to protein structure recognition. POLYMER 2004. [DOI: 10.1016/j.polymer.2003.10.091] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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46
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A quantitative analyses of the viscometric data of the coil-to-globule and globule-to-coil transition of poly(N-isopropylacrylamide) in water. POLYMER 2003. [DOI: 10.1016/j.polymer.2003.09.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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47
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Pokarowski P, Kolinski A, Skolnick J. A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. Biophys J 2003; 84:1518-26. [PMID: 12609858 PMCID: PMC1302725 DOI: 10.1016/s0006-3495(03)74964-9] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2002] [Accepted: 10/30/2002] [Indexed: 11/29/2022] Open
Abstract
A simple protein model restricted to the face-centered cubic lattice has been studied. The model interaction scheme includes attractive interactions between hydrophobic (H) residues, repulsive interactions between hydrophobic and polar (P) residues, and orientation-dependent P-P interactions. Additionally, there is a potential that favors extended beta-type conformations. A sequence has been designed that adopts a native structure, consisting of an antiparallel, six-member Greek-key beta-barrel with protein-like structural degeneracy. It has been shown that the proposed model is a minimal one, i.e., all the above listed types of interactions are necessary for cooperative (all-or-none) type folding to the native state. Simulations were performed via the Replica Exchange Monte Carlo method and the numerical data analyzed via a multihistogram method.
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Affiliation(s)
- Piotr Pokarowski
- Institute of Applied Mathematics and Mechanics, Warsaw University, Banacha 2, Poland
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48
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Nakamura Y, Sasaki N, Nakata M. Kinetics of the Coil−Globule Transition of Poly(methyl methacrylate) in a Mixed Solvent. Macromolecules 2001. [DOI: 10.1021/ma010063h] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yoshiki Nakamura
- Department of Polymer Science, Faculty of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Naoki Sasaki
- Department of Polymer Science, Faculty of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
| | - Mitsuo Nakata
- Department of Polymer Science, Faculty of Science, Hokkaido University, Kita-ku, Sapporo 060-0810, Japan
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49
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Zhang G, Wu C. Reentrant coil-to-globule-to-coil transition of a single linear homopolymer chain in a water/methanol mixture. PHYSICAL REVIEW LETTERS 2001; 86:822-825. [PMID: 11177949 DOI: 10.1103/physrevlett.86.822] [Citation(s) in RCA: 120] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2000] [Indexed: 05/23/2023]
Abstract
Both water and methanol are good solvents for poly( N-isopropylacrylamide) (PNIPAM) at room temperature, but strangely not a mixture of them. Using narrowly distributed linear PNIPAM chains (M(w) = 2.6x10(7) g/mol and M(w)/M(n)<1.1), we have, for the first time, observed a coil-to-globule-to-coil transition of a single PNIPAM chain when methanol was gradually added into water. This novel reentrant transition leads to insight into the complexation between methanol and water. We also found that the chain was crumpled in its globule state and the globule still contained approximately 80% of solvent in its hydrodynamic volume.
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Affiliation(s)
- G Zhang
- The Open Laboratory of Bond Selective Chemistry, Department of Chemical Physics, University of Science and Technology of China, Hefei, Anhui, China
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50
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Currie EPK, M. A. Cohen Stuart, and, Borisov OV. Phase Separation in Polymer Solutions with Annealed Excluded Volume Interactions. Macromolecules 2001. [DOI: 10.1021/ma991540n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- E. P. K. Currie
- Department of Physical and Colloid Chemistry, University of Wageningen, 6703 HB Wageningen, The Netherlands; and ZOI/ZC, BASF AG, 67056 Ludwigshafen, Germany
| | - M. A. Cohen Stuart, and
- Department of Physical and Colloid Chemistry, University of Wageningen, 6703 HB Wageningen, The Netherlands; and ZOI/ZC, BASF AG, 67056 Ludwigshafen, Germany
| | - O. V. Borisov
- Department of Physical and Colloid Chemistry, University of Wageningen, 6703 HB Wageningen, The Netherlands; and ZOI/ZC, BASF AG, 67056 Ludwigshafen, Germany
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