1
|
Collette D, Dunlap D, Finzi L. Macromolecular Crowding and DNA: Bridging the Gap between In Vitro and In Vivo. Int J Mol Sci 2023; 24:17502. [PMID: 38139331 PMCID: PMC10744201 DOI: 10.3390/ijms242417502] [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: 09/13/2023] [Revised: 11/29/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
The cellular environment is highly crowded, with up to 40% of the volume fraction of the cell occupied by various macromolecules. Most laboratory experiments take place in dilute buffer solutions; by adding various synthetic or organic macromolecules, researchers have begun to bridge the gap between in vitro and in vivo measurements. This is a review of the reported effects of macromolecular crowding on the compaction and extension of DNA, the effect of macromolecular crowding on DNA kinetics, and protein-DNA interactions. Theoretical models related to macromolecular crowding and DNA are briefly reviewed. Gaps in the literature, including the use of biologically relevant crowders, simultaneous use of multi-sized crowders, empirical connections between macromolecular crowding and liquid-liquid phase separation of nucleic materials are discussed.
Collapse
Affiliation(s)
| | | | - Laura Finzi
- Department of Physics, College of Arts & Sciences, Emory University, Atlanta, GA 30322, USA; (D.C.); (D.D.)
| |
Collapse
|
2
|
Erenpreisa J, Giuliani A, Yoshikawa K, Falk M, Hildenbrand G, Salmina K, Freivalds T, Vainshelbaum N, Weidner J, Sievers A, Pilarczyk G, Hausmann M. Spatial-Temporal Genome Regulation in Stress-Response and Cell-Fate Change. Int J Mol Sci 2023; 24:ijms24032658. [PMID: 36769000 PMCID: PMC9917235 DOI: 10.3390/ijms24032658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/17/2023] [Accepted: 01/22/2023] [Indexed: 02/04/2023] Open
Abstract
Complex functioning of the genome in the cell nucleus is controlled at different levels: (a) the DNA base sequence containing all relevant inherited information; (b) epigenetic pathways consisting of protein interactions and feedback loops; (c) the genome architecture and organization activating or suppressing genetic interactions between different parts of the genome. Most research so far has shed light on the puzzle pieces at these levels. This article, however, attempts an integrative approach to genome expression regulation incorporating these different layers. Under environmental stress or during cell development, differentiation towards specialized cell types, or to dysfunctional tumor, the cell nucleus seems to react as a whole through coordinated changes at all levels of control. This implies the need for a framework in which biological, chemical, and physical manifestations can serve as a basis for a coherent theory of gene self-organization. An international symposium held at the Biomedical Research and Study Center in Riga, Latvia, on 25 July 2022 addressed novel aspects of the abovementioned topic. The present article reviews the most recent results and conclusions of the state-of-the-art research in this multidisciplinary field of science, which were delivered and discussed by scholars at the Riga symposium.
Collapse
Affiliation(s)
| | - Alessandro Giuliani
- Istituto Superiore di Sanita Environment and Health Department, 00161 Roma, Italy
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto 610-0394, Japan
| | - Martin Falk
- Institute of Biophysics, The Czech Academy of Sciences, 612 65 Brno, Czech Republic
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Georg Hildenbrand
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Faculty of Engineering, University of Applied Science Aschaffenburg, 63743 Aschaffenburg, Germany
| | - Kristine Salmina
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
| | - Talivaldis Freivalds
- Institute of Cardiology and Regenerative Medicine, University of Latvia, LV1004 Riga, Latvia
| | - Ninel Vainshelbaum
- Latvian Biomedicine Research and Study Centre, LV1067 Riga, Latvia
- Doctoral Study Program, University of Latvia, LV1004 Riga, Latvia
| | - Jonas Weidner
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Aaron Sievers
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Institute for Human Genetics, University Hospital Heidelberg, 69117 Heidelberg, Germany
| | - Götz Pilarczyk
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
| | - Michael Hausmann
- Kirchhoff Institute for Physics, Heidelberg University, 69120 Heidelberg, Germany
- Correspondence:
| |
Collapse
|
3
|
Osada K. Structural Polymorphism of Single pDNA Condensates Elicited by Cationic Block Polyelectrolytes. Polymers (Basel) 2020; 12:polym12071603. [PMID: 32707655 PMCID: PMC7408586 DOI: 10.3390/polym12071603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 07/15/2020] [Accepted: 07/16/2020] [Indexed: 12/17/2022] Open
Abstract
DNA folding is a core phenomenon in genome packaging within a nucleus. Such a phenomenon is induced by polyelectrolyte complexation between anionic DNA and cationic proteins of histones. In this regard, complexes formed between DNA and cationic polyelectrolytes have been investigated as models to gain insight into genome packaging. Upon complexation, DNA undergoes folding to reduce its occupied volume, which often results in multi-complex associated aggregates. However, when cationic copolymers comprising a polycation block and a neutral hydrophilic polymer block are used instead, DNA undergoes folding as a single molecule within a spontaneously formed polyplex micelle (PM), thereby allowing the observation of the higher-order structures that DNA forms. The DNA complex forms polymorphic structures, including globular, rod-shaped, and ring-shaped (toroidal) structures. This review focuses on the polymorphism of DNA, particularly, to elucidate when, how, and why DNA organizes into these structures with cationic copolymers. The interactions between DNA and the copolymers, and the specific nature of DNA in rigidity; i.e., rigid but foldable, play significant roles in the observed polymorphism. Moreover, PMs serve as potential gene vectors for systemic application. The significance of the controlled DNA folding for such an application is addressed briefly in the last part.
Collapse
Affiliation(s)
- Kensuke Osada
- Quantum Medical Science Directorate, National Institutes for Quantum and Radiological Science and Technology (QST), Anagawa, Inage-ku, Chiba-shi, Chiba 263-8555, Japan
| |
Collapse
|
4
|
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.
Collapse
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
| | | |
Collapse
|
5
|
Rassou S, Illy N, Tezgel O, Guégan P. Anionic ring-opening polymerization of N
-glycidylphthalimide: Combination of phosphazene base and activated monomer mechanism. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/pola.28988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Somasoudrame Rassou
- Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères; Sorbonne Université, CNRS, 4 Place Jussieu; Paris F-75005 France
| | - Nicolas Illy
- Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères; Sorbonne Université, CNRS, 4 Place Jussieu; Paris F-75005 France
| | - Ozgul Tezgel
- Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères; Sorbonne Université, CNRS, 4 Place Jussieu; Paris F-75005 France
| | - Philippe Guégan
- Institut Parisien de Chimie Moléculaire, Equipe Chimie des Polymères; Sorbonne Université, CNRS, 4 Place Jussieu; Paris F-75005 France
| |
Collapse
|
6
|
Japaridze A, Muskhelishvili G, Benedetti F, Gavriilidou AFM, Zenobi R, De Los Rios P, Longo G, Dietler G. Hyperplectonemes: A Higher Order Compact and Dynamic DNA Self-Organization. NANO LETTERS 2017; 17:1938-1948. [PMID: 28191853 DOI: 10.1021/acs.nanolett.6b05294] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Bacterial chromosome has a compact structure that dynamically changes its shape in response to bacterial growth rate and growth phase. Determining how chromatin remains accessible to DNA binding proteins, and transcription machinery is crucial to understand the link between genetic regulation, DNA structure, and topology. Here, we study very large supercoiled dsDNA using high-resolution characterization, theoretical modeling, and molecular dynamics calculations. We unveil a new type of highly ordered DNA organization forming in the presence of attractive DNA-DNA interactions, which we call hyperplectonemes. We demonstrate that their formation depends on DNA size, supercoiling, and bacterial physiology. We compare structural, nanomechanic, and dynamic properties of hyperplectonemes bound by three highly abundant nucleoid-associated proteins (FIS, H-NS, and HU). In all these cases, the negative supercoiling of DNA determines molecular dynamics, modulating their 3D shape. Overall, our findings provide a mechanistic insight into the critical role of DNA topology in genetic regulation.
Collapse
Affiliation(s)
- Aleksandre Japaridze
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Georgi Muskhelishvili
- Jacobs University , D-28759 Bremen, Germany
- Agricultural University of Georgia , 0159 Tbilisi, Georgia
| | - Fabrizio Benedetti
- Center for Integrative Genomics, University of Lausanne , 1015 Lausanne, Switzerland
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
| | - Agni F M Gavriilidou
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich , 8093 Zurich, Switzerland
| | - Paolo De Los Rios
- Vital-IT, SIB Swiss Institute of Bioinformatics , 1015 Lausanne, Switzerland
- Laboratoire de Biophysique Statistique, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| | - Giovanni Longo
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
- Istituto di Struttura della Materia, Consiglio Nazionale delle Ricerche , Rome, Italy
| | - Giovanni Dietler
- Laboratory of Physics of Living Matter, Ecole Polytechnique Fédérale de Lausanne , 1015 Lausanne, Switzerland
| |
Collapse
|
7
|
Herzberger J, Niederer K, Pohlit H, Seiwert J, Worm M, Wurm FR, Frey H. Polymerization of Ethylene Oxide, Propylene Oxide, and Other Alkylene Oxides: Synthesis, Novel Polymer Architectures, and Bioconjugation. Chem Rev 2015; 116:2170-243. [PMID: 26713458 DOI: 10.1021/acs.chemrev.5b00441] [Citation(s) in RCA: 451] [Impact Index Per Article: 50.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The review summarizes current trends and developments in the polymerization of alkylene oxides in the last two decades since 1995, with a particular focus on the most important epoxide monomers ethylene oxide (EO), propylene oxide (PO), and butylene oxide (BO). Classical synthetic pathways, i.e., anionic polymerization, coordination polymerization, and cationic polymerization of epoxides (oxiranes), are briefly reviewed. The main focus of the review lies on more recent and in some cases metal-free methods for epoxide polymerization, i.e., the activated monomer strategy, the use of organocatalysts, such as N-heterocyclic carbenes (NHCs) and N-heterocyclic olefins (NHOs) as well as phosphazene bases. In addition, the commercially relevant double-metal cyanide (DMC) catalyst systems are discussed. Besides the synthetic progress, new types of multifunctional linear PEG (mf-PEG) and PPO structures accessible by copolymerization of EO or PO with functional epoxide comonomers are presented as well as complex branched, hyperbranched, and dendrimer like polyethers. Amphiphilic block copolymers based on PEO and PPO (Poloxamers and Pluronics) and advances in the area of PEGylation as the most important bioconjugation strategy are also summarized. With the ever growing toolbox for epoxide polymerization, a "polyether universe" may be envisaged that in its structural diversity parallels the immense variety of structural options available for polymers based on vinyl monomers with a purely carbon-based backbone.
Collapse
Affiliation(s)
- Jana Herzberger
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.,Graduate School Materials Science in Mainz , Staudingerweg 9, D-55128 Mainz, Germany
| | - Kerstin Niederer
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Hannah Pohlit
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.,Graduate School Materials Science in Mainz , Staudingerweg 9, D-55128 Mainz, Germany.,Max Planck Graduate Center , Staudingerweg 6, D-55128 Mainz, Germany.,Department of Dermatology, University Medical Center , Langenbeckstraße 1, D-55131 Mainz, Germany
| | - Jan Seiwert
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany
| | - Matthias Worm
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.,Max Planck Graduate Center , Staudingerweg 6, D-55128 Mainz, Germany
| | - Frederik R Wurm
- Max Planck Graduate Center , Staudingerweg 6, D-55128 Mainz, Germany.,Max Planck Institute for Polymer Research , Ackermannweg 10, D-55128 Mainz, Germany
| | - Holger Frey
- Institute of Organic Chemistry, Johannes Gutenberg-University Mainz , Duesbergweg 10-14, D-55128 Mainz, Germany.,Graduate School Materials Science in Mainz , Staudingerweg 9, D-55128 Mainz, Germany
| |
Collapse
|
8
|
Uda RM, Matsui T. Photoinduced conformational changes in DNA by poly(vinyl alcohol) carrying a malachite green moiety for protecting DNA against attack by nuclease. SOFT MATTER 2015; 11:8246-8252. [PMID: 26339777 DOI: 10.1039/c5sm01874a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Light is a highly advantageous means of specific cell targeting. Though targeted gene delivery is an important characteristic of an ideal delivery vehicle, there has been little effort to develop a photoresponsive vector. Among nonviral vectors, cationic substances interact effectively with negatively charged DNA. With this property in mind, we designed copolymers of poly(vinyl alcohol) carrying a malachite green moiety (PVAMG) with different molecular weights. Though PVAMG has no affinity for DNA in the absence of light, it undergoes photoionization in the presence of light to afford cationic DNA binding sites. The DNA-PVAMG complex was investigated with respect to DNA conformational changes and its protective nature, which are important properties for nonviral vectors. PVAMG irradiation promoted DNA conformational transitions from coils to partial globules to compacted globules. The complex had a protective effect against DNase I after PVAMG irradiation, while DNA was degraded under dark conditions. The effect on DNA transition and the protective nature were sensitive to the molecular weight of PVAMG. The data regarding binding constants and binding mode provided insight into the structure of the DNA-PVAMG complex. To withstand DNase I attacks, complexation results in the compaction of DNA, which is further covered with PVAMG.
Collapse
Affiliation(s)
- Ryoko M Uda
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
| | - Takashi Matsui
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama, Nara 639-1080, Japan.
| |
Collapse
|
9
|
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.
Collapse
Affiliation(s)
- Chao Cheng
- Department of Physics, Wenzhou University, Wenzhou 325035, China.
| | | | | |
Collapse
|
10
|
Chen Y, Abrams ES, Boles TC, Pedersen JN, Flyvbjerg H, Austin RH, Sturm JC. Concentrating genomic length DNA in a microfabricated array. PHYSICAL REVIEW LETTERS 2015; 114:198303. [PMID: 26024203 DOI: 10.1103/physrevlett.114.198303] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2014] [Indexed: 05/19/2023]
Abstract
We demonstrate that a microfabricated bump array can concentrate genomic-length DNA molecules efficiently at continuous, high flow velocities, up to 40 μm/s, if the single-molecule DNA globule has a sufficiently large shear modulus. Increase in the shear modulus is accomplished by compacting the DNA molecules to minimal coil size using polyethylene glycol (PEG) derived depletion forces. We map out the sweet spot, where concentration occurs, as a function of PEG concentration and flow speed using a combination of theoretical analysis and experiment. Purification of DNA from enzymatic reactions for next-generation DNA-sequencing libraries will be an important application of this development.
Collapse
Affiliation(s)
- Yu Chen
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
| | - Ezra S Abrams
- Sage Science, Inc., Beverly, Massachusetts 01915, USA
| | | | - Jonas N Pedersen
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Henrik Flyvbjerg
- Department of Micro- and Nanotechnology, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Robert H Austin
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Physics, Princeton University, Princeton, New Jersey 08544, USA
| | - James C Sturm
- Princeton Institute for Science and Technology of Materials (PRISM), Princeton, New Jersey 08540, USA
- Department of Electrical Engineering, Princeton University, Princeton, New Jersey 08544, USA
| |
Collapse
|
11
|
Isono T, Asai S, Satoh Y, Takaoka T, Tajima K, Kakuchi T, Satoh T. Controlled/Living Ring-Opening Polymerization of Glycidylamine Derivatives Using t-Bu-P4/Alcohol Initiating System Leading to Polyethers with Pendant Primary, Secondary, and Tertiary Amino Groups. Macromolecules 2015. [DOI: 10.1021/acs.macromol.5b00556] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Takuya Isono
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Shunsuke Asai
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Yusuke Satoh
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toshimitsu Takaoka
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Kenji Tajima
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toyoji Kakuchi
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| | - Toshifumi Satoh
- Division of Biotechnology and Macromolecular Chemistry, Faculty of
Engineering, and ‡Graduate School of Chemical Sciences and Engineering, Hokkaido University, Sapporo 060-8628, Japan
| |
Collapse
|
12
|
Satpathi S, Sengupta A, Hridya VM, Gavvala K, Koninti RK, Roy B, Hazra P. A Green Solvent Induced DNA Package. Sci Rep 2015. [PMCID: PMC5378943 DOI: 10.1038/srep09137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Mechanistic details of DNA compaction is essential blue print for gene regulation in living organisms. Many in vitro studies have been implemented using several compaction agents. However, these compacting agents may have some kinds of cytotoxic effects to the cells. To minimize this aspect, several research works had been performed, but people have never focused green solvent, i.e. room temperature ionic liquid as DNA compaction agent. To the best of our knowledge, this is the first ever report where we have shown that guanidinium tris(pentafluoroethyl)trifluorophosphate (Gua-IL) acts as a DNA compacting agent. The compaction ability of Gua-IL has been verified by different spectroscopic techniques, like steady state emission, circular dichroism, dynamic light scattering and UV melting. Notably, we have extensively probed this compaction by Gua-IL through field emission scanning electron microscopy (FE-SEM) and fluorescence microscopy images. We also have discussed the plausible compaction mechanism process of DNA by Gua-IL. Our results suggest that Gua-IL forms a micellar kind of self aggregation above a certain concentration (≥1 mM), which instigates this compaction process. This study divulges the specific details of DNA compaction mechanism by a new class of compaction agent, which is highly biodegradable and eco friendly in nature.
Collapse
|
13
|
Promoting DNA loading on magnetic nanoparticles using a DNA condensation strategy. Colloids Surf B Biointerfaces 2015; 125:247-54. [DOI: 10.1016/j.colsurfb.2014.10.036] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 10/13/2014] [Accepted: 10/16/2014] [Indexed: 11/24/2022]
|
14
|
Brocas AL, Mantzaridis C, Tunc D, Carlotti S. Polyether synthesis: From activated or metal-free anionic ring-opening polymerization of epoxides to functionalization. Prog Polym Sci 2013. [DOI: 10.1016/j.progpolymsci.2012.09.007] [Citation(s) in RCA: 188] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
15
|
González-Pérez A, Ruso JM. A Versatile Approach towards the Compaction, Decompaction, and Immobilization of DNA at Interfaces by Using Cyclodextrins. Chemphyschem 2013; 14:2544-53. [DOI: 10.1002/cphc.201300234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2013] [Indexed: 12/19/2022]
|
16
|
Lee BF, Wolffs M, Delaney KT, Sprafke JK, Leibfarth FA, Hawker CJ, Lynd NA. Reactivity ratios, and mechanistic insight for anionic ring-opening copolymerization of epoxides. Macromolecules 2012; 45:3722-3731. [PMID: 23226879 PMCID: PMC3514019 DOI: 10.1021/ma300634d] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactivity ratios were evaluated for anionic ring-opening copolymerizations of ethylene oxide (EO) with either allyl glycidyl ether (AGE) or ethylene glycol vinyl glycidyl ether (EGVGE) using a benzyl alkoxide initiator. The chemical shift for the benzylic protons of the initiator, as measured by (1)H NMR spectroscopy, were observed to be sensitive to the sequence of the first two monomers added to the initiator during polymer growth. Using a simple kinetic model for initiation and the first propagation step, reactivity ratios for the copolymerization of AGE and EGVGE with EO could be determined by analysis of the (1)H NMR spectroscopy for the resulting copolymer. For the copolymerization between EO and AGE, the reactivity ratios were determined to be r(AGE) = 1.31 ± 0.26 and r(EO) = 0.54 ± 0.03, while for EO and EGVGE, the reactivity ratios were r(EGVGE) = 3.50 ± 0.90 and r(EO) = 0.32 ± 0.10. These ratios were consistent with the compositional drift observed in the copolymerization between EO and EGVGE, with EGVGE being consumed early in the copolymerization. These experimental results, combined with density functional calculations, allowed a mechanism for oxyanionic ring-opening polymerization that begins with coordination of the Lewis-basic epoxide to the cation to be proposed. The calculated transition-state energies agree qualitatively with the observed relative rates for polymerization.
Collapse
Affiliation(s)
- Bongjae F Lee
- Materials Research Laboratory, University of California, Santa Barbara ; Materials Department, University of California, Santa Barbara ; Chemical Research Institute, Samsung Cheil Industries Inc., Republic of Korea
| | | | | | | | | | | | | |
Collapse
|
17
|
Uda RM, Ohshita M. Phototriggered DNA Complexation and Compaction Using Poly(vinyl alcohol) Carrying a Malachite Green Moiety. Biomacromolecules 2012; 13:1510-4. [DOI: 10.1021/bm3001952] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryoko M. Uda
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama,
Nara 639-1080, Japan
| | - Minami Ohshita
- Department of Chemical Engineering, Nara National College of Technology, Yata 22, Yamato-koriyama,
Nara 639-1080, Japan
| |
Collapse
|
18
|
Yoshikawa Y, Suzuki Y, Yamada K, Fukuda W, Yoshikawa K, Takeyasu K, Imanaka T. Critical behavior of megabase-size DNA toward the transition into a compact state. J Chem Phys 2012; 135:225101. [PMID: 22168726 DOI: 10.1063/1.3666845] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.
Collapse
Affiliation(s)
- Yuko Yoshikawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | | | | | | | | | | | | |
Collapse
|
19
|
Obermeier B, Wurm F, Mangold C, Frey H. Multifunctional Poly(ethylene glycol)s. Angew Chem Int Ed Engl 2011; 50:7988-97. [DOI: 10.1002/anie.201100027] [Citation(s) in RCA: 158] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2011] [Indexed: 11/10/2022]
|
20
|
Obermeier B, Wurm F, Mangold C, Frey H. Multifunktionelle Poly(ethylenglycole). Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
21
|
Meyer J, Keul H, Möller M. Poly(glycidyl amine) and Copolymers with Glycidol and Glycidyl Amine Repeating Units: Synthesis and Characterization. Macromolecules 2011. [DOI: 10.1021/ma200757v] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jörg Meyer
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen and DWI an der RWTH Aachen e.V., Pauwelsstrasse 8, D-52056 Aachen, Germany
| | - Helmut Keul
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen and DWI an der RWTH Aachen e.V., Pauwelsstrasse 8, D-52056 Aachen, Germany
| | - Martin Möller
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen and DWI an der RWTH Aachen e.V., Pauwelsstrasse 8, D-52056 Aachen, Germany
| |
Collapse
|
22
|
Brocas AL, Cendejas G, Caillol S, Deffieux A, Carlotti S. Controlled synthesis of polyepichlorohydrin with pendant cyclic carbonate functions for isocyanate-free polyurethane networks. ACTA ACUST UNITED AC 2011. [DOI: 10.1002/pola.24699] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
23
|
Sonda N, Hirano M, Shimada N, Kano A, Kidoaki S, Maruyama A. Cationic Comb-type Copolymers Do Not Cause Collapse but Shrinkage of DNA Molecules. CHEM LETT 2011. [DOI: 10.1246/cl.2011.250] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
24
|
Giguère G, Zhu XX. Functional star polymers with a cholic acid core and their thermosensitive properties. Biomacromolecules 2010; 11:201-6. [PMID: 19994878 DOI: 10.1021/bm9010694] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Star polymers derived from cholic acid with poly(allyl glycidyl ether) arms have been prepared via anionic polymerization, yielding polymers with well-defined molecular weight and low polydispersity. The double bonds of the allyl groups on the polymer are used to introduce either amine or carboxylic acid groups to obtain amphiphilic polymers with cationic and anionic groups, respectively. The polymers can aggregate in water above a certain critical concentration, which was found to vary with the arm length of the star polymers. The star polymers bearing amino groups showed interesting thermosensitivity, which also depends on the pH of the media. A simple acetylation of the amine groups can sharpen the transition and vary the cloud point from 15 to 48 degrees C, depending on the degree of acetylation. Such polymers offer useful alternatives to the existing thermosensitive polymers.
Collapse
Affiliation(s)
- Guillaume Giguère
- Department of Chemistry, Université de Montrééal, P.O. Box 6128, Downtown Station, Montreal, Quebec, H3C 3J7, Canada
| | | |
Collapse
|
25
|
Obermeier B, Wurm F, Frey H. Amino Functional Poly(ethylene glycol) Copolymers via Protected Amino Glycidol. Macromolecules 2010. [DOI: 10.1021/ma902245d] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Boris Obermeier
- Institute of Organic Chemistry, Organic and Macromolecular Chemistry, Duesbergweg 10-14, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Frederik Wurm
- Institute of Organic Chemistry, Organic and Macromolecular Chemistry, Duesbergweg 10-14, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Holger Frey
- Institute of Organic Chemistry, Organic and Macromolecular Chemistry, Duesbergweg 10-14, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| |
Collapse
|
26
|
Robic A, Gaillard C, Sassi JF, Lerat Y, Lahaye M. Ultrastructure of ulvan: a polysaccharide from green seaweeds. Biopolymers 2009; 91:652-64. [PMID: 19353644 DOI: 10.1002/bip.21195] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ultrastructural analysis of the gel forming green seaweed sulfated polysaccharide ulvan revealed a spherical-based morphology (10-18 nm diameter) more or less aggregated in aqueous solution. At pH 13 in TBAOH (tetrabutyl ammonium hydroxyde) or NaOH, ulvan formed an open gel-like structure or a continuous film by fusion or coalescence of bead-like structures, while in acidic pH conditions, ulvan appeared as dispersed beads. Low concentrations of sodium chloride, copper or boric acid induced the formation of aggregates. These results highlight the hydrophobic and aggregative behavior of ulvan that are discussed in regard to the peculiar gel formation and the low intrinsic viscosity of the polysaccharide in aqueous solution. (c) 2009 Wiley Periodicals, Inc. Biopolymers 91: 652-664, 2009.This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com.
Collapse
Affiliation(s)
- Audrey Robic
- Centre d'Etudes et de Valorisation des Algues, Presqu'île de Pen Lan, Pleubian, France
| | | | | | | | | |
Collapse
|
27
|
Liu YC, Le Ny ALM, Schmidt J, Talmon Y, Chmelka BF, Lee CT. Photo-assisted gene delivery using light-responsive catanionic vesicles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:5713-5724. [PMID: 19435291 DOI: 10.1021/la803588d] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Photoresponsive catanionic vesicles have been developed as a novel gene delivery vector combining enhanced cellular uptake with phototriggered release of vesicle payload following entry into cells. Vesicles with diameters ranging from 50 to 200 nm [measured using cryo-transmission electron microscopy (TEM) and light-scattering techniques] form spontaneously, following mixing of positively charged azobenzene-containing surfactant and negatively charged alkyl surfactant species. Fluorescent probe measurements showed that the catanionic vesicles at a cation/anion ratio of 7:3 formed at surfactant concentrations as low as 10 microM of the azobenzene surfactant under visible light (with the azobenzene surfactant species principally in the trans configuration), while 50-60 microM of the azobenzene surfactant is required to form vesicles under UV illumination (with the azobenzene surfactant species principally in the cis configuration). At intermediate surfactant concentrations (ca. 15-45 microM) under visible light conditions, transport of DNA-vesicle complexes occurred past the cell membrane of murine fibroblast NIH 3T3 cells through endocytosis. Subsequent UV illumination induced rupture of the vesicles and release of uncomplexed DNA into the cell interiors, where it was capable of passing through the nuclear membrane and thereby contributing to enhanced expression. Single-molecule fluorescent images of T4-DNA demonstrated that the formation of vesicles with a net positive charge led to compaction of DNA molecules via complex formation within a few seconds, while UV-induced disruption of the vesicle-DNA complexes led to DNA re-expansion to the elongated-coil state, also within a few seconds. Transfection experiments with eGFP DNA revealed that photoresponsive catanionic vesicles are more effectively taken up by cells compared to otherwise identical alkyl (i.e., nonazobenzene-containing and thus nonlight-responsive) catanionic vesicles, presumably because of pi-pi stacking interactions that enhance bilayer rigidity in the photoresponsive vesicles. Subsequent UV illumination following endocytosis leads to further dramatic enhancements in the transfection efficiencies, demonstrating that vector unpacking and release of DNA from the carrier complex can be the limiting step in the overall process of gene delivery.
Collapse
Affiliation(s)
- Yu-Chuan Liu
- Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, California 90089, USA
| | | | | | | | | | | |
Collapse
|
28
|
Hirano K, Aoyagi M, Ishido T, Ooie T, Frusawa H, Asakawa M, Shimizu T, Ishikawa M. Measuring the Length Distribution of Self-Assembled Lipid Nanotubes by Orientation Control with a High-Frequency Alternating Current Electric Field in Aqueous Solutions. Anal Chem 2009; 81:1459-64. [DOI: 10.1021/ac8022795] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ken Hirano
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Masaru Aoyagi
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Tomomi Ishido
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Toshihiko Ooie
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Hiroshi Frusawa
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Masumi Asakawa
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Toshimi Shimizu
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| | - Mitsuru Ishikawa
- Health Technology Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2217-14, Hayashi-cho, Takamatsu, Kagawa, 761-0395, Japan, Nanotube Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, 305-8565, Japan, and Department of Environmental Systems Engineering, Graduate School of Engineering, Kochi University of Technology, Tosayamada-cho, Kochi, 782-8502, Japan
| |
Collapse
|
29
|
Wan L, Manickam DS, Oupický D, Mao G. DNA release dynamics from reducible polyplexes by atomic force microscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2008; 24:12474-82. [PMID: 18839970 PMCID: PMC2825055 DOI: 10.1021/la802088y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Controlled intracellular disassembly of polyelectrolyte complexes of polycations and DNA (polyplexes) is a crucial step for the success of nonviral gene delivery. Motivated by our previous observation of different gene delivery performances among multiblock reducible copolypeptide vectors ( Manickam, D. S. ; Oupicky, D. Bioconjugate Chem. 2006, 17, 1395- 1403 ), atomic force microscopy is used to visualize plasmid DNA in various decondensed states from reducible polypeptide polyplexes under simulated physiological reducing conditions. DNA decondensation is triggered by reductive degradation of disulfide-containing cationic polypeptides. Striking differences in DNA release dynamics between polyplexes based on polypeptides of histidine-rich peptide (HRP, CKHHHKHHHKC) and nuclear localization signal (NLS, CGAGPKKKRKVC) peptide are presented. The HRP and NLS polyplexes are similar to each other in their initial morphology with a majority of them containing only one DNA plasmid. Upon reductive degradation by dithiothreitol, DNA is released from NLS abruptly regardless of the initial polyplex morphology, while DNA release from HRP polyplexes displays a gradual decondensation that is dependent on the size of polyplexes. The release rate is higher for larger HRP polyplexes. The smaller HRP polyplexes become unstable when they are in contact with expanding chains nearby. The results reveal potentially rich DNA release dynamics that can be controlled by subtle variation in multivalent counterion binding to DNA as well as the cellular matrix.
Collapse
Affiliation(s)
- Lei Wan
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
| | - Devika S. Manickam
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - David Oupický
- Department of Pharmaceutical Sciences, Wayne State University, Detroit, MI 48202
| | - Guangzhao Mao
- Department of Chemical Engineering and Materials Science, Wayne State University, Detroit, MI 48202
- Corresponding author:
| |
Collapse
|
30
|
Cao M, Deng M, Wang XL, Wang Y. Decompaction of Cationic Gemini Surfactant-Induced DNA Condensates by β-Cyclodextrin or Anionic Surfactant. J Phys Chem B 2008; 112:13648-54. [DOI: 10.1021/jp803244f] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Meiwen Cao
- Key Laboratory of Colloid and Interface Science, Institute of Chemistry, and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, Peopleʼs Republic of China
| | - Manli Deng
- Key Laboratory of Colloid and Interface Science, Institute of Chemistry, and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, Peopleʼs Republic of China
| | - Xiao-Ling Wang
- Key Laboratory of Colloid and Interface Science, Institute of Chemistry, and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, Peopleʼs Republic of China
| | - Yilin Wang
- Key Laboratory of Colloid and Interface Science, Institute of Chemistry, and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, Peopleʼs Republic of China
| |
Collapse
|
31
|
On Mechanism of Intermediate-Sized Circular DNA Compaction Mediated by Spermine: Contribution of Fluorescence Lifetime Correlation Spectroscopy. J Fluoresc 2008; 18:679-84. [DOI: 10.1007/s10895-008-0345-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
|
32
|
Huang D, Korolev N, Eom KD, Tam JP, Nordenskiöld L. Design and Biophysical Characterization of Novel Polycationic ϵ-Peptides for DNA Compaction and Delivery. Biomacromolecules 2007; 9:321-30. [DOI: 10.1021/bm700882g] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Dandan Huang
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, Singapore 637551, and Biochemistry, The Scripps Research Institute, Parkside Drive, Jupiter, Florida 33458
| | - Nikolay Korolev
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, Singapore 637551, and Biochemistry, The Scripps Research Institute, Parkside Drive, Jupiter, Florida 33458
| | - Khee Dong Eom
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, Singapore 637551, and Biochemistry, The Scripps Research Institute, Parkside Drive, Jupiter, Florida 33458
| | - James P. Tam
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, Singapore 637551, and Biochemistry, The Scripps Research Institute, Parkside Drive, Jupiter, Florida 33458
| | - Lars Nordenskiöld
- School of Biological Sciences, Nanyang Technological University, 60, Nanyang Drive, Singapore 637551, and Biochemistry, The Scripps Research Institute, Parkside Drive, Jupiter, Florida 33458
| |
Collapse
|
33
|
Shew CY, Yoshikawa K. Mean field theory for the intermolecular and intramolecular conformational transitions of a single flexible polyelectrolyte chain. J Chem Phys 2007; 126:144913. [PMID: 17444749 DOI: 10.1063/1.2714552] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The diMarzio theory has been extended to elucidate the intermolecular and intramolecular phase segregations of a single flexible chain polyelectrolyte in dilute salt-free solutions. At the long chain limit, this theory yields the formalism obtained from the more sophisticated Edward Hamiltonian for polyelectrolyte problems. The calculated phase diagram exhibits the features of a first-order phase transition, with continuous and discontinuous transitions separated by a critical point. Under the discontinuous transition, the polyelectrolyte chain exhibits coexistent expanded and collapsed conformational states, same as intermolecular phase segregation. For a limiting long chain, the mean chain size at critical point is roughly 90% of the size of an ideal chain. Such a result implies that partial contraction within a chain molecule is required to collapse a flexible polyelectrolyte chain. Moreover, the theory predicts that for a longer chain, intramolecular segregated conformations differ significantly from intermolecular segregated conformations, but the difference becomes small for shorter chains. Besides, the charge needed to induce intramolecular segregation is smaller than that of intermolecular segregation for a given chain length. These findings are consistent with previous literature results.
Collapse
Affiliation(s)
- Chwen-Yang Shew
- Department of Chemistry, College of Staten Island and Graduate Center, City University of New York, Staten Island, New York 10314, USA.
| | | |
Collapse
|
34
|
Ayoubi MA, Zinchenko AA, Philippova OE, Khokhlov AR, Yoshikawa K. Visualization of Different Pathways of DNA Release from Interpolyelectrolyte Complex. J Phys Chem B 2007; 111:8373-8. [PMID: 17432898 DOI: 10.1021/jp070261w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The release of double-stranded DNA from its interpolyelectrolyte complex with positively charged poly(allylamine hydrochloride) via exchange reaction with added polyanion, poly(sodium styrenesulfonate), is directly observed by fluorescence microscopy. It is shown that the pathways of DNA release depend essentially on the amount of added low-molecular-weight salt. At low salt content, the DNA release proceeds via the formation of an intermediate "beads-on-string" structure, whereas at high salt content the release goes directly from globule to coil states without any intermediate structures. The reasons for different character of DNA release are discussed.
Collapse
Affiliation(s)
- Mehran Asad Ayoubi
- Physics Department, Moscow State University, Moscow 119992, Russia, and Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | | | | | | | |
Collapse
|
35
|
Nakanishi H, Tsuchiya K, Okubo T, Sakai H, Abe M. Cationic surfactant changes the morphology of DNA molecules. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:345-7. [PMID: 17209572 DOI: 10.1021/la051443p] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The effect of cetyltrimethylammonium bromide (CTAB), a cationic surfactant, was investigated on the aggregated form of DNA molecules in water at a given temperature. CTAB caused changes in the aggregated form of DNA molecules from loosely packed spherical to rodlike through toroidal one with increasing concentration below the critical micelle concentration (CMC). The change was suggested to arise from the ion complex formation between CTAB and DNA molecules due to the electrostatic interaction, thereby reducing the surface charge and solubility in water of the latter.
Collapse
Affiliation(s)
- Hisanori Nakanishi
- Faculty of Science and Technology, Tokyo University of Science, Yamazaki 2641, Noda, Chiba 278-8510, Japan
| | | | | | | | | |
Collapse
|
36
|
Sakaue T, Yoshikawa K. On the formation of rings-on-a-string conformations in a single polyelectrolyte chain: A possible scenario. J Chem Phys 2007; 125:074904. [PMID: 16942377 DOI: 10.1063/1.2244555] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Recent single-molecular observations have revealed that a single giant DNA molecule assumes (micro) phase separated structures upon the addition of condensing agents. Electron and atomic force microscopy have clearly shown the coexistence of ordered tori and disordered coil structures within a single DNA molecule. Motivated by these experimental findings, we theoretically investigated the collapse transition of a single polyelectrolyte chain driven by the addition of condensing guest molecules. We found that the transition behavior critically depends on the degree of the surviving charge inside the torus. When the torus is charged, even slightly, "rings-on-a-string" structures are expected for a sufficiently long chain, owing to the combinational entropy of segment state distribution along the chain and the unique property of the stability of charged torus.
Collapse
Affiliation(s)
- Takahiro Sakaue
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
| | | |
Collapse
|
37
|
Kobori T, Iwamoto S, Takeyasu K, Ohtani T. Chromatin dynamics of unfolding and refolding controlled by the nucleosome repeat length and the linker and core histones. Biopolymers 2007; 85:295-307. [PMID: 17211885 DOI: 10.1002/bip.20671] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Chromatin is composed of genomic DNA and histones, forming a hierarchical architecture in the nucleus. The chromatin hierarchy is common among eukaryotes despite different intrinsic properties of the genome. To investigate an effect of the differences in genome organization, chromatin unfolding processes were comparatively analyzed using Schizosaccaromyces pombe, Saccharomyces cerevisiae, and chicken erythrocyte. NaCl titration showed dynamic changes of the chromatin. 400-1000 mM NaCl facilitated beads with approximately 115 nm in diameter in S. pombe chromatin. A similar transition was also observed in S. cerevisiae chromatin. This process did not involve core histone dissociation from the chromatin, and the persistence length after the transition was approximately 26 nm for S. pombe and approximately 28 nm for S. cerevisiae, indicating a salt-induced unfolding to "beads-on-a-string" fibers. Reduced salt concentration recovered the original structure, suggesting that electrostatic interaction would regulate this discrete folding-unfolding process. On the other hand, the linker histone was extracted from chicken chromatin at 400 mM NaCl, and AFM observed the "beads-on-a-string" fibers around a nucleus. Unlike yeast chromatin, therefore, this unfolding was irreversible because of linker histone dissociation. These results indicate that the chromatin unfolding and refolding depend on the presence and absence of the linker histone, and the length of the linker DNA.
Collapse
Affiliation(s)
- Toshiro Kobori
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan.
| | | | | | | |
Collapse
|
38
|
Frerix A, Schönewald M, Geilenkirchen P, Müller M, Kula MR, Hubbuch J. Exploitation of the coil-globule plasmid DNA transition induced by small changes in temperature, pH salt, and poly(ethylene glycol) compositions for directed partitioning in aqueous two-phase systems. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:4282-90. [PMID: 16618176 DOI: 10.1021/la052745u] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
In this study, the interplay of two linked equilibria is examined, one concerning an aqueous two-phase system (ATPS) composed of poly(ethylene glycol) (PEG) and salt employed to partition plasmid DNA (pDNA), and the other a potential structural transition of pDNA depending on PEG and salt concentration and other system parameters. The boundary conditions for pDNA partitioning are set by PEG and salt concentrations, PEG molecular weight, pH, and temperature. While investigating these parameters, it was found that a small increase/decrease of the respective values led to a drastic and significant change in pDNA behavior. This behavior could be attributed to a coil-globule transition of the pDNA triggered by the respective phase conditions. The combination of this structural change, aggregation effects linked to the transition process, and the electrostatic potential difference found in PEG-salt systems thus offers a sensitive way to separate nucleic acid forms on the basis of their unique property to undergo coil-globule transitions under distinct system properties.
Collapse
Affiliation(s)
- Andreas Frerix
- Institut für Biotechnologie 2, Forschungszentrum Jülich, 52426 Jülich, Germany
| | | | | | | | | | | |
Collapse
|
39
|
Zhou X, Chen S, Zhang D, Guo X, Ding W, Chen Y. Microsphere organization of nanorods directed by PEG linear polymer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2006; 22:1383-7. [PMID: 16460048 DOI: 10.1021/la052105r] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We demonstrate the sphere organization of ZnO, Bi2S3, MnO2, and La(OH)3 nanorods directed by PEG linear polymer. Our study shows that zinc, bismuth, manganese, or lanthanum species added to PEG solutions, in which PEG molecules are well dissolved in a coil state, convert the polymer coils to aggregate structures, which further aggregate into micrometer-sized M(n+)-PEG globules. The concentration of metallic species is higher in the globules than in bulk solutions. The surfaces of the globules act as soft templates for the initial nucleation and thereafter the growth of the nanorods. Finally, echinus-type assemblies of single-crystalline nanorods form by the metallic species hydrolyzing or reacting with deposition agents. This approach opens the possibility of using polymers as soft templates to control the organization of nano building units into designed structures.
Collapse
Affiliation(s)
- Xingfu Zhou
- Lab of Mesoscopic Chemistry, Department of Chemistry, Nanjing University, Nanjing 210093, China
| | | | | | | | | | | |
Collapse
|
40
|
Sarraguça JMG, Pais AACC. Polyelectrolytes in solutions with multivalent salt. Effects of flexibility and contour length. Phys Chem Chem Phys 2006; 8:4233-41. [PMID: 16971992 DOI: 10.1039/b606087k] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
It has been experimentally observed that trivalent ions are capable of promoting compaction of semi-flexible polyelectrolyte chains. In this work we perform Monte Carlo simulations on single chain model systems with varying chain size and stiffness and evaluate the action of multivalent salt on the chain conformation. It is observed that longer chains tend to achieve relatively more compact conformations than shorter ones, and the dimensions of the collapsed structures do not significantly vary with contour length. The influence of contour length and intrinsic stiffness in the process of ion condensation is studied by analysis of the ion-ion nearest-neighbor distribution. The general trend is an increase of the degree of ion condensation as the chain length increases, in accordance with experimental evidence. A decreased importance of end-effects and, especially, larger volume charge densities are responsible for such behavior. The influence of chain stiffness is nontrivial, and depends on salt concentration. The results emphasize the complex nature of ion-correlation phenomena in flexible or semi-flexible chains and call for the development of more sophisticated analytical theories.
Collapse
Affiliation(s)
- J M G Sarraguça
- Departamento de Química, Universidade de Coimbra, 3004-535, Coimbra, Portugal
| | | |
Collapse
|
41
|
Single macromolecules: hierarchic thermodynamics, irreversibility and biological function. J Biol Phys 2005; 31:243-8. [PMID: 23345896 DOI: 10.1007/s10867-005-7285-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
Single homo-polymers show two different paths in the folding transition; a liquid-like spherical globule is generated for flexible polymers, whereas a rich variety of ordered structures are formed for semi-flexible polymers. This unique characteristic is discussed in relation to its biological significance.
Collapse
|
42
|
Krízová J, Spanová A, Rittich B, Horák D. Magnetic hydrophilic methacrylate-based polymer microspheres for genomic DNA isolation. J Chromatogr A 2005; 1064:247-53. [PMID: 15739893 DOI: 10.1016/j.chroma.2004.12.014] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Carboxyl groups containing magnetic and non-magnetic microspheres were used in solid-phase reversible immobilization (SPRI) of genomic DNA. Magnetic non-porous poly(2-hydroxyethyl methacrylate-co-ethylene dimethacrylate)--P(HEMA-co-EDMA), poly(glycidyl methacrylate)--PGMA and P(HEMA-co-GMA) microspheres with hydrophilic properties were prepared by dispersion copolymerization of the respective monomers in the presence of colloidal iron oxides. DNA from chicken erythrocytes and DNA isolated from bacterial cells of Bifidobacterium longum was used for testing of adsorption/desorption properties of magnetic microspheres. The occurrence of false negative results in polymerase chain reaction (PCR) caused by the presence of extracellular inhibitors in DNA samples has been solved using SPRI. The P(HEMA-co-EDMA) and P(HEMA-co-GMA) microspheres were used for isolation of DNA from different dairy products followed by PCR identification of Bifidobacterium strains.
Collapse
Affiliation(s)
- Jana Krízová
- Masaryk University Brno, Faculty of Science, Department of Microbiology, Tvrdého 14, 60200 Brno, Czech Republic
| | | | | | | |
Collapse
|
43
|
Abstract
Using fluorescence microscopy (FM), which permits the observation of single molecules, we found that a pearling structure is generated on a single long DNA molecule upon the addition of a gemini (dimeric) surfactant. This pearling structure was further investigated by performing atomic force microscopy measurements on the same DNA molecules as observed by FM. These observations revealed that the pearling structure is composed of many rings that are interconnected by elongated coil parts along a single DNA molecule, i.e., rings-on-a-string structure. The mechanism of the formation of such an intrachain segregated structure in terms of microphase separation on a single polyelectrolyte chain is discussed.
Collapse
Affiliation(s)
- Naomi Miyazawa
- Department of Environmental Engineering, Nagoya University, Nagoya 464-8601, Japan
| | | | | | | |
Collapse
|
44
|
Koyama Y, Ito T, Matsumoto H, Tanioka A, Okuda T, Yamaura N, Aoyagi H, Niidome T. Novel poly(ethylene glycol) derivatives with carboxylic acid pendant groups: synthesis and their protection and enhancing effect on non-viral gene transfection systems. JOURNAL OF BIOMATERIALS SCIENCE. POLYMER EDITION 2004; 14:515-31. [PMID: 12901435 DOI: 10.1163/15685620360674227] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Novel carboxylic acid pendant-containing poly(ethylene glycol) (PEG) derivatives (PEG-Cs) were synthesized by the chemical modification of the carbon-carbon double-bond side chain of copoly(allyl glycidyl ether/ethylene oxide) (copoly(AGE/EO)). PEG-C showed a protecting ability for the DNA/polycation complex from the albumin-induced aggregation. It also expressed the enhanced efficiency on the polycation-mediated gene transfection on the cultured cells (up to 3-4-times higher), probably due to its disperse-stabilizing property and also the proton-sponge effect.
Collapse
Affiliation(s)
- Yoshiyuki Koyama
- Department of Home Economics, Otsuma Women's University, Chiyoda-ku, Tokyo 102-8357, Japan.
| | | | | | | | | | | | | | | |
Collapse
|
45
|
Iwataki T, Kidoaki S, Sakaue T, Yoshikawa K, Abramchuk SS. Competition between compaction of single chains and bundling of multiple chains in giant DNA molecules. J Chem Phys 2004; 120:4004-11. [PMID: 15268566 DOI: 10.1063/1.1642610] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
It has been established that in a dilute solution individual giant DNA molecules undergo a large discrete transition between an elongated coil state and a folded compact state. On the other hand, in concentrated solutions, DNA molecules assemble into various characteristic states, including multichain aggregate, liquid crystalline, ionic crystal, etc. In this study, we compared single-chain and multiple-chain events by observing individual chains using fluorescence microscopy. We used spermidine, SPD(3+), as a condensing agent for giant DNA. When the concentration of DNA is below 1 microM in base-pair units, individual DNA molecules exhibit a transition from an elongated state to a compact state. When the concentration of DNA is increased to 10 microM, a thick fiberlike assembly of multiple chains appears. AFM measurements of this thick fiber revealed that more than tens of DNA molecules form a bundle structure with parallel ordering of the chains. The transition between single-chain compaction and bundle formation with multiple-chain assemblies was reproduced by a theoretical calculation.
Collapse
Affiliation(s)
- Toshio Iwataki
- Department of Physics, Graduate School of Science, Kyoto University, 606-8502, Japan
| | | | | | | | | |
Collapse
|
46
|
Itaka K, Yamauchi K, Harada A, Nakamura K, Kawaguchi H, Kataoka K. Polyion complex micelles from plasmid DNA and poly(ethylene glycol)-poly(L-lysine) block copolymer as serum-tolerable polyplex system: physicochemical properties of micelles relevant to gene transfection efficiency. Biomaterials 2003; 24:4495-506. [PMID: 12922159 DOI: 10.1016/s0142-9612(03)00347-8] [Citation(s) in RCA: 183] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Polyion complex (PIC) micelles composed of the poly(ethylene glycol)-poly(L-lysine) (PEG-PLL) block copolymer and plasmid DNA (pDNA) were investigated in this study from a physicochemical viewpoint to get insight into the structural feature of the PIC micellar vector system to show practical gene transfection efficacy particularly under serum-containing medium. The residual ratio (r) of the lysine units in PEG-PLL to the phosphate units of pDNA in the system significantly affects the size of the PIC micelles evaluated from dynamic light scattering, being decreased from approximately 120 to 80 nm with an increase in the r value for the region with r > or = 1.0. The zeta potential of the complexes slightly increased with r in the same region, yet maintained a very small absolute value and leveled off to a few mV at r approximately 2.0. These results suggest that the micelles are most likely to take the core-shell structure with dense PEG palisades surrounding the PIC core to compartmentalize the condensed pDNA. Furthermore, an increasing r value in the region of r > or = 1 induces a rearrangement of the stoichiometric complex formed at r=1.0 to the non-stoichiometric complex composed of the excess block copolymer. The association number of pDNA and the block copolymer in the micelle was estimated from the apparent micellar molecular weight determined by static light scattering measurements, indicating that a single pDNA molecule was incorporated in each of the micelles prepared from the PEG (Mw=12,000 g/mol)-PLL (polymerization degree of PLL segment: 48) (12-48) block copolymer at r=2.0. These 12-48/pDNA micelles showed a gene expression comparable to the lipofection toward cultured 293 cells, though 100 microM chloroquine was required in the transfection medium. Notably, even in the presence of serum, the PIC micelles achieved appreciable cellular association to attain a high gene expression, which is in sharp contrast with the drastic decrease in the gene expression for lipoplex system in the presence of serum. A virus-comparable size (approximately 100 nm) with a serum-tolerable property of the PIC micelles indeed suggests their promising feasibility as non-viral gene-vector systems used for clinical gene therapy.
Collapse
Affiliation(s)
- Keiji Itaka
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | | | | | | | | | | |
Collapse
|
47
|
Iwaki T, Yoshikawa K. Competition between interchain and intrachain phase segregation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2003; 68:031902. [PMID: 14524798 DOI: 10.1103/physreve.68.031902] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2003] [Indexed: 05/24/2023]
Abstract
Single-molecule observations of giant DNA have clarified that individual molecules undergo a marked discrete transition between an elongated coil state and a compact globule state. There is a relatively wide region of coexistence between the coil and the globule states, i.e., interchain phase segregation, with a change in intensive variables such as the concentration of the condensing agent, salt concentration, temperature. Very recently, the coexistence of coil and globule conformations within a single long DNA chain, i.e., intrachain phase segregation, has been reported under certain experimental conditions. In this study, we investigated general conditions for intrachain phase segregation in a single polyelectrolyte molecule, based on a simple statistical model. We consider the contribution of condensed counterions and the interaction energy of a charged coiled region. Intrachain phase segregation is stable with regard to free energy within a suitable parameter region. Our results suggest that intrachain phase segregation occurs when the electrostatic screening effect by the salt solution is negligible or when the screening effect is large and there is attractive interaction between polyelectrolyte segments.
Collapse
Affiliation(s)
- T Iwaki
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
| | | |
Collapse
|
48
|
Yoshikawa Y, Suzuki M, Chen N, Zinchenko AA, Murata S, Kanbe T, Nakai T, Oana H, Yoshikawa K. Ascorbic acid induces a marked conformational change in long duplex DNA. EUROPEAN JOURNAL OF BIOCHEMISTRY 2003; 270:3101-6. [PMID: 12846844 DOI: 10.1046/j.1432-1033.2003.03699.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Ascorbic acid is often regarded as an antioxidant in vivo, where it protects against cancer by scavenging DNA-damaging reactive oxygen species. However, the detailed mechanism of the action of ascorbic acid on genetic DNA is still unclear. We examined the effect of ascorbic acid on the higher-order structure of DNA through real-time observation by fluorescence microscopy. We found that ascorbic acid generates a pearling structure in single giant DNA molecules, with elongated and compact regions coexisting along a molecular chain. Results from electron microscopy and atomic force microscopy indicate that the compact regions assume a loosely packed conformation. A possible mechanism for the induction of this conformational change is discussed in relation to the interplay between the higher-order and second-order structures of DNA.
Collapse
Affiliation(s)
- Yuko Yoshikawa
- Department of Food and Nutrition, Nagoya Bunri College, Japan.
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
|
50
|
Mikhailenko SV, Sergeyev VG, Zinchenko AA, Gallyamov MO, Yaminsky IV, Yoshikawa K. Interplay between folding/unfolding and helix/coil transitions in giant DNA. Biomacromolecules 2002; 1:597-603. [PMID: 11710187 DOI: 10.1021/bm0055403] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
It has been well established that double-stranded DNA undergoes a melting, or helix/coil, transition into a single-stranded coil state with an increase in temperature. On the other hand, it has recently been found that, at a fixed temperature, long DNA, larger than several kilobase pairs, exhibits a discrete transition, or switching, between elongated and folded states, preserving its double-stranded structure, with the addition of various condensation agents, such as alcohol, hydrophilic polymer, multivalent cation, and cationic surfactant. In the present study, we examined the interplay between the folding/unfolding transition and the helix/coil transition in individual giant DNA molecules, by observing the conformation of single molecular chains with fluorescence microscopy. The results indicate that the helix-to-coil transition tightly cooperates with the unfolding transition in DNA.
Collapse
Affiliation(s)
- S V Mikhailenko
- Graduate School of Human Informatics, Nagoya University, Nagoya 464-8601, Japan.
| | | | | | | | | | | |
Collapse
|