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Kim YH, Jeon N, Park S, Choi SQ, Lee E, Li S. Complexation of Poly(ethylene glycol)-(ds)OligoDNA Conjugates with Ionic Liquids. ACS Macro Lett 2024; 13:528-536. [PMID: 38629344 DOI: 10.1021/acsmacrolett.4c00028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
We report the complexation of poly(ethylene glycol) conjugated double-stranded oligoDNA (PEG-(ds)oligoDNA) with imidazolium-based ionic liquids (ILs) to form polyelectrolyte complex aggregates (PCAs). The PEG-(ds)oligoDNA conjugates are prepared following a solution-phase coupling reaction. The binding of PEG-(ds)oligoDNA with either 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) or 1-hexyl-3-methylimidazolium tetrafluoroborate ([HMIM][BF4]) is confirmed by a fluorescence displacement assay. Both ILs show stronger binding affinity to PEG-(ds)oligoDNA than bare (ds)oligoDNA due to the PEG-assisted increase in IL cation concentration in the vicinity of (ds)oligoDNA. The complex morphology formed at various amine (N) to phosphate (P) ratios is also examined. At high N/P ratios above 4, nanosized PCAs are formed, driven by a counterion-mediated attraction among the IL-bound (ds)oligoDNA segments and stabilized by the conjugated PEG segments. The PCAs exhibit near-neutral surface charges and resistance to DNase degradation, suggesting their potential use in gene delivery applications.
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Affiliation(s)
- Young Hun Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Nayeong Jeon
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sujin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Eunji Lee
- School of Materials Science and Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Sheng Li
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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Sarkar S, Dey U, Khohliwe TB, Yella VR, Kumar A. Analysis of nucleoid-associated protein-binding regions reveals DNA structural features influencing genome organization in Mycobacterium tuberculosis. FEBS Lett 2021; 595:2504-2521. [PMID: 34387867 DOI: 10.1002/1873-3468.14178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/01/2021] [Accepted: 08/11/2021] [Indexed: 11/10/2022]
Abstract
Nucleoid-associated proteins (NAPs) maintain bacterial nucleoid configuration through their architectural properties of DNA bending, wrapping, and bridging. However, the contribution of DNA structural alterations to DNA-NAP recognition at the genomic scale remains unresolved. Present work dissects the DNA sequence, shape and altered structural preferences at a genomic scale for six NAPs in Mycobacterium tuberculosis. Results suggest narrower minor groove width (MGW) and higher DNA rigidity are marked for the binding sites of EspR and Lsr2, while mIHF, MtHU and NapM have heterogeneous DNA structural predilections. In contrast, WhiB4-DNA-binding sites were characterized by wider MGW, highly deformable and less curved DNA. This work provides systematic insight into NAP-mediated genome organization as a function of DNA structural features.
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Affiliation(s)
- Sharmilee Sarkar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | - Upalabdha Dey
- Department of Molecular Biology and Biotechnology, Tezpur University, India
| | | | - Venkata Rajesh Yella
- Department of Biotechnology, Koneru Lakshmaiah Education Foundation, Guntur, India
| | - Aditya Kumar
- Department of Molecular Biology and Biotechnology, Tezpur University, India
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Wong JTY. Architectural Organization of Dinoflagellate Liquid Crystalline Chromosomes. Microorganisms 2019; 7:microorganisms7020027. [PMID: 30678153 PMCID: PMC6406473 DOI: 10.3390/microorganisms7020027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/12/2019] [Accepted: 01/17/2019] [Indexed: 12/12/2022] Open
Abstract
Dinoflagellates have some of the largest genome sizes, but lack architectural nucleosomes. Their liquid crystalline chromosomes (LCCs) are the only non-architectural protein-mediated chromosome packaging systems, having high degrees of DNA superhelicity, liquid crystalline condensation and high levels of chromosomal divalent cations. Recent observations on the reversible decompaction–recompaction of higher-order structures implicated that LCCs are composed of superhelical modules (SPMs) comprising highly supercoiled DNA. Orientated polarizing light photomicrography suggested the presence of three compartments with different packaging DNA density in LCCs. Recent and previous biophysical data suggest that LCCs are composed of: (a) the highly birefringent inner core compartment (i) with a high-density columnar-hexagonal mesophase (CH-m); (b) the lower-density core surface compartment (ii.1) consisting of a spiraling chromonema; (c) the birefringent-negative periphery compartment (ii.2) comprising peripheral chromosomal loops. C(ii.1) and C(ii.2) are in dynamic equilibrium, and can merge into a single compartment during dinomitosis, regulated through multiphasic reversible soft-matter phase transitions.
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Affiliation(s)
- Joseph Tin Yum Wong
- Division of Life Science, Hong Kong University of Life Science, Clearwater Bay, Kowloon, Hong Kong.
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Li Y, Manzano I, Zydney AL. Effects of polyamines on the ultrafiltration of plasmid DNA. Biotechnol Prog 2018; 35:e2765. [DOI: 10.1002/btpr.2765] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Revised: 12/06/2018] [Accepted: 12/07/2018] [Indexed: 01/14/2023]
Affiliation(s)
- Ying Li
- Dept. of Chemical Engineering The Pennsylvania State University University Park PA 16802
| | - Ivan Manzano
- Dept. of Chemical Engineering The Pennsylvania State University University Park PA 16802
| | - Andrew L. Zydney
- Dept. of Chemical Engineering The Pennsylvania State University University Park PA 16802
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Calcium enhances gene expression when using low molecular weight poly-l-lysine delivery vehicles. Int J Pharm 2018; 547:274-281. [DOI: 10.1016/j.ijpharm.2018.05.067] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 05/23/2018] [Accepted: 05/28/2018] [Indexed: 11/17/2022]
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6
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Importance of hydrophobic interactions in the single-chained cationic surfactant-DNA complexation. J Colloid Interface Sci 2018; 521:197-205. [PMID: 29571101 DOI: 10.1016/j.jcis.2018.03.048] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/10/2018] [Accepted: 03/14/2018] [Indexed: 12/12/2022]
Abstract
The goal of this work was to understand the key factors determining the DNA compacting capacity of single-chained cationic surfactants. Fluorescence, zeta potential, circular dichroism, gel electrophoresis and AFM measurements were carried out in order to study the condensation of the nucleic acid resulting from the formation of the surfactant-DNA complexes. The apparent equilibrium binding constant of the surfactants to the nucleic acid, Kapp, estimated from the experimental results obtained in the ethidium bromide competitive binding experiments, can be considered directly related to the ability of a given surfactant as a DNA compacting agent. The plot of ln(Kapp) vs. ln(cmc), cmc being the critical micelle concentration, for all the bromide and chloride surfactants studied, was found to be a reasonably good linear correlation. This result shows that hydrophobic interactions mainly control the surfactant DNA compaction efficiency.
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Choi G, Eom S, Vinu A, Choy JH. 2D Nanostructured Metal Hydroxides with Gene Delivery and Theranostic Functions; A Comprehensive Review. CHEM REC 2018; 18:1033-1053. [DOI: 10.1002/tcr.201700091] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/26/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Goeun Choi
- Center for Intelligent Nano-Bio Materials (CINBM) Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Republic of Korea
| | - Sairan Eom
- Center for Intelligent Nano-Bio Materials (CINBM) Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Republic of Korea
| | - Ajayan Vinu
- Global Innovative Center for Advanced Nanomaterials Faculty of Engineering and Natural Built Environment The University of Newcastle; University Drive; Callaghan NSW 2308 Australia
| | - Jin-Ho Choy
- Center for Intelligent Nano-Bio Materials (CINBM) Department of Chemistry and Nano Science; Ewha Womans University; Seoul 03760 Republic of Korea
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Unksov IN, Kasyanenko NA. Conformational changes in the DNA molecule in solution caused by the binding of a light-sensitive cationic surfactant. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020287] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Direct Evidence of Divalent Manganese Ion-Induced DNA Condensation at Room Temperature. MACROMOL CHEM PHYS 2016. [DOI: 10.1002/macp.201600123] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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10
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Batoulis H, Schmidt TH, Weber P, Schloetel JG, Kandt C, Lang T. Concentration Dependent Ion-Protein Interaction Patterns Underlying Protein Oligomerization Behaviours. Sci Rep 2016; 6:24131. [PMID: 27052788 PMCID: PMC4823792 DOI: 10.1038/srep24131] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 03/21/2016] [Indexed: 11/09/2022] Open
Abstract
Salts and proteins comprise two of the basic molecular components of biological materials. Kosmotropic/chaotropic co-solvation and matching ion water affinities explain basic ionic effects on protein aggregation observed in simple solutions. However, it is unclear how these theories apply to proteins in complex biological environments and what the underlying ionic binding patterns are. Using the positive ion Ca2+ and the negatively charged membrane protein SNAP25, we studied ion effects on protein oligomerization in solution, in native membranes and in molecular dynamics (MD) simulations. We find that concentration-dependent ion-induced protein oligomerization is a fundamental chemico-physical principle applying not only to soluble but also to membrane-anchored proteins in their native environment. Oligomerization is driven by the interaction of Ca2+ ions with the carboxylate groups of aspartate and glutamate. From low up to middle concentrations, salt bridges between Ca2+ ions and two or more protein residues lead to increasingly larger oligomers, while at high concentrations oligomers disperse due to overcharging effects. The insights provide a conceptual framework at the interface of physics, chemistry and biology to explain binding of ions to charged protein surfaces on an atomistic scale, as occurring during protein solubilisation, aggregation and oligomerization both in simple solutions and membrane systems.
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Affiliation(s)
- Helena Batoulis
- Membrane Biochemistry, Life &Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Thomas H Schmidt
- Membrane Biochemistry, Life &Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Pascal Weber
- Membrane Biochemistry, Life &Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jan-Gero Schloetel
- Membrane Biochemistry, Life &Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Christian Kandt
- Life Science Informatics B-IT, Computational Structural Biology, University of Bonn, Germany
| | - Thorsten Lang
- Membrane Biochemistry, Life &Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
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Kopaczynska M, Schulz A, Fraczkowska K, Kraszewski S, Podbielska H, Fuhrhop JH. Selective condensation of DNA by aminoglycoside antibiotics. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 45:287-99. [PMID: 26646261 PMCID: PMC4823326 DOI: 10.1007/s00249-015-1095-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 10/05/2015] [Accepted: 10/29/2015] [Indexed: 11/30/2022]
Abstract
The condensing effect of aminoglycoside antibiotics on the structure of double-stranded DNA was examined. The selective condensation of DNA by small molecules is an interesting approach in biotechnology. Here, we present the interaction between calf thymus DNA and three types of antibiotic molecules: tobramycin, kanamycin, and neomycin. Several techniques were applied to study this effect. Atomic force microscopy, transmission electron microscopy images, and nuclear magnetic resonance spectra showed that the interaction of tobramycin with double-stranded DNA caused the rod, toroid, and sphere formation and very strong condensation of DNA strands, which was not observed in the case of other aminoglycosides used in the experiment. Studies on the mechanisms by which small molecules interact with DNA are important in understanding their functioning in cells, in designing new and efficient drugs, or in minimizing their adverse side effects. Specific interactions between tobramycin and DNA double helix was modeled using molecular dynamics simulations. Simulation study shows the aminoglycoside specificity to bend DNA double helix, shedding light on the origins of toroid formation. This phenomenon may lighten the ototoxicity or nephrotoxicity issues, but also other adverse reactions of aminoglycoside antibiotics in the human body.
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Affiliation(s)
- M Kopaczynska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland.
| | - A Schulz
- Institut für Chemie and Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
| | - K Fraczkowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - S Kraszewski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - H Podbielska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Technology, Wybrzeże Wyspiańskiego 27, 50-370, Wrocław, Poland
| | - J H Fuhrhop
- Institut für Chemie and Biochemie, Organische Chemie, Freie Universität Berlin, Takustr. 3, 14195, Berlin, Germany
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Danilevich VN, Machulin AV, Lipkin AV, Kulakovskaya TV, Smith SS, Mulyukin AL. New insight into formation of DNA-containing microparticles during PCR: the scaffolding role of magnesium pyrophosphate crystals. J Biomol Struct Dyn 2015; 34:625-39. [PMID: 25891071 DOI: 10.1080/07391102.2015.1040842] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
This work aims to study molecular mechanisms involved in the formation of DNA-containing microparticles and nanoparticles during PCR. Both pyrophosphate and Mg(2+) ions proved to play an important role in the generation of DNA microparticles (MPs) with a unique and sophisticated structure in PCR with Taq polymerase. Thus, the addition of Tli thermostable pyrophosphatase to a PCR mixture inhibited this process and caused the destruction of synthesized DNA MPs. Thermal cycling of Na-pyrophosphate (Na-PPi)- and Mg(2+)-containing mixtures (without DNA polymerase and dNTPs) under the standard PCR regime yielded crystalline oval or lenticular microdisks and 3D MPs composed from magnesium pyrophosphate (Mg-PPi). As shown by scanning electron microscopy (SEM), the produced Mg-PPi microparticles consisted of intersecting disks or their segments. They were morphologically similar but simpler than DNA-containing MPs generated in PCR. The incorporation of dNTPs, primers, or dsDNA into Mg-pyrophosphate particles resulted in the structural diversification of 3D microparticles. Thus, the unusual and complex structure of DNA MPs generated in PCR is governed by the unique feature of Mg-pyrophosphate to form supramolecular particles during thermal cycling. We hypothesize the Mg-pyrophosphate particles that are produced during thermal cycling serve as scaffolds for amplicon DNA condensation.
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Affiliation(s)
- Vasily N Danilevich
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
| | - Andrey V Machulin
- b Skryabin Institute of Biochemistry and Physiology of Microorganisms , Russian Academy of Sciences , Pr. Nauki 5, 142290 Pushchino , Moscow Region, Russia
| | - Alexey V Lipkin
- a Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry , Russian Academy of Science , ul. Miklukho-Maklaya 16/10, Moscow 117997 , Russia
| | - Tatyana V Kulakovskaya
- b Skryabin Institute of Biochemistry and Physiology of Microorganisms , Russian Academy of Sciences , Pr. Nauki 5, 142290 Pushchino , Moscow Region, Russia
| | - Steven S Smith
- c Beckman Research Institute and Division of Urology and Urologic Oncology , City of Hope National Medical Center , 1500 E. Duarte Rd., Duarte , CA 91010 , USA
| | - Andrey L Mulyukin
- d Winogradsky Institute of Microbiology , Russian Academy of Science , Pr. 60-letiya Oktyabrya 7/2, Moscow 117312 , Russia
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Ostos F, Lebron J, Moyá M, Deasy M, López-Cornejo P. Binding of DNA by a dinitro-diester calix[4]arene: Denaturation and condensation of DNA. Colloids Surf B Biointerfaces 2015; 127:65-72. [DOI: 10.1016/j.colsurfb.2015.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Revised: 12/12/2014] [Accepted: 01/12/2015] [Indexed: 12/27/2022]
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García JP, Marrón E, Martín VI, Moyá ML, Lopez-Cornejo P. Conformational changes of DNA in the presence of 12-s-12 gemini surfactants (s=2 and 10). Role of the spacer's length in the interaction surfactant-polynucleotide. Colloids Surf B Biointerfaces 2014; 118:90-100. [PMID: 24736044 DOI: 10.1016/j.colsurfb.2014.03.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 02/22/2014] [Accepted: 03/16/2014] [Indexed: 12/27/2022]
Abstract
A multifaceted study on the interaction of calf-thymus DNA with two different cationic gemini surfactants alkanediyl-α-ω-bis(dodecyldimethyl-amonium)bromide, 12-s-12,2Br(-) (with s=2, G2, and 10, G10) was carried out. The measurements were done at different molar ratios X=[surfactant]/[DNA]. Results show two different conformational changes in DNA: a first compaction of the polynucleotide corresponding to a partial conformational (not total) change of DNA from an extended coil state to a globular state that happens at the lower molar ratio X. A second change corresponds to a breaking of the partial condensation, that is, the transition from the compacted state to a new more extended conformation (for the higher X values) different to the initial extension. According to circular dichroism spectra and dynamic light scattering measurements, this new state of DNA seems to be similar to a ψ-phase. Measurements confirm that interactions involved in the compaction are different to those previously obtained for the analog surfactant CTAB. X values at which the conformational changes happen depend on the length of the spacer in the surfactant along with the charge of the polar heads.
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Affiliation(s)
- J P García
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, c/Prof. García González n° 1, Sevilla 41012, Spain
| | - E Marrón
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, c/Prof. García González n° 1, Sevilla 41012, Spain
| | - V I Martín
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, c/Prof. García González n° 1, Sevilla 41012, Spain
| | - M L Moyá
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, c/Prof. García González n° 1, Sevilla 41012, Spain
| | - P Lopez-Cornejo
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, c/Prof. García González n° 1, Sevilla 41012, Spain.
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Janmey PA, Slochower DR, Wang YH, Wen Q, Cēbers A. Polyelectrolyte properties of filamentous biopolymers and their consequences in biological fluids. SOFT MATTER 2014; 10:1439-49. [PMID: 24651463 PMCID: PMC4009494 DOI: 10.1039/c3sm50854d] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Anionic polyelectrolyte filaments are common in biological cells. DNA, RNA, the cytoskeletal filaments F-actin, microtubules, and intermediate filaments, and polysaccharides such as hyaluronan that form the pericellular matrix all have large net negative charge densities distributed over their surfaces. Several filamentous viruses with diameters and stiffnesses similar to those of cytoskeletal polymers also have similar negative charge densities. Extracellular protein filaments such collagen, fibrin and elastin, in contrast, have notably smaller charge densities and do not behave as highly charged polyelectrolytes in solution. This review summarizes data that demonstrate generic counterion-mediated effects on four structurally unrelated biopolymers of similar charge density: F-actin, vimentin, Pf1 virus, and DNA, and explores the possible biological and pathophysiological consequences of the polyelectrolyte properties of biological filaments.
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Affiliation(s)
- Paul A Janmey
- Institute for Medicine and Engineering, University of Pennsylvania, 1010 Vagelos Laboratories, 3340 Smith Walk, Philadelphia, PA 19104, USA
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Kikuchi T, Sato S, Fujita D, Fujita M. Stepwise DNA condensation by a histone-mimic peptide-coated M12L24 spherical complex. Chem Sci 2014. [DOI: 10.1039/c4sc00656a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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Danilevich VN, Artemov VV, Smith SS, Gainutdinov RV, Mulyukin AL. The structural peculiarities of condensed DNA micro- and nanoparticles formed in PCR. J Biomol Struct Dyn 2013; 32:1979-92. [DOI: 10.1080/07391102.2013.848411] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Zhou T, Llizo A, Wang C, Xu G, Yang Y. Nanostructure-induced DNA condensation. NANOSCALE 2013; 5:8288-8306. [PMID: 23838744 DOI: 10.1039/c3nr01630g] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The control of the DNA condensation process is essential for compaction of DNA in chromatin, as well as for biological applications such as nonviral gene therapy. This review endeavours to reflect the progress of investigations on DNA condensation effects of nanostructure-based condensing agents (such as nanoparticles, nanotubes, cationic polymer and peptide agents) observed by using atomic force microscopy (AFM) and other techniques. The environmental effects on structural characteristics of nanostructure-induced DNA condensates are also discussed.
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Affiliation(s)
- Ting Zhou
- National Center for Nanoscience and Technology (NCNST), Beijing 100190, PR China
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Grueso E, Cerrillos C, Hidalgo J, Lopez-Cornejo P. Compaction and decompaction of DNA induced by the cationic surfactant CTAB. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:10968-10979. [PMID: 22755509 DOI: 10.1021/la302373m] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
A multifaceted study on the interaction of the cationic surfactant CTAB with calf thymus DNA was carried out by using different techniques. The measurements were done at different molar ratios X = [CTAB]/[DNA]. Results show the conformational change that DNA suffers due to the interaction with surfactant molecules at low molar ratios: the condensation of the polynucleotide, from an extended coil state to a globular state. The effect observed at the higher molar ratios is worth noting: the decondensation of DNA, that is, the transition from a compact state to a more extended conformation. Experimental data obtained confirm that this latter state is not exactly the same as that found in the absence of the surfactant. Attractive interactions between different parts of the molecule by ion correlation effects are the driving force to produce both the compaction and decompaction events. Results also show the importance of choosing both a proper system for the study and the most seeming measuring technique to use. The study demonstrates that, in some cases, the use of several techniques is desirable in obtaining reliable and accurate results.
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Affiliation(s)
- E Grueso
- Department of Physical Chemistry, Faculty of Chemistry, University of Seville, Sevilla, Spain
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Danilevich VN. Rapid and efficient technique for the production of condensed DNA and RNA nanoparticles using thermal cycling. DOKL BIOCHEM BIOPHYS 2012; 443:71-5. [DOI: 10.1134/s1607672912020044] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Indexed: 11/23/2022]
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Derakhshankhah H, Saboury AA, Bazl R, Tajmir-Riahi HA, Falahati M, Ajloo D, Mansoori-Torshizi H, Divsalar A, Hekmat A, Moosavi-Movahedi AA. Synthesis, cytotoxicity and spectroscopy studies of a new copper (II) complex: calf thymus DNA and T47D as targets. JOURNAL OF THE IRANIAN CHEMICAL SOCIETY 2012. [DOI: 10.1007/s13738-012-0086-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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.
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Affiliation(s)
- Yuko Yoshikawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
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Danilevich VN, Vasilenko EA, Pechnikova EV, Grishin EV. New morphotypes of condensed DNA microparticles formed in PCR with KlenTaq and Taq polymerases and plasmid DNA as a template. Microbiology (Reading) 2012. [DOI: 10.1134/s002626171106004x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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26
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Yoshikawa Y, Komeda S, Uemura M, Kanbe T, Chikuma M, Yoshikawa K, Imanaka T. Highly Efficient DNA Compaction Mediated by an In Vivo Antitumor-Active Tetrazolato-Bridged Dinuclear Platinum(II) Complex. Inorg Chem 2011; 50:11729-35. [DOI: 10.1021/ic2017165] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yuko Yoshikawa
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
| | - Seiji Komeda
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670,
Japan
| | - Masako Uemura
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670,
Japan
| | - Toshio Kanbe
- Laboratory of Medical
Mycology,
Research Institute for Disease Mechanism and Control, School of Medicine, Nagoya University, Nagoya 464-0064, Japan
| | - Masahiko Chikuma
- Faculty of Pharmaceutical Sciences, Osaka University of Pharmaceutical Sciences, Takatsuki
569-1094, Japan
| | - Kenichi Yoshikawa
- Department of Physics, Graduate School of Science, Kyoto University, Kyoto 606-8501, Japan
| | - Tadayuki Imanaka
- Department of Biotechnology, College of Life Sciences, Ritsumeikan University, Kusatsu 525-8577, Japan
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Danilevich VN, Vasilenko EA, Pechnikova EV, Sokolova OS, Grishin EV. Micro- and nanoparticles of condensed DNA Formed in PCR with Taq polymerase and plasmid DNA as a template. Microbiology (Reading) 2011. [DOI: 10.1134/s0026261711030088] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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29
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Cherstvy AG. Electrostatic interactions in biological DNA-related systems. Phys Chem Chem Phys 2011; 13:9942-68. [DOI: 10.1039/c0cp02796k] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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31
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Tan ZJ, Chen SJ. Importance of diffuse metal ion binding to RNA. Met Ions Life Sci 2011; 9:101-24. [PMID: 22010269 PMCID: PMC4883094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
RNAs are highly charged polyanionic molecules. RNA structure and function are strongly correlated with the ionic condition of the solution. The primary focus of this article is on the role of diffusive ions in RNA folding. Due to the long-range nature of electrostatic interactions, the diffuse ions can contribute significantly to RNA structural stability and folding kinetics. We present an overview of the experimental findings as well as the theoretical developments on the diffuse ion effects in RNA folding. This review places heavy emphasis on the effect of magnesium ions. Magnesium ions play a highly efficient role in stabilizing RNA tertiary structures and promoting tertiary structural folding. The highly efficient role goes beyond the mean-field effect such as the ionic strength. In addition to the effects of specific ion binding and ion dehydration, ion-ion correlation for the diffuse ions can contribute to the efficient role of the multivalent ions such as the magnesium ions in RNA folding.
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Affiliation(s)
- Zhi-Jie Tan
- Department of Physics and Key Laboratory of Artificial Micro- and Nano-Structures of the Ministry of Education, School of Physics and Technology, Wuhan University, Wuhan 430 072, China
| | - Shi-Jie Chen
- Department of Physics & Astronomy and Department of Biochemistry, University of Missouri, Columbia MO 65211, USA
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Theory of crystallization of a closed macromolecule. Int J Biol Macromol 2010; 47:439-44. [DOI: 10.1016/j.ijbiomac.2010.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2010] [Revised: 06/16/2010] [Accepted: 06/21/2010] [Indexed: 11/16/2022]
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33
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Danilevich VN, Kadykov VA, Grishin EV. Condensed DNA particles formed in a PCR with plasmid templates: An electron microscopy study. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:535-46. [DOI: 10.1134/s1068162010040084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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34
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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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Danilevich VN, Kadykov VA, Grishin EV. Micro- and nanoparticles of condensed DNA formed in a PCR with yeast genomic DNA as a template. Electron microscopy data. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010; 36:375-86. [DOI: 10.1134/s106816201003009x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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36
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Yoshikawa K, Kidoaki S, Takahashi M, Vasilevskaya VV, Khokhlov AR. Marked discreteness on the coil-globule transition of single duplex DNA. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19961000631] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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37
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Danilevich VN, Barinova ES, Grishin EV. [Microparticles from coupled DNA formed in the process of polymerase chain reaction]. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2009; 35:226-38. [PMID: 19537174 DOI: 10.1134/s1068162009020095] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
DNA microparticle formation in the course of a polymerase chain reaction (PCR) is reported. PCR with gene-specific and partially complementary primers and yeast genomic DNA as a template was shown to yield spherical DNA-composed microparticles as well as their aggregates and conglomerates, along with routine linear DNA. Microparticles were formed at late PCR stages and could be easily identified by the reaction with fluorescently labeled oligonucleotide primers or by staining of the PCR mixture with fluorescent dyes (acridine orange, propidium iodide or DAPI). According to the data of epifluorescent and electron microscopy, the microparticle size varied from 500 nm to 3-4 microm and the particles were multimeric star-shaped spheres or aggregates formed by several fused microspheres. Some properties of the microspheres were studied. It was found that the Mg2+ cations comprising the PCR buffer played a key role in the formation of microparticles and the stabilization of their structures.
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38
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Danilevich VN, Grishin EV. Characteristics of microspheres formed in PCR with bacterial genomic DNA or plasmid DNA as templates. Microbiology (Reading) 2009. [DOI: 10.1134/s0026261709030114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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39
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Katsuda Y, Yoshikawa Y, Sato T, Saito Y, Chikuma M, Suzuki M, Yoshikawa K. Cisplatin and its analogues induce a significant change in the higher-order structure of long duplex DNA. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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40
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Napirei M, Ludwig S, Mezrhab J, Klöckl T, Mannherz HG. Murine serum nucleases--contrasting effects of plasmin and heparin on the activities of DNase1 and DNase1-like 3 (DNase1l3). FEBS J 2009; 276:1059-73. [PMID: 19154352 DOI: 10.1111/j.1742-4658.2008.06849.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNase1 is regarded as the major serum nuclease; however, a systematic investigation into the presence of additional serum nuclease activities is lacking. We have demonstrated directly that serum contains DNase1-like 3 (DNase1l3) in addition to DNase1 by an improved denaturing SDS-PAGE zymography method and anti-murine DNase1l3 immunoblotting. Using DNA degradation assays, we compared the activities of recombinant murine DNase1 and DNase1l3 (rmDNase1, rmDNase1l3) with the serum of wild-type and DNase1 knockout mice. Serum and rmDNase1 degrade chromatin effectively only in cooperation with serine proteases, such as plasmin or thrombin, which remove DNA-bound proteins. This can be mimicked by the addition of heparin, which displaces histones from chromatin. In contrast, serum and rmDNase1l3 degrade chromatin without proteolytic help and are directly inhibited by heparin and proteolysis by plasmin. In previous studies, serum DNase1l3 escaped detection because of its sensitivity to proteolysis by plasmin after activation of the plasminogen system in the DNA degradation assays. In contrast, DNase1 is resistant to plasmin, probably as a result of its di-N-glycosylation, which is lacking in DNase1l3. Our data demonstrate that secreted rmDNase1 and murine parotid DNase1 are mixtures of three different di-N-glycosylated molecules containing two high-mannose, two complex N-glycans or one high-mannose and one complex N-glycan moiety. In summary, serum contains two nucleases, DNase1 and DNase1l3, which may substitute or cooperate with each other during DNA degradation, providing effective clearance after exposure or release from dying cells.
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Affiliation(s)
- Markus Napirei
- Abteilung für Anatomie und Embryologie, Medizinische Fakultät, Ruhr-Universität Bochum, Germany.
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41
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Danilevich VN, Petrovskaya LE, Grishin EV. DNA nano- and microparticles: new products of polymerase chain reaction. DOKL BIOCHEM BIOPHYS 2008; 421:168-70. [PMID: 18853764 DOI: 10.1134/s1607672908040029] [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]
Affiliation(s)
- V N Danilevich
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, ul. Miklukho-Maklaya 16/10, Moscow, 117997 Russia
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42
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Wang F, Li D, Li G, Liu X, Dong S. Electrodissolution of Inorganic Ions/DNA Multilayer Film for Tunable DNA Release. Biomacromolecules 2008; 9:2645-52. [DOI: 10.1021/bm800766t] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fuan Wang
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, Peopleʼs Republic of China, Graduate School of the Chinese Academy of Sciences, Beijing 10039, Peopleʼs Republic of China
| | - Dan Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, Peopleʼs Republic of China, Graduate School of the Chinese Academy of Sciences, Beijing 10039, Peopleʼs Republic of China
| | - Gaiping Li
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, Peopleʼs Republic of China, Graduate School of the Chinese Academy of Sciences, Beijing 10039, Peopleʼs Republic of China
| | - Xiaoqing Liu
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, Peopleʼs Republic of China, Graduate School of the Chinese Academy of Sciences, Beijing 10039, Peopleʼs Republic of China
| | - Shaojun Dong
- State Key Laboratory of Electroanalytical Chemistry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, Peopleʼs Republic of China, Graduate School of the Chinese Academy of Sciences, Beijing 10039, Peopleʼs Republic of China
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43
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Hou S, Yang K, Liu Z, Feng XZ. A method to increase the bioactivity of plasmid DNA by heat treatment. ACTA ACUST UNITED AC 2008; 70:1066-72. [DOI: 10.1016/j.jprot.2008.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 10/22/2007] [Accepted: 01/30/2008] [Indexed: 10/22/2022]
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44
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Utsuno K. Thermodynamics of DNA Condensation Caused by Mn2+ Binding. Chem Pharm Bull (Tokyo) 2008; 56:247-9. [DOI: 10.1248/cpb.56.247] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Kuniharu Utsuno
- Department of Science and Engineering for Materials, Tomakomai National College of Technology
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45
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Kuznetsov SV, Ren CC, Woodson SA, Ansari A. Loop dependence of the stability and dynamics of nucleic acid hairpins. Nucleic Acids Res 2007; 36:1098-112. [PMID: 18096625 PMCID: PMC2275088 DOI: 10.1093/nar/gkm1083] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Hairpin loops are critical to the formation of nucleic acid secondary structure, and to their function. Previous studies revealed a steep dependence of single-stranded DNA (ssDNA) hairpin stability with length of the loop (L) as approximately L(8.5 +/- 0.5), in 100 mM NaCl, which was attributed to intraloop stacking interactions. In this article, the loop-size dependence of RNA hairpin stabilities and their folding/unfolding kinetics were monitored with laser temperature-jump spectroscopy. Our results suggest that similar mechanisms stabilize small ssDNA and RNA loops, and show that salt contributes significantly to the dependence of hairpin stability on loop size. In 2.5 mM MgCl2, the stabilities of both ssDNA and RNA hairpins scale as approximately L(4 +/- 0.5), indicating that the intraloop interactions are weaker in the presence of Mg2+. Interestingly, the folding times for ssDNA hairpins (in 100 mM NaCl) and RNA hairpins (in 2.5 mM MgCl2) are similar despite differences in the salt conditions and the stem sequence, and increase similarly with loop size, approximately L(2.2 +/- 0.5) and approximately L(2.6 +/- 0.5), respectively. These results suggest that hairpins with small loops may be specifically stabilized by interactions of the Na+ ions with the loops. The results also reinforce the idea that folding times are dominated by an entropic search for the correct nucleating conformation.
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Affiliation(s)
- Serguei V Kuznetsov
- Department of Physics (M/C 273), University of Illinois at Chicago, 845 W. Taylor St., Chicago, IL 60607, USA
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46
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Wei YF, Hsiao PY. Role of chain stiffness on the conformation of single polyelectrolytes in salt solutions. J Chem Phys 2007; 127:064901. [PMID: 17705621 DOI: 10.1063/1.2751195] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Conformation of single polyelectrolytes in tetravalent salt solutions is investigated under the framework of a coarse-grained model, using Langevin dynamics simulations. The chain size, studied by the radius of gyration, shows three different variational behaviors with salt concentration, depending on the chain stiffness. According to the size variations, polyelectrolytes of fixed chain length are classified into three categories: (1) flexible chain, for which the variation shows a curve similar to a tilted L, (2) semiflexible chain, whose curve resembles U, and (3) rigid chain, for which the curve is a straight line. The wormlike chain model with persistence length predicted by the Odijk-Skolnick-Fixman theory is found to be able to qualitatively describe the end-to-end distance at low salt concentration not only for semiflexible and rigid chains but also for flexible chain. In a low salt region, a flexible polyelectrolyte extends more significantly than a semiflexible chain, in reference of the size of their uncharged counterparts, and in a high salt region, regardless of chain stiffness, a chain attains a dimension comparable to that of its neutral polymer. The chain stiffness influences both the local and the global chain structures. A flexible chain exhibits a zigzagged local structure in the presence of salt ions, and the condensed structure is a disordered, random globule. A semiflexible chain is locally smooth, and the condensed structure is orderly packed, taking a form such as hairpin or toroid. Moreover, the chain stiffness can also affect the nature of the coil-globule transition. The transition occurred in a discrete manner for semiflexible chain, whereas it occurred in a continuous way for flexible chain. This discrete feature happened not only at low salt concentration when a semiflexible chain collapsed but also at high salt concentration when the collapsed chain is reexpanded. At the end, the effects of chain stiffness and salt concentration on the conformation of single polyelectrolytes are summarized in a schematic state diagram.
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Affiliation(s)
- Yu-Fu Wei
- Department of Engineering and System Science, National Tsing Hua University, Hsinchu, Taiwan 300, Republic of China
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47
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Spring BQ, Clegg RM. Fluorescence Measurements of Duplex DNA Oligomers under Conditions Conducive for Forming M−DNA (a Metal−DNA Complex). J Phys Chem B 2007; 111:10040-52. [PMID: 17665942 DOI: 10.1021/jp0725782] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
M-DNA (a metal complex of DNA with millimolar concentrations of Zn2+, Co2+, or Ni2+ and basic pH) has been proposed to undergo electron transfer over long distances along the helix and has generated interest as a potential building block for nanoelectronics. We show that DNA aggregates form under solvent conditions favorable for M-DNA (millimolar zinc and pH = 8.6) by fluorescence correlation spectroscopy. We have performed steady-state Förster resonance energy transfer (FRET) experiments with DNA oligomers conjugated with 6-carboxyfluorescein and tetramethylrhodamine to the opposite ends of double-stranded DNA (dsDNA) molecules. Enhanced acceptor emission is observed for distances larger than expected for identical DNA molecules with no zinc. To avoid intermolecular FRET, the fluorescently labeled dsDNA is diluted with a 100-fold excess of unlabeled dsDNA. The intramolecular FRET efficiency increases 25-fold for a 30-mer doubly labeled duplex DNA molecule upon addition of millimolar concentrations of zinc ions. Without zinc, this oligomer has less than 1% FRET efficiency. This dramatic increase in the FRET efficiency points to either significant changes in the Förster radius or fraying of the ends of the DNA helices. The latter hypothesis is supported by our experiments with a 9-mer that show dissociation of the duplex by zinc ions.
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Affiliation(s)
- Bryan Q Spring
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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48
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Ou Z, Muthukumar M. Langevin dynamics of semiflexible polyelectrolytes: rod-toroid-globule-coil structures and counterion distribution. J Chem Phys 2007; 123:074905. [PMID: 16229618 DOI: 10.1063/1.1940054] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We have investigated the nature of counterion condensation on uniformly charged semiflexible polyelectrolyte chains and the concomitant configurations by monitoring the role of chain stiffness, chain length, counterion valency, and the strength of electrostatic interaction. The counterion condensation is seen to follow the adsorption process and the effective polymer charge increases with chain stiffness. Size and shape, as calculated through the radius of gyration, effective persistence length, and hydrodynamic radius, are studied. Stable coil-like, globular, folded-chain, toroidal, and rodlike configurations are possible at suitable combinations of values of chain stiffness, chain length, electrostatic interaction strength, and the valency of counterion. For high strengths of electrostatic interactions, sufficiently stiff polyelectrolytes form toroids in the presence of multivalent counterions, whereas flexible polyelectrolytes form disordered globules. The kinetic features of the nucleation and growth of toroids are monitored. Several metastable structures are found to frustrate the formation of toroids. The generic pathway involves the nucleation of one primary loop somewhere along the chain contour, followed by a growth process where the rest of the chain is folded continuously on top of the primary loop. The dependence of the average radii of toroids on the chain length is found to be roughly linear, in disagreement with existing scaling arguments.
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Affiliation(s)
- Zhaoyang Ou
- Department of Polymer Science and Engineering, Materials Research Science and Engineering Center, University of Massachusetts, Amherst, Massachusetts 01003, USA
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49
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Study the effects of divalent metallic ions on the combination of DNA and histones with fluorescence anisotropy assays. CHINESE SCIENCE BULLETIN-CHINESE 2007. [DOI: 10.1007/s11434-007-0141-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Xu ZP, Walker TL, Liu KL, Cooper HM, Lu GQM, Bartlett PF. Layered double hydroxide nanoparticles as cellular delivery vectors of supercoiled plasmid DNA. Int J Nanomedicine 2007; 2:163-74. [PMID: 17722544 PMCID: PMC2673978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
We prepared stable homogeneous suspensions with layered double hydroxide (LDH) nanoparticles for in vitro gene delivery tests. The viability of HEK 293T cells in the presence of LDH nanoparticles at different concentrations was investigated. This revealed 50% cell viability at 500 microg/mL of LDH nanoparticles that is much higher than 50-100 microg/mL used for the delivery tests. The supercoiled pEF-eGFP plasmid (ca. 6100 base pairs) was mixed with LDH nanoparticle suspensions for anion exchange at a weight ratio of DNA/LDH between 1:25 and 1:100. In vitro experiments show that GFP expression in HEK 293T cells starts in the first day, reaches the maximum levels by the second day and continues in the third day. The GFP expression generally increases with the increase in DNA loading in DNA-LDH nanohybrids. However, the delivery efficiency with LDH nanoparticles as the agent is low. For example, the relative efficiency is 7%-15% of that of the commercial agent FuGENE 6. Three to 6% of total cells expressed GFP in an amount detectable by the FACS cytometry 2 days after transfection at 1 microg/mL of plasmid DNA with 25 microg/mL of LDH nanomaterial. The lower delivery efficiency could be attributed to the aggregation of LDH nanoparticles caused by the long-chain plasmid DNA.
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Affiliation(s)
- Zhi Ping Xu
- ARC Centre for Functional Nanomaterials, Australian Institute of Bioengineering and Nanotechnology
| | - Tara L Walker
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kerh-lin Liu
- ARC Centre for Functional Nanomaterials, Australian Institute of Bioengineering and Nanotechnology
| | - Helen M Cooper
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
| | - GQ Max Lu
- ARC Centre for Functional Nanomaterials, Australian Institute of Bioengineering and Nanotechnology
| | - Perry F Bartlett
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD 4072, Australia
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