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Cajili MKM, Prieto EI. Interplay between Alba and Cren7 Regulates Chromatin Compaction in Sulfolobus solfataricus. Biomolecules 2022; 12:biom12040481. [PMID: 35454068 PMCID: PMC9030869 DOI: 10.3390/biom12040481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 03/03/2022] [Accepted: 03/15/2022] [Indexed: 01/06/2023] Open
Abstract
Chromatin compaction and regulation are essential processes for the normal function of all organisms, yet knowledge on how archaeal chromosomes are packed into higher-order structures inside the cell remains elusive. In this study, we investigated the role of archaeal architectural proteins Alba and Cren7 in chromatin folding and dynamics. Atomic force microscopy revealed that Sulfolobus solfataricus chromatin is composed of 28 nm fibers and 60 nm globular structures. In vitro reconstitution showed that Alba can mediate the formation of folded DNA structures in a concentration-dependent manner. Notably, it was demonstrated that Alba on its own can form higher-order structures with DNA. Meanwhile, Cren7 was observed to affect the formation of Alba-mediated higher-order chromatin structures. Overall, the results suggest an interplay between Alba and Cren7 in regulating chromatin compaction in archaea.
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Maruyama H, Nambu T, Mashimo C, Okinaga T, Takeyasu K. Single-Molecule/Cell Analyses Reveal Principles of Genome-Folding Mechanisms in the Three Domains of Life. Int J Mol Sci 2021; 22:13432. [PMID: 34948225 PMCID: PMC8707338 DOI: 10.3390/ijms222413432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 11/21/2022] Open
Abstract
Comparative structural/molecular biology by single-molecule analyses combined with single-cell dissection, mass spectroscopy, and biochemical reconstitution have been powerful tools for elucidating the mechanisms underlying genome DNA folding. All genomes in the three domains of life undergo stepwise folding from DNA to 30-40 nm fibers. Major protein players are histone (Eukarya and Archaea), Alba (Archaea), and HU (Bacteria) for fundamental structural units of the genome. In Euryarchaeota, a major archaeal phylum, either histone or HTa (the bacterial HU homolog) were found to wrap DNA. This finding divides archaea into two groups: those that use DNA-wrapping as the fundamental step in genome folding and those that do not. Archaeal transcription factor-like protein TrmBL2 has been suggested to be involved in genome folding and repression of horizontally acquired genes, similar to bacterial H-NS protein. Evolutionarily divergent SMC proteins contribute to the establishment of higher-order structures. Recent results are presented, including the use of Hi-C technology to reveal that archaeal SMC proteins are involved in higher-order genome folding, and the use of single-molecule tracking to reveal the detailed functions of bacterial and eukaryotic SMC proteins. Here, we highlight the similarities and differences in the DNA-folding mechanisms in the three domains of life.
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Affiliation(s)
- Hugo Maruyama
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Takayuki Nambu
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Chiho Mashimo
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Toshinori Okinaga
- Department of Bacteriology, Osaka Dental University, Hirakata 573-1121, Japan; (T.N.); (C.M.); (T.O.)
| | - Kunio Takeyasu
- Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan;
- Center for Biotechnology, National Taiwan University, Taipei 10672, Taiwan
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3
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Parlane NA, Wedlock DN, Han JH, Park JH. Heterologous peptide display on chromatin nanofibers: A new strategy for peptide vaccines. Biochem Biophys Res Commun 2020; 524:825-831. [PMID: 32037086 DOI: 10.1016/j.bbrc.2020.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 02/02/2020] [Indexed: 12/22/2022]
Abstract
Chromatin organization starts from a "beads-on-a string" 10 nm fiber, a basic nucleosomal structure consisting of DNA and core histones. Given its regular nucleosome array on DNA backbone where N-terminal tails of each histone are exposed on the surface of chromatin fiber, we hypothesized that chromatin can be utilized as a heterologous peptide carrier to elicit a peptide-specific immune response. The plasmid DNA containing the Widom's clone 601 sequence and the recombinant chimeric histones containing the peptide derived from ras oncogene (G12V) were used to assemble the chromatin fiber in vitro. The immunogenicity of the assembled chromatin was tested in mice as a single vaccine component or formulated with adjuvants. G12V tagged-chromatin co-administered with adjuvants induced higher antibody responses against the G12V peptide than vaccination with adjuvant alone, while chimeric histones did not generate a significant antibody response. Interestingly, splenocytes from mice vaccinated with the G12V tagged-chromatin vaccine did not generate significant antigen-specific cytokine responses. Our studies suggest that chromatin can be utilized as an effective carrier of antigenic peptides for inducing specific antibody responses.
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Affiliation(s)
- Natalie A Parlane
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - D Neil Wedlock
- AgResearch, Hopkirk Research Institute, Palmerston North, New Zealand
| | - Jun-Hee Han
- EpiCentre, School of Veterinary Science, Massey University, New Zealand
| | - Jeong Hyeon Park
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.
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4
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Identification of autoreactive B cells with labeled nucleosomes. Sci Rep 2017; 7:602. [PMID: 28377609 PMCID: PMC5428865 DOI: 10.1038/s41598-017-00664-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 02/28/2017] [Indexed: 12/15/2022] Open
Abstract
The pathogenesis of autoimmune diseases has not been completely elucidated yet, and only a few specific treatments have been developed so far. In autoimmune diseases mediated by pathogenic autoantibodies, such as systemic lupus erythematosus, the specific detection and analysis of autoreactive B cells is crucial for a better understanding of the physiopathology. Biological characterization of these cells may help to define new therapeutic targets. Very few techniques allowing the precise detection of autoreactive B cells have been described so far. Herein we propose a new flow cytometry technique for specific detection of anti-nucleosome B cells, which secrete autoantibodies in systemic lupus erythematosus, using labeled nucleosomes. We produced different fluorochrome-labeled nucleosomes, characterized them, and finally tested them in flow cytometry. Nucleosomes labeled via the cysteines present in H3 histone specifically bind to autoreactive B cells in the anti-DNA transgenic B6.56R mice model. The present work validates the use of fluorochrome-labeled nucleosomes via cysteines to identify anti-nucleosome B cells and offers new opportunities for the description of autoreactive B cell phenotype.
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Zhang H, Li T. Presence of negative supercoiling in aggregates of histone H1-plasmidic polynucleosome complexes. Bioorg Med Chem Lett 2017; 27:168-170. [DOI: 10.1016/j.bmcl.2016.11.088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 11/26/2016] [Accepted: 11/30/2016] [Indexed: 11/29/2022]
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6
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Liu Y, Guthold M, Snyder MJ, Lu H. AFM of self-assembled lambda DNA-histone networks. Colloids Surf B Biointerfaces 2015; 134:17-25. [PMID: 26141439 DOI: 10.1016/j.colsurfb.2015.06.026] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Revised: 06/09/2015] [Accepted: 06/11/2015] [Indexed: 11/20/2022]
Abstract
Atomic force microscopy (AFM) was used to investigate the self-assembly behavior of λ-DNA and histones at varying histone:DNA ratios. Without histones and at the lowest histone:DNA ratio (less than one histone per 1000 base pairs of DNA), the DNA appeared as individual (uncomplexed), double-stranded DNA molecules. At increasing histone concentrations (one histone per 500, 250 and 167 base pairs of DNA), the DNA molecules started to form extensive polygonal networks of mostly pentagons and hexagons. The observed networks might be one of the naturally occurring, stable DNA-histone structures. The condensing effects of the divalent cations Mg(2+) and Ca(2+) on the DNA-histone complexes were also investigated. The networks persisted at high Mg(2+) concentration (20mM) and the highest histone concentration. At high Ca(2+) concentration and the highest histone concentration, the polygonal network disappeared and, instead, individual, tightly condensed aggregates were formed.
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Affiliation(s)
- YuYing Liu
- Department of Physics, College of Science, China Agricultural University, Beijing 100083, China
| | - Martin Guthold
- Department of Physics, Wake Forest University, Winston Salem 27109, USA.
| | - Matthew J Snyder
- Department of Physics, Wake Forest University, Winston Salem 27109, USA
| | - HongFeng Lu
- Department of Physics, College of Science, China Agricultural University, Beijing 100083, China.
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7
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Analyses of nuclear proteins and nucleic acid structures using atomic force microscopy. Methods Mol Biol 2015; 1262:119-53. [PMID: 25555579 DOI: 10.1007/978-1-4939-2253-6_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Since the inception of atomic force microscopy (AFM) in 1986, the value of this technology for exploring the structure and biophysical properties of a variety of biological samples has been increasingly recognized. AFM provides the opportunity to both image samples at nanometer resolution and also measure the forces on the surface of the sample. Here, we describe a variety of methods for studying nuclear samples including single nucleic acid molecules, higher-order chromatin structures, the nucleolus, and the nucleus. Protocols to prepare nucleic acids, nucleic acid-protein complexes, reconstituted chromatin, the cell nucleus, and the nucleolus are included, as well as protocols describing how to prepare the AFM substrate and the AFM tip. Finally, we describe how to perform conventional imaging, high-speed imaging, recognition imaging, force spectroscopy, and nanoindentation experiments.
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Brackley CA, Allan J, Keszenman-Pereyra D, Marenduzzo D. Topological constraints strongly affect chromatin reconstitution in silico. Nucleic Acids Res 2015; 43:63-73. [PMID: 25432958 PMCID: PMC4288149 DOI: 10.1093/nar/gku1085] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 10/15/2014] [Accepted: 10/17/2014] [Indexed: 12/22/2022] Open
Abstract
The fundamental building block of chromatin, and of chromosomes, is the nucleosome, a composite material made up from DNA wrapped around a histone octamer. In this study we provide the first computer simulations of chromatin self-assembly, starting from DNA and histone proteins, and use these to understand the constraints which are imposed by the topology of DNA molecules on the creation of a polynucleosome chain. We take inspiration from the in vitro chromatin reconstitution protocols which are used in many experimental studies. Our simulations indicate that during self-assembly, nucleosomes can fall into a number of topological traps (or local folding defects), and this may eventually lead to the formation of disordered structures, characterised by nucleosome clustering. Remarkably though, by introducing the action of topological enzymes such as type I and II topoisomerase, most of these defects can be avoided and the result is an ordered 10-nm chromatin fibre. These findings provide new insight into the biophysics of chromatin formation, both in the context of reconstitution in vitro and in terms of the topological constraints which must be overcome during de novo nucleosome formation in vivo, e.g. following DNA replication or repair.
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Affiliation(s)
- C A Brackley
- SUPA, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - J Allan
- Institute of Cell Biology, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - D Keszenman-Pereyra
- Edinburgh Genomics, Ashworth Laboratories, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - D Marenduzzo
- SUPA, School of Physics & Astronomy, University of Edinburgh, Edinburgh, EH9 3FD, UK
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Kizaki S, Suzuki Y, Takenaka T, Endo M, Sugiyama H. AFM analysis of changes in nucleosome wrapping induced by DNA epigenetic modification. Biomater Sci 2014; 2:1399-1403. [DOI: 10.1039/c4bm00113c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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10
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Kalle W, Strappe P. Atomic force microscopy on chromosomes, chromatin and DNA: a review. Micron 2012; 43:1224-31. [PMID: 22633852 DOI: 10.1016/j.micron.2012.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Revised: 04/06/2012] [Accepted: 04/08/2012] [Indexed: 01/19/2023]
Abstract
The purpose of this review is to discuss the achievements and progress that has been made in the use of atomic force microscopy in DNA related research in the last 25 years. For this review DNA related research is split up in chromosomal-, chromatin- and DNA focused research to achieve a logical flow from large- to smaller structures. The focus of this review is not only on the AFM as imaging tool but also on the AFM as measuring tool using force spectroscopy, as therein lays its greatest advantage and future. The amazing technological and experimental progress that has been made during the last 25 years is too extensive to fully cover in this review but some key developments and experiments have been described to give an overview of the evolution of AFM use from 'imaging tool' to 'measurement tool' on chromosomes, chromatin and DNA.
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Affiliation(s)
- Wouter Kalle
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, Australia.
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11
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Suzuki Y, Yoshikawa Y, Yoshimura SH, Yoshikawa K, Takeyasu K. Unraveling DNA dynamics using atomic force microscopy. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2011; 3:574-88. [PMID: 21618449 DOI: 10.1002/wnan.150] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The elucidation of structure-function relationships of biological samples has become important issue in post-genomic researches. In order to unveil the molecular mechanisms controlling gene regulations, it is essential to understand the interplay between fundamental DNA properties and the dynamics of the entire molecule. The wide range of applicability of atomic force microscopy (AFM) has allowed us to extract physicochemical properties of DNA and DNA-protein complexes, as well as to determine their topographical information. Here, we review how AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics. We begin by illustrating the application of AFM to investigate the fundamental feature of DNA molecules; topological transition of DNA, length dependent properties of DNA molecules, flexibility of double-stranded DNA, and capability of the formation of non-Watson-Crick base pairing. These properties of DNA are critical for the DNA folding and enzymatic reactions. The technical advancement in the time-resolution of AFM and sample preparation methods enabled visual analysis of DNA-protein interactions at sub-second time region. DNA tension-dependent enzymatic reaction and DNA looping dynamics by restriction enzymes were examined at a nanoscale in physiological environments. Contribution of physical properties of DNA to dynamics of nucleosomes and transition of the higher-order structure of reconstituted chromatin are also reviewed.
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Affiliation(s)
- Yuki Suzuki
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto, Japan.
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12
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Modern Atomic Force Microscopy and Its Application to the Study of Genome Architecture. SCANNING PROBE MICROSCOPY IN NANOSCIENCE AND NANOTECHNOLOGY 2010. [DOI: 10.1007/978-3-642-03535-7_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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13
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Hizume K, Nakai T, Araki S, Prieto E, Yoshikawa K, Takeyasu K. Removal of histone tails from nucleosome dissects the physical mechanisms of salt-induced aggregation, linker histone H1-induced compaction, and 30-nm fiber formation of the nucleosome array. Ultramicroscopy 2009; 109:868-73. [PMID: 19328628 DOI: 10.1016/j.ultramic.2009.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
In order to reveal the roles of histone tails in the formation of higher-order chromatin structures, we employed atomic force microscopy (AFM), and an in vitro reconstitution system to examine the properties of reconstituted chromatin composed of tail-less histones and a long DNA (106-kb plasmid) template. The tail-less nucleosomes did not aggregate at high salt concentrations or with an excess amount of core histones, in contrast with the behavior of nucleosomal arrays composed of nucleosomes containing normal, N-terminal tails. Analysis of our nucleosome distributions reveals that the attractive interaction between tail-less nucleosomes is weakened. Addition of linker histone H1 into the tail-less nucleosomal array failed to promote the formation of 30nm chromatin fibers that are usually formed in the normal nucleosomal array. These results demonstrate that the attractive interaction between nucleosomes via histone tails plays a critical role in the formation of the uniform 30-nm chromatin fiber.
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Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Yoshida Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
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Hizume K, Yoshimura SH, Kumeta M, Takeyasu K. Structural organization of dynamic chromatin. Subcell Biochem 2007; 41:3-28. [PMID: 17484121 DOI: 10.1007/1-4020-5466-1_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- Kohji Hizume
- Laboratory of Plasma Membrane and Nuclear Signaling, Graduate School of Biostudies, Kyoto University, Kitashirakawa-oiwake-cho, Sakyo-ku, Kyoto, 606-8502, Japan
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Limanskaya LA, Limanskii AP. Compaction of single supercoiled DNA molecules adsorbed onto amino mica. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2006. [DOI: 10.1134/s1068162006050074] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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16
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Limanskaya LA, Limansky AP. S-DNA, over-supercoiled DNA with a 1.94-to 2.19-Å rise per base pair. Mol Biol 2006. [DOI: 10.1134/s0026893306010158] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Yoshikawa Y, Hizume K, Oda Y, Takeyasu K, Araki S, Yoshikawa K. Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation. Biophys J 2005; 90:993-9. [PMID: 16284271 PMCID: PMC1367124 DOI: 10.1529/biophysj.105.069963] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Direct attack to genomic DNA by reactive oxygen species causes various types of lesions, including base modifications and strand breaks. The most significant lesion is considered to be an unrepaired double-strand break that can lead to fatal cell damage. We directly observed double-strand breaks of DNA in reconstituted chromatin stained by a fluorescent cyanine dye, YOYO (quinolinium, 1,1'-[1,3- propanediylbis[(dimethyliminio)-3,1- propanediyl]]bis[4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]]-, tetraiodide), in solution, where YOYO is known to have the ability to photo-cleave DNAs by generating reactive oxygen species. Reconstituted chromatin was assembled from large circular DNA (106 kbp) with core histone proteins. We also investigated the effect of vitamin C (ascorbic acid) on preventing photo-induced double-strand breaks in a quantitative manner. We found that DNA is protected against double-strand breaks by the addition of ascorbic acid, and this protective effect is dose dependent. The effective kinetic constant of the breakage reaction in the presence of 5 mM ascorbic acid is 20 times lower than that in the absence of ascorbic acid. This protective effect of ascorbic acid in reconstituted chromatin is discussed in relation to the highly compacted polynucleosomal structure. The results highlight the fact that single-molecule observation is a useful tool for studying double-strand breaks in giant DNA and chromatin.
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Affiliation(s)
- Yuko Yoshikawa
- Department of Food and Nutrition, Nagoya Bunri College, Nagoya 451-0077, Japan.
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18
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USHIKI T, HOSHI O. 走査型プローブ顕微鏡の生物学応用. ELECTROCHEMISTRY 2005. [DOI: 10.5796/electrochemistry.73.908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Hansma HG, Kasuya K, Oroudjev E. Atomic force microscopy imaging and pulling of nucleic acids. Curr Opin Struct Biol 2004; 14:380-5. [PMID: 15193320 DOI: 10.1016/j.sbi.2004.05.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Recent advances in atomic force microscopy (AFM) imaging of nucleic acids include the visualization of DNA and RNA incorporated into devices and patterns, and into structures based on their sequences or sequence recognition. AFM imaging of nuclear structures has contributed to advances in telomere research and to our understanding of nucleosome formation. Highlights of force spectroscopy or pulling of nucleic acids include the use of DNA as a programmable force sensor, and the analysis of RNA flexibility and drug binding to DNA.
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Affiliation(s)
- Helen G Hansma
- Department of Physics, University of California, Santa Barbara, CA 93106, USA.
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