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Abstract
The behavior of benzoic acid in polyethylene inspired me to reflect on why water is a unique molecule that all living organisms depend upon. From properties of DNA in aqueous solution a seemingly counter-intuitive conjecture emerges: water is needed for the creation of certain dry low-dielectric nm-size environments where hydrogen bonding exerts strong recognition power. Such environments seem to be functionally crucial, and their interactions with other hydrophobic environments, or with hydrophobic agents that modulate the chemical potential of water, can cause structural transformations via ‘hydrophobic catalysis’. Possibly combined with an excluded volume osmosis effect (EVO), hydrophobic catalysis may have important biological roles, e.g., in genetic recombination. Hydrophobic agents are found to strongly accelerate spontaneous DNA strand exchange as well as certain other DNA rearrangement reactions. It is hypothesized that hydrophobic catalysis be involved in gene recognition and gene recombination mediated by bacterial RecA (one of the oldest proteins we know of) as well as in sexual recombination in higher organisms, by Rad51. Hydrophobically catalyzed unstacking fluctuations of DNA bases can favor elongated conformations, such as the recently proposed [Formula: see text]-DNA, with potential regulatory roles. That living cells can survive as dormant spores, with very low water content and in principle as such travel far in space is reflected upon: a random walk model with solar photon pressure as driving force indicates our life on earth could not have originated outside our galaxy but possibly from many solar systems within it — at some place, though, where there was plenty of liquid water.
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Affiliation(s)
- Bengt Nordén
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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2
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Volodin AA, Bocharova TN, Smirnova EA. Polycationic ligands of different chemical classes stimulate DNA strand displacement between short oligonucleotides in a protein-free system. Biopolymers 2016; 105:633-41. [DOI: 10.1002/bip.22859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 03/26/2016] [Accepted: 04/19/2016] [Indexed: 11/07/2022]
Affiliation(s)
- Alexander A. Volodin
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
| | - Tatiana N. Bocharova
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
| | - Elena A. Smirnova
- Institute of Molecular Genetics of the Russian Academy of Sciences; Kurchatov Sq, 2 Moscow 123182 Russia
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3
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Kitts CC, Beke-Somfai T, Nordén B. Michler’s Hydrol Blue: A Sensitive Probe for Amyloid Fibril Detection. Biochemistry 2011; 50:3451-61. [DOI: 10.1021/bi102016p] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Catherine C. Kitts
- Department of Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-41296 Göteborg, Sweden
| | - Tamás Beke-Somfai
- Department of Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-41296 Göteborg, Sweden
| | - Bengt Nordén
- Department of Physical Chemistry, Chalmers University of Technology, Kemivägen 10, SE-41296 Göteborg, Sweden
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4
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Shibata T, Nishinaka T, Mikawa T, Aihara H, Kurumizaka H, Yokoyama S, Ito Y. Homologous genetic recombination as an intrinsic dynamic property of a DNA structure induced by RecA/Rad51-family proteins: a possible advantage of DNA over RNA as genomic material. Proc Natl Acad Sci U S A 2001; 98:8425-32. [PMID: 11459985 PMCID: PMC37453 DOI: 10.1073/pnas.111005198] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heteroduplex joints are general intermediates of homologous genetic recombination in DNA genomes. A heteroduplex joint is formed between a single-stranded region (or tail), derived from a cleaved parental double-stranded DNA, and homologous regions in another parental double-stranded DNA, in a reaction mediated by the RecA/Rad51-family of proteins. In this reaction, a RecA/Rad51-family protein first forms a filamentous complex with the single-stranded DNA, and then interacts with the double-stranded DNA in a search for homology. Studies of the three-dimensional structures of single-stranded DNA bound either to Escherichia coli RecA or Saccharomyces cerevisiae Rad51 have revealed a novel extended DNA structure. This structure contains a hydrophobic interaction between the 2' methylene moiety of each deoxyribose and the aromatic ring of the following base, which allows bases to rotate horizontally through the interconversion of sugar puckers. This base rotation explains the mechanism of the homology search and base-pair switch between double-stranded and single-stranded DNA during the formation of heteroduplex joints. The pivotal role of the 2' methylene-base interaction in the heteroduplex joint formation is supported by comparing the recombination of RNA genomes with that of DNA genomes. Some simple organisms with DNA genomes induce homologous recombination when they encounter conditions that are unfavorable for their survival. The extended DNA structure confers a dynamic property on the otherwise chemically and genetically stable double-stranded DNA, enabling gene segment rearrangements without disturbing the coding frame (i.e., protein-segment shuffling). These properties may give an extensive evolutionary advantage to DNA.
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Affiliation(s)
- T Shibata
- Cellular and Molecular Biology Laboratory, RIKEN, The Institute of Physical and Chemical Research, Hirosawa 2-1, Wako-shi, Saitama 351-0198, Japan.
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5
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Yasuda T, Morimatsu K, Kato R, Usukura J, Takahashi M, Ohmori H. Physical interactions between DinI and RecA nucleoprotein filament for the regulation of SOS mutagenesis. EMBO J 2001; 20:1192-202. [PMID: 11230142 PMCID: PMC145485 DOI: 10.1093/emboj/20.5.1192] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Escherichia coli dinI gene is one of the LexA-regulated genes, which are induced upon DNA damage. Its overexpression conferred severe UV sensitivity on wild-type cells and resulted in the inhibition of LexA and UmuD processing, reactions that are normally dependent on activated RecA in a complex with single-stranded (ss)DNA. Here, we study the mechanism by which DinI inhibits the activities of RecA. While DinI neither binds to ssDNA nor prevents the formation of RecA nucleoprotein filament, it binds to active RecA filament, thereby inhibiting its coprotease activity but not the ATPase activity. Furthermore, even under in vitro conditions where UmuD cleavage dependent on RecA-ssDNA-adeno sine-5'-(3-thiotriphosphate) is blocked in the presence of DinI, LexA is cleaved normally. This result, taken together with electron microscopy observations and linear dichroism measurements, indicates that the ternary complex remains intact in the presence of DinI, and that the affinity to the RecA filament decreases in the order LexA, DinI and UmuD. DinI is thus suited to modulating UmuD processing so as to limit SOS mutagenesis.
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Affiliation(s)
- Takeshi Yasuda
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
| | - Katsumi Morimatsu
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
| | - Ryuichi Kato
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
| | - Jiro Usukura
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
| | - Masayuki Takahashi
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
| | - Haruo Ohmori
- Institute for Virus Research, Kyoto University, Department of Biology, Graduate School of Science, Osaka University, Nagoya University Postgraduate School of Medicine, Japan and Institut Curie and Centre National de la Recherche Scientifique, France Present address: Cellular Physiology Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan Present address: Division of Biological Sciences, Sections of Microbiology and of Molecular and Cellular Biology, University of California, Davis, CA 95616-8665, USA Present address: FRE 2230, CNRS and Universite de Nantes, F44322 Nantes, France Corresponding author e-mail:
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6
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Kurumizaka H, Aihara H, Ikawa S, Shibata T. Specific defects in double-stranded DNA unwinding and homologous pairing of a mutant RecA protein. FEBS Lett 2000; 477:129-34. [PMID: 10899323 DOI: 10.1016/s0014-5793(00)01781-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The DNA molecules bound to RecA filaments are extended 1.5-fold relative to B-form DNA. This extended DNA structure may be important in the recognition of homology between single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). In this study, we show that the K286N mutation specifically impaired the dsDNA unwinding and homologous pairing activities of RecA, without an apparent effect on dsDNA binding itself. In contrast, the R243Q mutation caused defective dsDNA unwinding, due to the defective dsDNA binding of the C-terminal domain of RecA. These results provide new evidence that dsDNA unwinding is essential to homology recognition between ssDNA and dsDNA during homologous pairing.
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Affiliation(s)
- H Kurumizaka
- Cellular and Molecular Biology Laboratory, RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan.
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7
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Bergmeier M, Gradzielski M, Hoffmann H, Mortensen K. Behavior of Ionically Charged Lamellar Systems under the Influence of a Shear Field. J Phys Chem B 1999. [DOI: 10.1021/jp983480d] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Bergmeier
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany, and Condensed Matter Physics and Chemistry Department, Risø National Laboratory, DK-4000 Roskilde, Denmark
| | - M. Gradzielski
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany, and Condensed Matter Physics and Chemistry Department, Risø National Laboratory, DK-4000 Roskilde, Denmark
| | - H. Hoffmann
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany, and Condensed Matter Physics and Chemistry Department, Risø National Laboratory, DK-4000 Roskilde, Denmark
| | - K. Mortensen
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany, and Condensed Matter Physics and Chemistry Department, Risø National Laboratory, DK-4000 Roskilde, Denmark
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8
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Nishinaka T, Shinohara A, Ito Y, Yokoyama S, Shibata T. Base pair switching by interconversion of sugar puckers in DNA extended by proteins of RecA-family: a model for homology search in homologous genetic recombination. Proc Natl Acad Sci U S A 1998; 95:11071-6. [PMID: 9736691 PMCID: PMC21597 DOI: 10.1073/pnas.95.19.11071] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Escherichia coli RecA is a representative of proteins from the RecA family, which promote homologous pairing and strand exchange between double-stranded DNA and single-stranded DNA. These reactions are essential for homologous genetic recombination in various organisms. From NMR studies, we previously reported a novel deoxyribose-base stacking interaction between adjacent residues on the extended single-stranded DNA bound to RecA protein. In this study, we found that the same DNA structure was induced by the binding to Saccharomyces cerevisiae Rad51 protein, indicating that the unique DNA structure induced by the binding to RecA-homologs was conserved from prokaryotes to eukaryotes. On the basis of this structure, we have formulated the structure of duplex DNA within filaments formed by RecA protein and its homologs. Two types of molecular structures are presented. One is the duplex structure that has the N-type sugar pucker. Its helical pitch is approximately 95 A (18.6 bp/turn), corresponding to that of an active, or ATP-form of the RecA filament. The other is one that has the S-type sugar pucker. Its helical pitch is approximately 64 A (12.5 bp/turn), corresponding to that of an inactive, or ADP-form of the RecA filament. During this modeling, we found that the interconversion of sugar puckers between the N-type and the S-type rotates bases horizontally, while maintaining the deoxyribose-base stacking interaction. We propose that this base rotation enables base pair switching between double-stranded DNA and single-stranded DNA to take place, facilitating homologous pairing and strand exchange. A possible mechanism for strand exchange involving DNA rotation also is discussed.
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Affiliation(s)
- T Nishinaka
- Cellular and Molecular Biology Laboratory, The Institute of Physical and Chemical Research (RIKEN), Saitama 351-0198, Japan
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9
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Bergmeier M, Gradzielski M, Hoffmann H, Mortensen K. Behavior of a Charged Vesicle System under the Influence of a Shear Gradient: A Microstructural Study. J Phys Chem B 1998. [DOI: 10.1021/jp9734484] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Bergmeier
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - M. Gradzielski
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - H. Hoffmann
- Lehrstuhl für Physikalische Chemie I, Universität Bayreuth, D-95440 Bayreuth, Germany
| | - K. Mortensen
- Condensed Matter Physics and Chemistry Department, Riso National Laboratory, DK-4000 Roskilde, Denmark
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10
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Ellouze C, Kim HK, Maeshima K, Tuite E, Morimatsu K, Horii T, Mortensen K, Nordén B, Takahashi M. Nucleotide cofactor-dependent structural change of Xenopus laevis Rad51 protein filament detected by small-angle neutron scattering measurements in solution. Biochemistry 1997; 36:13524-9. [PMID: 9354620 DOI: 10.1021/bi971000n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Rad51 protein, a eukaryotic homologue of RecA protein, forms a filamentous complex with DNA and catalyzes homologous recombination. We have analyzed the structure of Xenopus Rad51 protein (XRad51.1) in solution by small-angle neutron scattering (SANS). The measurements showed that XRad51.1 forms a helical filament independently of DNA. The sizes of the cross-sectional and helical pitch of the filament could be determined, respectively, from a Guinier plot and the position of the subsidiary maximum of SANS data. We observed that the helical structure is modified by nucleotide binding as in the case of RecA. Upon ATP binding under high-salt conditions (600 mM NaCl), the helical pitch of XRad51.1 filament was increased from 8 to 10 nm and the cross-sectional diameter decreased from 7 to 6 nm. The pitch sizes of XRad51.1 are similar to, though slightly larger than, those of RecA filament under corresponding conditions. A similar helical pitch size was observed by electron microscopy for budding yeast Rad51 [Ogawa, T., et al. (1993) Science 259, 1896-1899]. In contrast to the RecA filament, the structure of XRad51.1 filament with ADP is not significantly different from that with ATP. Thus, the hydrolysis of ATP to ADP does not modify the helical filament of XRad51.1. Together with our recent observation that ADP does not weaken the XRad51.1/DNA interaction, the effect of ATP hydrolysis on XRad51.1 nucleofilament should be very different from that on RecA.
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Affiliation(s)
- C Ellouze
- UMR 216, Institut Curie and CNRS, F-91405 Orsay, France
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11
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Roca AI, Cox MM. RecA protein: structure, function, and role in recombinational DNA repair. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1997; 56:129-223. [PMID: 9187054 DOI: 10.1016/s0079-6603(08)61005-3] [Citation(s) in RCA: 324] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- A I Roca
- Department of Biochemistry, College of Agriculture and Life Sciences, University of Wisconsin, Madison 53706, USA
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12
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Simonson T, Kubista M, Sjöback R, Ryberg H, Takahashi M. Properties of RecA-oligonucleotide complexes. J Mol Recognit 1994; 7:199-206. [PMID: 7880544 DOI: 10.1002/jmr.300070307] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The interaction of RecA protein with short single-stranded oligonucleotides is characterised by flow linear dichroism (LD), isoelectric focusing (IEF) and electron microscopy (EM). From LD and EM it is evident that RecA forms long filaments with at least some 50 oligonucleotides in a 'train formation'. The tendency to form trains is substantially lower when an amino group is attached to the 5' end of the oligonucleotide, suggesting that the modification impairs protein-protein interactions at the interface between two oligomers. From LD it is also evident that no bridging occurs between RecA-oligonucleotide complexes containing more than one oligomer strand per RecA filament. This property make them manageable in polyacrylamide gels, hence allowing characterisation by IEF. RecA was found acidic with a pI of 5.0. The pI was not dependent on the presence of bound cofactor (ATP gamma S) and oligonucleotides suggesting that protonation of the protein readily occurs to compensate for the negative charges provided by bound cofactor and DNA.
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Affiliation(s)
- T Simonson
- Department of Biochemistry and Biophysics, Chalmers University of Technology, Gothenburg, Sweden
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14
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15
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Kim S, Nordén B, Takahashi M. Role of DNA intercalators in the binding of RecA to double-stranded DNA. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)82404-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Bloemendal M, van Grondelle R. Linear-dichroism spectroscopy for the study of structural properties of proteins. Mol Biol Rep 1993; 18:49-69. [PMID: 8232293 DOI: 10.1007/bf01006895] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
This review gives an experiment directed survey of the application of linear-dichroism (LD) spectroscopy to the study of proteins. LD spectroscopy is a relatively simple technique that provides information on the orientation of chromophores in molecules, on molecular characteristics such as shape, size and electronic properties, and on binding parameters in molecular complexes. Since LD is only observed when the molecules are non-randomly oriented in the sample, particular attention is paid to various orientation techniques, viz. in electric and flow fields, in polymer films and gels, and by light induction (photoselection). Examples are given on bacteriorhodopsin and retinals, chlorosomes, lens crystallins, aspartate aminotransferase, and the interaction of gene32- and recA-protein with DNA.
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Affiliation(s)
- M Bloemendal
- Department of Protein and Molecular Biology, Royal Free Hospital School of Medicine, London, UK
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17
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18
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Eriksson S, Nordén B, Morimatsu K, Horii T, Takahashi M. Role of tyrosine residue 264 of RecA for the binding of cofactor and DNA. J Biol Chem 1993. [DOI: 10.1016/s0021-9258(18)53926-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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19
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Takahashi M, Nordén B. Coordination and internal exchange of two DNA molecules in a RecA filament in the presence of hydrolysing ATP. Information on ATP-RecA-DNA structure from linear dichroism spectroscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1992; 210:87-92. [PMID: 1446687 DOI: 10.1111/j.1432-1033.1992.tb17394.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Solution structure of complexes between DNA and recombinase RecA from Escherchia coli, in the presence of the physiological cofactor ATP, is probed by flow linear dichroism (LD) spectroscopy. A problem of ADP accumulation which promotes dissociation of DNA-RecA is circumvented by using an ATP-regenerating system. The LD features indicate that the local structure of the complex is very similar to that found in the presence of the non-hydrolysable analog of ATP, adenosine-5'-O-[gamma-thio]triphosphate (ATP[gamma S]); the DNA bases are oriented with their planes preferentially perpendicular to the long axis of the filament, while the indole chromophores of the two tryptophan residues of RecA are rather parallel to this reference direction. A much smaller overall amplitude of the LD spectrum, compared to ATP[gamma S], is interpreted as a result of fast dissociation of RecA due to hydrolysis of ATP, producing transiently naked DNA regions which act like flexible joints, diminishing the macroscopic orientation of the RecA filaments. However, the ATP hydrolysis is not found to prevent simultaneous accommodation of two non-complementary DNA molecules in the RecA complex, as judged from the LD behaviour upon successive addition of two different polynucleotides or modified DNA strands. A notable difference from corresponding complexes formed with ATP[gamma S] is that, in the presence of ATP hydrolysis, the order in which the two DNA molecules have been added is insignificant as judged from virtually identical resulting structures; this observation indicates that exchange of DNA occurs between the two DNA accommodation sites within the RecA filament.
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Affiliation(s)
- M Takahashi
- Institut de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique, Strasbourg, France
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20
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Nordén B, Elvingson C, Kubista M, Sjöberg B, Ryberg H, Ryberg M, Mortensen K, Takahashi M. Structure of RecA-DNA complexes studied by combination of linear dichroism and small-angle neutron scattering measurements on flow-oriented samples. J Mol Biol 1992; 226:1175-91. [PMID: 1518050 DOI: 10.1016/0022-2836(92)91060-3] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
By combining anisotropy of small-angle neutron scattering (SANS) and optical anisotropy (linear dichroism, l.d.) on flow-oriented RecA-DNA complexes, the average DNA-base orientation has been determined in RecA complexes with double-stranded (ds) as well as single-stranded (ss) DNA. From the anisotropy of the two-dimensional SANS intensity representation, the second moment orientation function S is obtained. Knowledge of S is crucial for the interpretation of l.d. spectra in terms of orientation of the DNA bases and the aromatic amino acid residues. The DNA-base planes are essentially perpendicular to the fibre axis of the complex between RecA and dsDNA in the presence of cofactor ATP gamma S. A somewhat tilted base geometry is found for the RecA-ATP gamma S complexes with single-stranded poly(dT) and poly(d epsilon A). This behaviour contrasts the RecA-ssDNA complex formed without cofactor which displays a poor orientation of the bases. Well-ordered bases in the ssDNA-RecA complex is possibly reflecting the role of RecA in preparing a nucleotide strand for base-pairing in the search-for-homology process. While the central SANS intensity is essentially independent of the pitch of the helical complex, a secondary intensity maximum, which becomes focused upon flow orientation, is found to be a sensitive measure of the pitch. The pitch values for the complexes compare well with cryo-electron microscopy results but are slightly larger than those seen for uranyl-stained samples.
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Affiliation(s)
- B Nordén
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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21
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Mortensen K, Brown W, Nordén B. Inverse melting transition and evidence of three-dimensional cubatic structure in a block-copolymer micellar system. PHYSICAL REVIEW LETTERS 1992; 68:2340-2343. [PMID: 10045370 DOI: 10.1103/physrevlett.68.2340] [Citation(s) in RCA: 159] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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Abstract
This review will consider solution studies of structure and interactions of DNA and DNA complexes using linear dichroism spectroscopy, with emphasis on the technique of orientation by flow. The theoretical and experimental background to be given may serve, in addition, as a general introduction into the state of the art of linear dichroism spectroscopy, particularly as it is applied to biophysical problems.
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Affiliation(s)
- B Norden
- Department of Physical Chemistry, Chalmers University of Technology, Gothenburg, Sweden
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23
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Takahashi M, Kubista M, Nordén B. Co-ordination of multiple DNA molecules in RecA fiber evidenced by linear dichroism spectroscopy. Biochimie 1991; 73:219-26. [PMID: 1883883 DOI: 10.1016/0300-9084(91)90205-f] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Polarized light spectroscopy has been used to study the interaction of RecA protein with DNA. Several different DNA complexes have been identified and characterized with respect to stoichiometries, base orientation and nuclease accessibility. By using spectroscopically distinguishable DNAs, we determined the number of DNA molecules co-ordinated by the RecA fiber in each of these complexes, and established their base pairing abilities. Based on these observations, we discuss the molecular mechanism of the RecA-mediated strand exchange reaction.
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Affiliation(s)
- M Takahashi
- Groupe de Cancérogenèse et de Mutagenèse Moléculaire et Structurale, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg, France
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