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Rajendran A, Endo M, Katsuda Y, Hidaka K, Sugiyama H. Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly. J Am Chem Soc 2011; 133:14488-91. [DOI: 10.1021/ja204546h] [Citation(s) in RCA: 152] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Arivazhagan Rajendran
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
| | - Masayuki Endo
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yousuke Katsuda
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Kumi Hidaka
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa-oiwakecho, Sakyo-ku, Kyoto 606-8502, Japan
- CREST, Japan Science and Technology Corporation (JST), Sanbancho, Chiyoda-ku, Tokyo 102-0075, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-ushinomiyacho, Sakyo-ku, Kyoto 606-8501, Japan
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Sastry SS, Spielmann HP, Hearst JE. Psoralens and their application to the study of some molecular biological processes. ADVANCES IN ENZYMOLOGY AND RELATED AREAS OF MOLECULAR BIOLOGY 2006; 66:85-148. [PMID: 8430517 DOI: 10.1002/9780470123126.ch3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- S S Sastry
- Department of Chemistry, University of California, Lawrence Berkeley Laboratory, Berkeley
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Streltsov SA, Beabealashvili RS, Grechishnikov SB. Thr-Val-Thr dansyl hydrazide: the first fluorescent tripeptide preferentially binding with at pairs in DNA. J Biomol Struct Dyn 2005; 23:347-56. [PMID: 16218759 DOI: 10.1080/07391102.2005.10507069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In 1991-1993 we amended a DNA-protein recognition model advanced in 1975. Here we test our assumptions with a specially designed tripeptide L-Thr-L-Val-L-Thr-NH-NH-Dns (Dns is 5-dimethylaminonaphthalene-1-sulfonic acid residue). It is shown to dimerize in solution (as evidenced by the nonlinear concentration dependence of its fluorescence) and to bind with DNA mainly in beta-dimeric form (S-shaped adsorption isotherm obtained by equilibrium dialysis). The tripeptide is bound in the DNA minor groove (whence it can be displaced with distamycin A), and such complexes become able to associate into 'biduplex' structures (nonlinear dependence of the linear dichroism of bound peptide on DNA concentration). The peptide dimers clearly prefer the AT pairs [half-saturating peptide concentrations are (0.6-0.7) x 10(-4) M for poly(dA).poly(dT) but exceed (2.5-2.8) x10(-4) M for poly(dG).poly(dC)]. These results agree nicely with our earlier suggestions. Since Dns-tagged trivaline has been shown to prefer the GC pairs, we think it now becomes possible to design oligopeptides that would specifically bind to any predefined nucleotide sequence.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 32 Vavilova st., Moscow 119991, Russia.
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Streltsov SA, Martinkina LP, Khorlin AA, Florentiev VL, Zhenodarova SM, Sedelnikova EA, Smolyaninova OA. Trivaline molecular complexes with trinucleotides form in solution the extended, about 1000 A in length structures. J Biomol Struct Dyn 1994; 11:1403-15. [PMID: 7946081 DOI: 10.1080/07391102.1994.10508075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The fluorescence, flow linear dichroism and electron microscopy (EM) have shown the trivaline ability to interact in solution with certain molecules of trinucleotides. This interaction results in formation of extended structures up to several thousand angstroms in length. Such structures were observed for trivaline complexes with homopurine, homopyrimidine or random sequences of deoxyribo- and ribonucleotides, independently of the presence or absence of the terminal 5'-phosphate residue. A model of such a structural organization is proposed. An elementary structural unit consists of a trivaline beta-dimer and adsorbed trinucleotide. So, "dimeric" complex is formed. Two such "dimeric" complexes combine with each other by means of peptide-peptide contacts (as with beta-sandwich). So, "tetrameric" complex is formed. It has a dyad axis. Two such structural units combine with each other by means of Hoogsteen's hydrogen bonds. So, "octameric" complex is formed. It has three mutually perpendicular dyad axes. The "octameric" complexes appear to be able to combine with each other by means of stacking interactions, and to form the regular organized aggregates consisting of many dozens of elementary units. So, "stacking" structure is formed. The "octameric" complex is the symmetry translational unit of such a structure. The spatial position of the bases in all these structures is additionally fixed by the nucleo-peptide interactions. These aggregates have the appearance of extended structures on electron micrographs.
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Affiliation(s)
- S A Streltsov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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Streltsov SA, Semenov TE, Moroz OV. Homology in trivaline complex formation with dsDNA and ssRNA. J Biomol Struct Dyn 1993; 10:763-84. [PMID: 7682081 DOI: 10.1080/07391102.1993.10508005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
It has been shown by the equilibrium dialysis that at a polyU concentration above the "critical" one, the complete polymer saturation with trivaline reaches approximately 0.7 trivaline molecules per one phosphate group. i.e. at these conditions peptide dimer occupies on polyU a site of three bases (phosphates) in length. The trivaline complex with polyU at a concentration lower than the "critical" one does not reveal any noticeable fluorescence, but has rather significant positive linear dichroism at 265 and 330 nm. The trivaline-nucleic acids complex has a significant fluorescence at any dsDNA concentration while with polyU it is only so at a concentration above the "critical" one. Electron microscopy has shown that at a rather high concentration of dsDNA molecules in solution a "biduplex" structure undergoes an additional stage of compaction, during which the extended particles more than 30 nm in diameter are formed.
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Affiliation(s)
- S A Streltsov
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow
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Downs WD, Cech TR. An ultraviolet-inducible adenosine-adenosine cross-link reflects the catalytic structure of the Tetrahymena ribozyme. Biochemistry 1990; 29:5605-13. [PMID: 2201409 DOI: 10.1021/bi00475a027] [Citation(s) in RCA: 46] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
When a shortened enzymatic version of the Tetrahymena self-splicing intervening sequence (IVS) RNA is placed under catalytic conditions and irradiated at 254 nm, a covalent cross-link forms with high efficiency. The position of the cross-link was mapped by using three independent methods: RNase H digestion, primer extension with reverse transcriptase, and partial hydrolysis of end-labeled RNA. The cross-link is chemically unusual in that it joins two adenosines, A57 and A95. Formation of this cross-link depends upon the identity and concentration of divalent cations present and upon heat-cool renaturation of the IVS in a manner that parallels conditions required for optimal catalytic activity. Furthermore, cross-linking requires the presence of sequences within the core structure, which is conserved among group I intervening sequences and necessary for catalytic activity. Together these correlations suggest that a common folded structure permits cross-linking and catalytic activity. The core can form this structure independent of the presence of P1 and elements at the 3' end of the IVS. The cross-linked RNA loses catalytic activity under destabilizing conditions, presumably due to disruption of the folded structure by the cross-link. One of the nucleotides participating in this cross-link is highly conserved (86%) within the secondary structure of group I intervening sequences. We conclude that A57 and A95 are precisely aligned in a catalytically active conformation of the RNA. A model is presented for the tertiary arrangement in the vicinity of the cross-link.
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Affiliation(s)
- W D Downs
- Department of Molecular, Cellular, and Developmental Biology, Howard Hughes Medical Institute, University of Colorado, Boulder 80309-0215
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8
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Shi YB, Griffith J, Gamper H, Hearst JE. Evidence for structural deformation of the DNA helix by a psoralen diadduct but not by a monoadduct. Nucleic Acids Res 1988; 16:8945-52. [PMID: 3174437 PMCID: PMC338644 DOI: 10.1093/nar/16.18.8945] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
We have investigated the structural change in a double-stranded DNA helix caused by covalent addition of a psoralen. A synthetic double-stranded DNA was constructed to contain either a psoralen furan-side monoadduct or an interstrand diadduct at a specific site. When the unmodified and psoralen modified DNAs were examined by electron microscopy in the presence of distamycin, which stiffens the DNA helix, the DNA containing the psoralen interstrand diadduct appeared bent (or kinked), whereas the furan-side monoadducted DNA appeared similar to the unmodified DNA. RecA protein from E. coli has been shown to preferentially bind UV (ultra violet) irradiated DNA presumably due to alterations in the normal DNA helical structure. Using a nitrocellulose filter binding assay, we have found that the psoralen interstrand diadduct enhances the binding of recA protein to the double-stranded DNA, whereas a furan-side monoadduct has little effect. Thus both the recA protein binding and the electron microscopic data suggest that a psoralen diadduct causes deformation of a DNA helix, most likely by kinking the helix, and that a monoadduct has little effect on the DNA helix structure.
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Affiliation(s)
- Y B Shi
- Department of Chemistry, University of California, Berkeley 94720
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Widmer RM, Koller T, Sogo JM. Analysis of the psoralen-crosslinking pattern in chromatin DNA by exonuclease digestion. Nucleic Acids Res 1988; 16:7013-24. [PMID: 2841647 PMCID: PMC338348 DOI: 10.1093/nar/16.14.7013] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
When chromatin is photoreacted with psoralen, crosslinks occur preferentially in the linker DNA between nucleosomes. The pattern of these crosslinks can be analysed by exonuclease digestion of random DNA fragments, since the exonucleases tested stop at sites of psoralen-crosslinks. Further digestion of these fragments with S1-nuclease leads to DNA fragments of nucleosomal and polynucleosomal size, which presumably carry psoralen-crosslinks at both ends. This method of analysis of chromatin structure complements the classical micrococcal nuclease digestion analysis, since it can be performed in vitro as well as in vivo, and since it is independent of pH and ionic conditions.
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Affiliation(s)
- R M Widmer
- Institut für Zellbiologie, Eidgenössische Technische Hochschule, ETHZ, Zürich, Switzerland
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Caffarelli E, De Santis P, Leoni L, Palleschi A, Savino M. Preferential positioning of nucleosomes on pBR322 as evaluated via Fourier transform of data from electron microscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 171:497-501. [PMID: 3345744 DOI: 10.1111/j.1432-1033.1988.tb13817.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleosome positioning on pBR322 DNA has been evaluated by electron microscopy visualization, after psoralen cross-linking. The distribution function of nucleosomes on pBR322 DNA has been calculated analyzing the data of the electron microscopy via Fourier transform. This function shows definite maxima, which indicate differential interactions of the histone octamer to different DNA sequences.
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Affiliation(s)
- E Caffarelli
- Centro di Studio per gli Acidi Nucleici del Consiglio Nazionale delle Ricerche, Roma, Italy
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Tomic MT, Wemmer DE, Kim SH. Structure of a psoralen cross-linked DNA in solution by nuclear magnetic resonance. Science 1987; 238:1722-5. [PMID: 3686011 DOI: 10.1126/science.3686011] [Citation(s) in RCA: 58] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
One- and two-dimensional nuclear magnetic resonance (NMR) methods were used to determine a three-dimensional model of an eight-base-pair DNA fragment (d-GGGTACCC) cross-linked with psoralen in solution. Two-dimensional nuclear Overhauser effect experiments were used to assign the spectrum and estimate distances for 171 proton pairs in the cross-linked DNA. The NMR-derived model shows a 53 degree bend into the major groove that occurs primarily at the site of drug addition and a 56 degree unwinding that spans the eight-base-pair duplex.
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Affiliation(s)
- M T Tomic
- Department of Chemistry, University of California, Berkeley 94720
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Piette J, Decuyper-Debergh D, Gamper H. Mutagenesis of the lac promoter region in M13 mp10 phage DNA by 4'-hydroxymethyl-4,5',8-trimethylpsoralen. Proc Natl Acad Sci U S A 1985; 82:7355-9. [PMID: 3864162 PMCID: PMC391343 DOI: 10.1073/pnas.82.21.7355] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Double-stranded M13 phage DNA (M13 mp10 replicative form) was photoreacted with 4'-hydroxymethyl-4,5',8-trimethylpsoralen, using light of wavelength greater than 320 nm or greater than 390 nm to generate predominantly crosslinks or monoadducts, respectively. The damaged DNAs were scored for inactivation and mutagenesis after transfection into Escherichia coli. The appearance of light-blue or colorless plaques on indicator medium showed that mutation had occurred in the lac insert of the viral DNA. A comparison of the consequences of the two phototreatments with psoralen supports the idea that crosslinks are both more lethal and more mutagenic than monoadducts. Numerous mutant clones partially or totally deficient in beta-galactosidase were plaque-purified and amplified. The viral DNA of each clone was sequenced by the dideoxy chain-terminating procedure. All of the observed base-pair changes were mapped to the lac promoter region and consisted of 3 transition, 14 transversion, and 6 single base-pair frame-shift mutations. The predominant mutation was a T.A----G.C transversion.
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Graetzer R, Morrison TW. Effects of 8-methoxypsoralen and near ultraviolet radiation on the survival of the lower eukaryote D. discoideum. Photochem Photobiol 1985; 42:275-9. [PMID: 4059364 DOI: 10.1111/j.1751-1097.1985.tb08942.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Ben-Hur E, Song PS. The Photochemistry and Photobiology of Furocoumarins (Psoralens). ADVANCES IN RADIATION BIOLOGY 1984. [DOI: 10.1016/b978-0-12-035411-5.50009-5] [Citation(s) in RCA: 148] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
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