메뉴 건너뛰기




Volumn 114, Issue 19, 2010, Pages 6713-6721

Binding of BOBO-3 intercalative dye to DNA homo-oligonucleotides with different base compositions

Author keywords

[No Author keywords available]

Indexed keywords

ABSORPTION SPECTROSCOPY; BINDING ENERGY; BIOCHEMISTRY; DNA; EQUILIBRIUM CONSTANTS; FLUORESCENCE; FLUORESCENCE SPECTROSCOPY; GENES; OLIGONUCLEOTIDES;

EID: 77952478055     PISSN: 15206106     EISSN: 15205207     Source Type: Journal    
DOI: 10.1021/jp1010742     Document Type: Article
Times cited : (10)

References (46)
  • 1
    • 0026696234 scopus 로고
    • Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: Properties and applications
    • Rye, H. S.; Yue, S.; Wemmer, D. E.; Quesada, M. A.; Haugland, R. P.; Mathies, R. A.; Glazer, A. N. Stable Fluorescent Complexes of Double-Stranded DNA with Bis-Intercalating Asymmetric Cyanine Dyes: Properties and Applications Nucleic Acids Res. 1992, 20, 2803-2812
    • (1992) Nucleic Acids Res. , vol.20 , pp. 2803-2812
    • Rye, H.S.1    Yue, S.2    Wemmer, D.E.3    Quesada, M.A.4    Haugland, R.P.5    Mathies, R.A.6    Glazer, A.N.7
  • 2
    • 0027129003 scopus 로고
    • Stable Dye-DNA intercalation complexes as reagents for high-sensitivity fluorescence detection
    • Glazer, A. N.; Rye, H. S. Stable Dye-DNA Intercalation Complexes As Reagents for High-Sensitivity Fluorescence Detection Nature 1992, 359, 859-861
    • (1992) Nature , vol.359 , pp. 859-861
    • Glazer, A.N.1    Rye, H.S.2
  • 4
    • 0000801665 scopus 로고
    • Viscosity dependent radiationless relaxation rate of cyanine dyes. A picosecond laser spectroscopy study
    • Sundström, V.; Gillbro, T. Viscosity Dependent Radiationless Relaxation Rate of Cyanine Dyes. A Picosecond Laser Spectroscopy Study Chem. Phys. 1981, 61 (3) 257-269
    • (1981) Chem. Phys. , vol.61 , Issue.3 , pp. 257-269
    • Sundström, V.1    Gillbro, T.2
  • 5
    • 0001353214 scopus 로고
    • Theoretical study of trans-cis photoisomerism in polymethine cyanines
    • Momicchioli, F.; Baraldi, I.; Berthier, G. Theoretical Study of Trans-Cis Photoisomerism in Polymethine Cyanines Chem. Phys. 1988, 123 (1) 103-112
    • (1988) Chem. Phys. , vol.123 , Issue.1 , pp. 103-112
    • Momicchioli, F.1    Baraldi, I.2    Berthier, G.3
  • 6
    • 33751157052 scopus 로고
    • Base-content dependence of emission enhancements, quantum yields, and lifetimes for cyanine dyes bound to double-strand DNA: Photophysical properties of monomeric and bichromomphoric DNA stains
    • Netzel, T. L.; Nafisi, K.; Zhao, M.; Lenhard, J. R.; Johnson, I. Base-Content Dependence of Emission Enhancements, Quantum Yields, and Lifetimes for Cyanine Dyes Bound to Double-Strand DNA: Photophysical Properties of Monomeric and Bichromomphoric DNA Stains J. Phys. Chem. 1995, 99 (51) 17936-17947
    • (1995) J. Phys. Chem. , vol.99 , Issue.51 , pp. 17936-17947
    • Netzel, T.L.1    Nafisi, K.2    Zhao, M.3    Lenhard, J.R.4    Johnson, I.5
  • 7
    • 0027499414 scopus 로고
    • Fluorometric assay using dimeric dyes for double- and single-stranded DNA and rna with picogram sensitivity
    • Rye, H. S.; Dabora, J. M.; Quesada, M. A.; Mathies, R. A.; Glazer, A. N. Fluorometric Assay Using Dimeric Dyes for Double- and Single-Stranded DNA and RNA with Picogram Sensitivity Anal. Biochem. 1993, 208 (1) 144-150
    • (1993) Anal. Biochem. , vol.208 , Issue.1 , pp. 144-150
    • Rye, H.S.1    Dabora, J.M.2    Quesada, M.A.3    Mathies, R.A.4    Glazer, A.N.5
  • 8
    • 0027243117 scopus 로고
    • Picogram detection of stable Dye-DNA intercalation complexes with two-color laser-excited confocal fluorescence gel scanner
    • Rye, H. S.; Yue, S.; Quesada, M. A.; Haugland, R. P.; Mathies, R. A.; Glazer, A. N. Picogram Detection of Stable Dye-DNA Intercalation Complexes with Two-Color Laser-Excited Confocal Fluorescence Gel Scanner Methods Enzymol. 1993, 217, 414-431
    • (1993) Methods Enzymol. , vol.217 , pp. 414-431
    • Rye, H.S.1    Yue, S.2    Quesada, M.A.3    Haugland, R.P.4    Mathies, R.A.5    Glazer, A.N.6
  • 9
    • 0027976331 scopus 로고
    • TOTO and YOYO: New very bright fluorochromes for DNA content analyses by flow cytometry
    • Hirons, G. T.; Fawcett, J. J.; Crissman, H. A. TOTO and YOYO: New Very Bright Fluorochromes for DNA Content Analyses by Flow Cytometry Cytometry 1994, 15, 129-140
    • (1994) Cytometry , vol.15 , pp. 129-140
    • Hirons, G.T.1    Fawcett, J.J.2    Crissman, H.A.3
  • 10
    • 0028902956 scopus 로고
    • Site selective bis-intercalation of a homodimeric thiazole orange dye in dna oligonucleotides
    • Jacobsen, J. P.; Pedersen, J. B.; Hansen, L. F.; Wemmer, D. E. Site Selective Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA Oligonucleotides Nucleic Acids Res. 1995, 23 (5) 753-760
    • (1995) Nucleic Acids Res. , vol.23 , Issue.5 , pp. 753-760
    • Jacobsen, J.P.1    Pedersen, J.B.2    Hansen, L.F.3    Wemmer, D.E.4
  • 11
    • 0000905821 scopus 로고
    • Groove binding of a styrylcyanine dye to the DNA double helix: The salt effect
    • Kumart, C. V.; Turner, R. S.; Asuncion, E. H. Groove Binding of a Styrylcyanine Dye to the DNA Double Helix: the Salt Effect J. Photochem. Photobiol. A: Chem. 1993, 74, 231-238
    • (1993) J. Photochem. Photobiol. A: Chem. , vol.74 , pp. 231-238
    • Kumart, C.V.1    Turner, R.S.2    Asuncion, E.H.3
  • 12
    • 0033199558 scopus 로고    scopus 로고
    • On the sequence selective bis-intercalation of a homodimeric thiazole orange Dye in DNA
    • Bunkenborg, J.; Stidsen, M. M.; Jacobsen, J. P. On the Sequence Selective Bis-Intercalation of a Homodimeric Thiazole Orange Dye in DNA Bioconjugate Chem. 1999, 10 (5) 824-831
    • (1999) Bioconjugate Chem. , vol.10 , Issue.5 , pp. 824-831
    • Bunkenborg, J.1    Stidsen, M.M.2    Jacobsen, J.P.3
  • 15
    • 0022098776 scopus 로고
    • Regularities in formation of the spine of hydration in the DNA minor groove and its influence on the DNA structure
    • Chuprina, V. P. Regularities in Formation of the Spine of Hydration in the DNA Minor Groove and Its Influence on the DNA Structure FEBS Lett. 1985, 186, 98-102
    • (1985) FEBS Lett. , vol.186 , pp. 98-102
    • Chuprina, V.P.1
  • 17
    • 34248365283 scopus 로고    scopus 로고
    • Fluorescence relaxation dynamics of acridine orange in nanosized micellar systems and DNA
    • Shaw, A. K.; Pal, S. K. Fluorescence Relaxation Dynamics of Acridine Orange in Nanosized Micellar Systems and DNA J. Phys. Chem. B 2007, 111 (16) 4189-4199
    • (2007) J. Phys. Chem. B , vol.111 , Issue.16 , pp. 4189-4199
    • Shaw, A.K.1    Pal, S.K.2
  • 18
    • 33751553558 scopus 로고
    • Short and excitation-independent fluorescence lifetimes of j-aggregates adsorbed on silver(I) bromide and silica
    • Kemnitz, K.; Yoshihara, K.; Tani, T. Short and Excitation-Independent Fluorescence Lifetimes of J-Aggregates Adsorbed on Silver(I) Bromide and Silica J. Phys. Chem. 1990, 94 (7) 3099-3104
    • (1990) J. Phys. Chem. , vol.94 , Issue.7 , pp. 3099-3104
    • Kemnitz, K.1    Yoshihara, K.2    Tani, T.3
  • 19
    • 0026766945 scopus 로고
    • One-electron-reduction potentials of pyrimidine bases, nucleosides, and nucleotides in aqueous solution. Consequences for DNA redox chemistry
    • Steenken, S.; Telo, J. P.; Novais, H. M.; Candeias, L. P. One-Electron-Reduction Potentials of Pyrimidine Bases, Nucleosides, and Nucleotides in Aqueous Solution. Consequences for DNA Redox Chemistry J. Am. Chem. Soc. 1992, 114 (12) 4701-4709
    • (1992) J. Am. Chem. Soc. , vol.114 , Issue.12 , pp. 4701-4709
    • Steenken, S.1    Telo, J.P.2    Novais, H.M.3    Candeias, L.P.4
  • 20
    • 0026458382 scopus 로고
    • Base-selective oxidation and cleavage of DNA by photochemical cosensitized electron transfer
    • Dunn, D. A.; Lin, V. H.; Kochevar, I. E. Base-Selective Oxidation and Cleavage of DNA by Photochemical Cosensitized Electron Transfer Biochemistry 1992, 31 (46) 11620-11625
    • (1992) Biochemistry , vol.31 , Issue.46 , pp. 11620-11625
    • Dunn, D.A.1    Lin, V.H.2    Kochevar, I.E.3
  • 21
    • 0345743716 scopus 로고    scopus 로고
    • Single-molecule fluorescence spectroscopy of TOTO on Poly-AT and Poly-GC DNA
    • Bowen, B. P.; Enderlein, J.; Woodbury, N. W. Single-Molecule Fluorescence Spectroscopy of TOTO on Poly-AT and Poly-GC DNA Photochem. Photobiol. 2003, 78 (6) 576-581
    • (2003) Photochem. Photobiol. , vol.78 , Issue.6 , pp. 576-581
    • Bowen, B.P.1    Enderlein, J.2    Woodbury, N.W.3
  • 22
    • 0346374832 scopus 로고    scopus 로고
    • TOTO binding affinity analysis using single-molecule fluorescence spectroscopy
    • Bowen, B. P.; Woodbury, N. W. TOTO Binding Affinity Analysis Using Single-Molecule Fluorescence Spectroscopy Photochem. Photobiol. 2003, 78 (6) 582-586
    • (2003) Photochem. Photobiol. , vol.78 , Issue.6 , pp. 582-586
    • Bowen, B.P.1    Woodbury, N.W.2
  • 23
    • 75649137304 scopus 로고    scopus 로고
    • Photophysics and binding constant determination of the homodimeric Dye BOBO-3 and DNA oligonucleotides
    • Ruedas-Rama, M. J.; Orte, A.; Crovetto, L.; Talavera, E. M.; Alvarez-Pez, J. M. Photophysics and Binding Constant Determination of the Homodimeric Dye BOBO-3 and DNA Oligonucleotides J. Phys. Chem. B 2010, 114, 1094-1103
    • (2010) J. Phys. Chem. B , vol.114 , pp. 1094-1103
    • Ruedas-Rama, M.J.1    Orte, A.2    Crovetto, L.3    Talavera, E.M.4    Alvarez-Pez, J.M.5
  • 24
  • 25
    • 0016175370 scopus 로고
    • Theoretical aspects of DNA-Protein interactions: Co-operative and Non-co-operative Binding of Large Ligands to a One-Dimensional Homogeneous Lattice
    • McGhee, J. D.; von Hippel, P. Theoretical aspects of DNA-Protein interactions: Co-operative and Non-co-operative Binding of Large Ligands to a One-Dimensional Homogeneous Lattice J. Mol. Biol. 1974, 86, 469-489
    • (1974) J. Mol. Biol. , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.2
  • 26
    • 0042823487 scopus 로고    scopus 로고
    • Formation pathways of a guanine-quadruplex dna revealed by molecular dynamics and thermodynamic analysis of the substates
    • Štefl, R.; Cheatham, T. E.; Špačková, N. a.; Fadrná, E.; Berger, I.; Koča, J.; Šponer, J. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates Biophys. J. 2003, 85, 1787-1804
    • (2003) Biophys. J. , vol.85 , pp. 1787-1804
    • Štefl, R.1    Cheatham, T.E.2    Špačková, N.A.3    Fadrná, E.4    Berger, I.5    Koča, J.6    Šponer, J.7
  • 27
    • 0034619427 scopus 로고    scopus 로고
    • Structural characterization of a guanine-quadruplex ligand complex
    • Read, M. A.; Neidle, S. Structural Characterization of a Guanine-Quadruplex Ligand Complex Biochemistry 2000, 39, 13422-13432
    • (2000) Biochemistry , vol.39 , pp. 13422-13432
    • Read, M.A.1    Neidle, S.2
  • 28
    • 84906404797 scopus 로고    scopus 로고
    • Time Tagged Time-Resolved Fluorescence Data Collection. PicoQuant Technical Note, (accessed 2010)
    • Wahl, M. Time Tagged Time-Resolved Fluorescence Data Collection. PicoQuant Technical Note 2004, http://www.picoquant.com/technotes/technote-tttr. pdf (accessed 2010).
    • (2004)
    • Wahl, M.1
  • 29
    • 0000469474 scopus 로고    scopus 로고
    • Solvent dependence of the fluorescence lifetimes of xanthene dyes
    • Magde, D.; Rojas, G. E.; Seybold, P. G. Solvent Dependence of the Fluorescence Lifetimes of Xanthene Dyes Photochem. Photobiol. 1999, 70 (5) 737-744
    • (1999) Photochem. Photobiol. , vol.70 , Issue.5 , pp. 737-744
    • Magde, D.1    Rojas, G.E.2    Seybold, P.G.3
  • 30
    • 0018116734 scopus 로고
    • DNA bifunctional intercalators. 2. Fluorescence properties and DNA binding interaction of an ethidium homodimer and an acridine ethidium heterodimer
    • Gaugain, B.; Barbet, J.; Capelle, N.; Roques, B. P.; Le Pecq, J. B. DNA Bifunctional Intercalators. 2. Fluorescence Properties and DNA Binding Interaction of an Ethidium Homodimer and an Acridine Ethidium Heterodimer Biochemistry 1978, 17, 5078-5088 (Pubitemid 9063046)
    • (1978) Biochemistry , vol.17 , Issue.24 , pp. 5078-5088
    • Gaugain, B.1    Barbet, J.2    Capelle, N.3
  • 31
    • 0028104651 scopus 로고
    • Characterization of the binding of the fluorescent dyes yo and yoyo to dna by polarized light spectroscopy
    • Larsson, A.; Carlsson, C.; Jonsson, M.; Albinsson, B. Characterization of the Binding of the Fluorescent Dyes YO and YOYO to DNA by Polarized Light Spectroscopy J. Am. Chem. Soc. 1994, 116, 8459-8465
    • (1994) J. Am. Chem. Soc. , vol.116 , pp. 8459-8465
    • Larsson, A.1    Carlsson, C.2    Jonsson, M.3    Albinsson, B.4
  • 32
    • 15544371286 scopus 로고    scopus 로고
    • Comparison of SYTO9 and SYBR Green i for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis
    • Monis, P. T.; Giglio, S.; Saint, C. P. Comparison of SYTO9 and SYBR Green I for Real-time Polymerase Chain Reaction and Investigation of the Effect of Dye Concentration on Amplification and DNA Melting Curve Analysis Anal. Biochem. 2005, 340 (1) 24-34
    • (2005) Anal. Biochem. , vol.340 , Issue.1 , pp. 24-34
    • Monis, P.T.1    Giglio, S.2    Saint, C.P.3
  • 33
    • 0037026872 scopus 로고    scopus 로고
    • DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel-based assay
    • Bjorndal, M. T.; Fygenson, D. K. DNA Melting in the Presence of Fluorescent Intercalating Oxazole Yellow Dyes Measured with a Gel-Based Assay Biopolymers 2002, 65 (1) 40-44
    • (2002) Biopolymers , vol.65 , Issue.1 , pp. 40-44
    • Bjorndal, M.T.1    Fygenson, D.K.2
  • 34
    • 38649136194 scopus 로고    scopus 로고
    • Characterization of evagreen and the implication of its physicochemical properties for qPCR applications
    • Mao, F.; Leung, W.-Y.; Xin, X. Characterization of EvaGreen and the Implication of Its Physicochemical Properties for qPCR Applications BMC Biotechnol. 2007, 7 (1) 76
    • (2007) BMC Biotechnol. , vol.7 , Issue.1 , pp. 76
    • Mao, F.1    Leung, W.-Y.2    Xin, X.3
  • 35
    • 84989065227 scopus 로고
    • Conformational and dynamic investigation in solution of inosine and its molecular complex, inosiplex, by proton and carbon NMR spectroscopy
    • Rossi, C.; Picchi, M.; Tiezzi, E.; Corbini, G.; Corti, P. Conformational and Dynamic Investigation in Solution of Inosine and Its Molecular Complex, Inosiplex, by Proton and Carbon NMR Spectroscopy Magn. Reson. Chem. 1990, 28 (4) 348-354
    • (1990) Magn. Reson. Chem. , vol.28 , Issue.4 , pp. 348-354
    • Rossi, C.1    Picchi, M.2    Tiezzi, E.3    Corbini, G.4    Corti, P.5
  • 36
    • 0028341190 scopus 로고
    • Fluorescence lifetime analysis of DNA intercalated ethidium bromide and quenching by free dye
    • Heller, D. P.; Greenstock, C. L. Fluorescence Lifetime Analysis of DNA Intercalated Ethidium Bromide and Quenching by Free Dye Biophys. Chem. 1994, 50, 305-312
    • (1994) Biophys. Chem. , vol.50 , pp. 305-312
    • Heller, D.P.1    Greenstock, C.L.2
  • 37
    • 0000444299 scopus 로고
    • Physical and chemical characterization of the ordered complexes formed between polyinosinic acid, polycytidylic acid and their deoxyribo-analogues
    • Chamberlin, M. J.; Patterson, D. L. Physical and Chemical Characterization of the Ordered Complexes Formed between Polyinosinic Acid, Polycytidylic Acid and Their Deoxyribo-Analogues J. Mol. Biol. 1965, 12, 410-428
    • (1965) J. Mol. Biol. , vol.12 , pp. 410-428
    • Chamberlin, M.J.1    Patterson, D.L.2
  • 38
    • 0031593411 scopus 로고    scopus 로고
    • H-1 NMR studies of the bisintercalation of a homodimeric oxazole yellow Dye in DNA oligonucleotides
    • Johansen, F.; Jacobsen, J. P. H-1 NMR Studies of the Bisintercalation of a Homodimeric Oxazole Yellow Dye in DNA Oligonucleotides J. Biomol. Struct. Dyn. 1998, 16, 205-222
    • (1998) J. Biomol. Struct. Dyn. , vol.16 , pp. 205-222
    • Johansen, F.1    Jacobsen, J.P.2
  • 39
    • 0029013864 scopus 로고
    • Solution structure of a DNA complex with the fluorescent bis-intercalator toto determined by NMR spectroscopy
    • Spielmann, H. P.; Wemmer, D. E.; Jacobsen, J. P. Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Determined by NMR Spectroscopy Biochemistry 1995, 34 (27) 8542-8553
    • (1995) Biochemistry , vol.34 , Issue.27 , pp. 8542-8553
    • Spielmann, H.P.1    Wemmer, D.E.2    Jacobsen, J.P.3
  • 40
    • 0032079881 scopus 로고    scopus 로고
    • Solution structure of a DNA complex with the fluorescent bis-intercalator toto modified on the benzothiazole ring
    • Petersen, M.; Jacobsen, J. P. Solution Structure of a DNA Complex with the Fluorescent Bis-Intercalator TOTO Modified on the Benzothiazole Ring Bioconjugate Chem. 1998, 9 (3) 331-340
    • (1998) Bioconjugate Chem. , vol.9 , Issue.3 , pp. 331-340
    • Petersen, M.1    Jacobsen, J.P.2
  • 41
    • 0028946629 scopus 로고
    • Interaction of dimeric intercalating dyes with single-stranded DNA
    • Rye, H. S.; Glazer, A. N. Interaction of Dimeric Intercalating Dyes with Single-stranded DNA. Nucleic Acids Res. 1995, 23, 1215-1222
    • (1995) Nucleic Acids Res. , vol.23 , pp. 1215-1222
    • Rye, H.S.1    Glazer, A.N.2
  • 43
    • 0014020739 scopus 로고
    • Modified intercalation model for the interaction of amino acridines and DNA
    • Pritchard, N. J.; Blake, A.; Peacocke, A. R. Modified Intercalation Model for the Interaction of Amino Acridines and DNA Nature 1966, 212 (5068) 1360-1361
    • (1966) Nature , vol.212 , Issue.5068 , pp. 1360-1361
    • Pritchard, N.J.1    Blake, A.2    Peacocke, A.R.3
  • 44
    • 0036118683 scopus 로고    scopus 로고
    • The effect of spermine on plasmid condensation and dye release observed by fluorescence correlation spectroscopy
    • Kral, T.; Hof, M.; Langner, M. The Effect of Spermine on Plasmid Condensation and Dye Release Observed by Fluorescence Correlation Spectroscopy Biol. Chem. 2002, 338, 331-335
    • (2002) Biol. Chem. , vol.338 , pp. 331-335
    • Kral, T.1    Hof, M.2    Langner, M.3
  • 45
    • 0034743730 scopus 로고    scopus 로고
    • Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra
    • Nygren, J.; Ogulchansky, T. Y.; Losytskyy, M. Y.; Kovalska, V. B.; Yashchuk, V. M.; Yarmoluk, S. M. Interactions of Cyanine Dyes with Nucleic Acids. XXIV. Aggregation of Monomethine Cyanine Dyes in Presence of DNA and Its Manifestation in Absorption and Fluorescence Spectra Spectrochim. Acta A 2001, 57, 1525-1532
    • (2001) Spectrochim. Acta A , vol.57 , pp. 1525-1532
    • Nygren, J.1    Ogulchansky, T.Y.2    Losytskyy, M.Y.3    Kovalska, V.B.4    Yashchuk, V.M.5    Yarmoluk, S.M.6
  • 46
    • 0028222102 scopus 로고    scopus 로고
    • Influence of base composition, base sequence, and duplex structure on DNA hydration: Apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 °c
    • Chalikian, T. V.; Sarvazyan, A. P.; Plum, G. E.; Breslauer, K. J. Influence of Base Composition, Base Sequence, and Duplex Structure on DNA Hydration: Apparent Molar Volumes and Apparent Molar Adiabatic Compressibilities of Synthetic and Natural DNA Duplexes at 25 °C Biochemistry 2002, 33 (9) 2394-2401
    • (2002) Biochemistry , vol.33 , Issue.9 , pp. 2394-2401
    • Chalikian, T.V.1    Sarvazyan, A.P.2    Plum, G.E.3    Breslauer, K.J.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.