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Volumn 96, Issue 1, 2013, Pages 81-91

Phenazinium dyes methylene violet 3RAX and indoine blue bind to DNA by intercalation: Evidence from structural and thermodynamic studies

Author keywords

Calorimetry; DNA; Indoine blue; Interaction; Methylene violet 3RAX; Spectroscopy

Indexed keywords

BINDING AFFINITIES; CAPACITY VALUE; DNA BINDING; EFFECT OF IONIC STRENGTH; ELECTROSTATIC ATTRACTIONS; ENERGETIC ASPECT; ENTHALPY CHANGE; ENTHALPY-ENTROPY COMPENSATION; HYDROPHOBIC FORCES; INDOINE BLUE; INTERACTION; METHYLENE VIOLET 3RAX; NEGATIVE ENTHALPY; TEMPERATURE DEPENDENCE; THERMODYNAMIC STUDIES;

EID: 84865410391     PISSN: 01437208     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.dyepig.2012.07.026     Document Type: Article
Times cited : (33)

References (47)
  • 2
    • 39749163983 scopus 로고    scopus 로고
    • Quantification of cationic anti-malaria agent methylene blue in different human biological matrices using cation exchange chromatography coupled to tandem mass spectrometry
    • J. Burhenne, K.D. Riedel, J. Rengelshausen, P. Meissner, O. Muller, and G. Mikus Quantification of cationic anti-malaria agent methylene blue in different human biological matrices using cation exchange chromatography coupled to tandem mass spectrometry J Chromatogr B 863 2008 273 282
    • (2008) J Chromatogr B , vol.863 , pp. 273-282
    • Burhenne, J.1    Riedel, K.D.2    Rengelshausen, J.3    Meissner, P.4    Muller, O.5    Mikus, G.6
  • 3
    • 0037012426 scopus 로고    scopus 로고
    • Detecting the adsorption of dye molecules in homogeneous poly(propylene imine) dendrimer monolayers by surface plasmon resonance sensor
    • S. Chen, Q. Yu, L. Li, C.L. Boozer, J. Homola, and S.S. Yee Detecting the adsorption of dye molecules in homogeneous poly(propylene imine) dendrimer monolayers by surface plasmon resonance sensor J Am Chem Soc 124 2002 3395 3401
    • (2002) J Am Chem Soc , vol.124 , pp. 3395-3401
    • Chen, S.1    Yu, Q.2    Li, L.3    Boozer, C.L.4    Homola, J.5    Yee, S.S.6
  • 4
    • 33646544085 scopus 로고    scopus 로고
    • Counterion-dye staining for DNA in electrophoresed gels using indoine blue and methyl orange
    • S.Y. Hwang, L.T. Jin, G.S. Yoo, and J.K. Choi Counterion-dye staining for DNA in electrophoresed gels using indoine blue and methyl orange Electrophoresis 27 2006 1739 1743
    • (2006) Electrophoresis , vol.27 , pp. 1739-1743
    • Hwang, S.Y.1    Jin, L.T.2    Yoo, G.S.3    Choi, J.K.4
  • 5
    • 33646170399 scopus 로고    scopus 로고
    • Structure basis for the inhibitory mechanism of a novel DNase γ-specific inhibitor, DR 396
    • S. Sunaga, A. Yoshimori, D. Shiokawa, and S.I. Tanuma Structure basis for the inhibitory mechanism of a novel DNase γ-specific inhibitor, DR 396 Bioorg Med Chem 14 2006 4217 4226
    • (2006) Bioorg Med Chem , vol.14 , pp. 4217-4226
    • Sunaga, S.1    Yoshimori, A.2    Shiokawa, D.3    Tanuma, S.I.4
  • 6
    • 3242749168 scopus 로고    scopus 로고
    • PH-dependent loading and release behavior of small hydrophilic molecules in weak polyelectrolyte multilayer films
    • S.E. Burke, and C.J. Barrett pH-dependent loading and release behavior of small hydrophilic molecules in weak polyelectrolyte multilayer films Macromolecules 37 2004 5375 5384
    • (2004) Macromolecules , vol.37 , pp. 5375-5384
    • Burke, S.E.1    Barrett, C.J.2
  • 7
    • 0033184696 scopus 로고    scopus 로고
    • Novel carbons from nanocomposites for high lithium storage
    • L. Duclaux, E. Frackowiak, and F. Beguin Novel carbons from nanocomposites for high lithium storage J Power Sources 81-82 1999 323 327
    • (1999) J Power Sources , vol.81-82 , pp. 323-327
    • Duclaux, L.1    Frackowiak, E.2    Beguin, F.3
  • 8
    • 1242299960 scopus 로고    scopus 로고
    • Clay/carbon nanocomposites as precursors of electrode materials for lithium-ion batteries and supercapacitors
    • L. Duclaux, E. Frackowiak, T. Gibinski, R. Benoit, and F. Beguin Clay/carbon nanocomposites as precursors of electrode materials for lithium-ion batteries and supercapacitors Mol Cryst Liq Cryst 340 2000 449 454
    • (2000) Mol Cryst Liq Cryst , vol.340 , pp. 449-454
    • Duclaux, L.1    Frackowiak, E.2    Gibinski, T.3    Benoit, R.4    Beguin, F.5
  • 9
    • 34247631618 scopus 로고    scopus 로고
    • Molecular recognition of DNA by small molecules: At base pair specific intercalative binding of cytotoxic plant alkaloid palmatine
    • K. Bhadra, M. Maiti, and G.S. Kumar Molecular recognition of DNA by small molecules: AT base pair specific intercalative binding of cytotoxic plant alkaloid palmatine Biochim Biophys Acta 1770 2007 1071 1080
    • (2007) Biochim Biophys Acta , vol.1770 , pp. 1071-1080
    • Bhadra, K.1    Maiti, M.2    Kumar, G.S.3
  • 10
    • 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
    • J.D. McGhee, and P.H. von Hippel 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 86 1974 469 489
    • (1974) J Mol Biol , vol.86 , pp. 469-489
    • McGhee, J.D.1    Von Hippel, P.H.2
  • 11
    • 0001511660 scopus 로고
    • Formation and stability of inorganic complexes in solution
    • P. Job Formation and stability of inorganic complexes in solution Ann Chim 9 1928 113 203
    • (1928) Ann Chim , vol.9 , pp. 113-203
    • Job, P.1
  • 13
    • 33846450257 scopus 로고    scopus 로고
    • RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium
    • M.M. Islam, R. Sinha, and G.S. Kumar RNA binding small molecules: studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium Biophys Chem 125 2007 508 520
    • (2007) Biophys Chem , vol.125 , pp. 508-520
    • Islam, M.M.1    Sinha, R.2    Kumar, G.S.3
  • 14
    • 44149108423 scopus 로고    scopus 로고
    • Self-structure induction in single stranded poly (A) by small molecules: Studies on DNA intercalators, partial intercalators and groove binding molecules
    • P. Giri, and G.S. Kumar Self-structure induction in single stranded poly (A) by small molecules: studies on DNA intercalators, partial intercalators and groove binding molecules Arch Biochem Biophys 474 2008 183 192
    • (2008) Arch Biochem Biophys , vol.474 , pp. 183-192
    • Giri, P.1    Kumar, G.S.2
  • 15
    • 33845374393 scopus 로고
    • Novel approach to job's method: An undergraduate experiment
    • Z.D. Hill, and M. Patrick Novel approach to job's method: an undergraduate experiment J Chem Educ 63 1986 162 167
    • (1986) J Chem Educ , vol.63 , pp. 162-167
    • Hill, Z.D.1    Patrick, M.2
  • 16
    • 36048941459 scopus 로고    scopus 로고
    • Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug-DNA binding
    • S. Das, and G.S. Kumar Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: model for intercalative drug-DNA binding J Mol Struct 872 2008 56 63
    • (2008) J Mol Struct , vol.872 , pp. 56-63
    • Das, S.1    Kumar, G.S.2
  • 17
    • 61949239352 scopus 로고    scopus 로고
    • Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides
    • M.M. Islam, S. Roy Chowdhury, and G.S. Kumar Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides J Phys Chem B 113 2009 1210 1224
    • (2009) J Phys Chem B , vol.113 , pp. 1210-1224
    • Islam, M.M.1    Roy Chowdhury, S.2    Kumar, G.S.3
  • 18
    • 49349105052 scopus 로고    scopus 로고
    • Binding interaction of cationic phenazinium dyes with calf thymus DNA: A comparative study
    • D. Sarkar, P. Das, S. Basak, and N. Chattopadhyay Binding interaction of cationic phenazinium dyes with calf thymus DNA: a comparative study J Phys Chem B 112 2008 9243 9249
    • (2008) J Phys Chem B , vol.112 , pp. 9243-9249
    • Sarkar, D.1    Das, P.2    Basak, S.3    Chattopadhyay, N.4
  • 19
    • 0028104651 scopus 로고
    • Characterization of the binding of the fluorescent dyes YO and YOYO to DNA by polarized light spectroscopy
    • A. Larsson, C. Carlsson, M. Jonsson, and B. Albinsson Characterization of the binding of the fluorescent dyes YO and YOYO to DNA by polarized light spectroscopy J Am Chem Soc 116 1994 8459 8465
    • (1994) J Am Chem Soc , vol.116 , pp. 8459-8465
    • Larsson, A.1    Carlsson, C.2    Jonsson, M.3    Albinsson, B.4
  • 20
    • 28844436476 scopus 로고    scopus 로고
    • The binding of DNA intercalating and non-intercalating compounds to A-form and protonated form of poly(rC).poly(rG): Spectroscopic and viscometric study
    • R. Sinha, M.M. Islam, K. Bhadra, G.S. Kumar, A. Banerjee, and M. Maiti The binding of DNA intercalating and non-intercalating compounds to A-form and protonated form of poly(rC).poly(rG): spectroscopic and viscometric study Bioorg Med Chem 14 2006 800 814
    • (2006) Bioorg Med Chem , vol.14 , pp. 800-814
    • Sinha, R.1    Islam, M.M.2    Bhadra, K.3    Kumar, G.S.4    Banerjee, A.5    Maiti, M.6
  • 21
    • 70349973209 scopus 로고    scopus 로고
    • DNA intercalation of methylene blue and quinacrine: New insights into base and sequence specificity from structural and thermodynamic studies with polynucleotides
    • M. Hossain, and G.S. Kumar DNA intercalation of methylene blue and quinacrine: new insights into base and sequence specificity from structural and thermodynamic studies with polynucleotides Mol BioSyst 5 2009 1311 1322
    • (2009) Mol BioSyst , vol.5 , pp. 1311-1322
    • Hossain, M.1    Kumar, G.S.2
  • 22
    • 38749106626 scopus 로고    scopus 로고
    • Spectroscopic and calorimetric studies on the binding of the phototoxic and cytotoxic plant alkaloid sanguinarine with double helical poly (A)
    • P. Giri, and G.S. Kumar Spectroscopic and calorimetric studies on the binding of the phototoxic and cytotoxic plant alkaloid sanguinarine with double helical poly (A) J Photochem Photobiol A Chem 194 2008 111 121
    • (2008) J Photochem Photobiol A Chem , vol.194 , pp. 111-121
    • Giri, P.1    Kumar, G.S.2
  • 24
    • 9244222243 scopus 로고    scopus 로고
    • Tuning of intercalation and electron-transfer processes between DNA and acridinium derivatives through steric effects
    • J. Joseph, E. Kuruvilla, A.T. Achuthan, D. Ramaiah, and G.B. Schuster Tuning of intercalation and electron-transfer processes between DNA and acridinium derivatives through steric effects Bioconjug Chem 15 2004 1230 1235
    • (2004) Bioconjug Chem , vol.15 , pp. 1230-1235
    • Joseph, J.1    Kuruvilla, E.2    Achuthan, A.T.3    Ramaiah, D.4    Schuster, G.B.5
  • 25
    • 0019941688 scopus 로고
    • Sanguinarine: A monofunctional intercalating alkaloid
    • M. Maiti, R. Nandi, and K. Chaudhuri Sanguinarine: a monofunctional intercalating alkaloid FEBS Lett 142 1982 280 284
    • (1982) FEBS Lett , vol.142 , pp. 280-284
    • Maiti, M.1    Nandi, R.2    Chaudhuri, K.3
  • 26
    • 85048645035 scopus 로고
    • Structural considerations in the interactions of deoxyribonucleic acid and acridines
    • L.S. Lerman Structural considerations in the interactions of deoxyribonucleic acid and acridines J Mol Biol 3 1961 18 30
    • (1961) J Mol Biol , vol.3 , pp. 18-30
    • Lerman, L.S.1
  • 27
    • 0024993904 scopus 로고
    • Differential scanning calorimetric study of the effect of intercalators and other kinds of DNA-binding drugs on the stepwise melting of plasmid DNA
    • Y. Maeda, K. Nunomura, and E. Ohtsubo Differential scanning calorimetric study of the effect of intercalators and other kinds of DNA-binding drugs on the stepwise melting of plasmid DNA J Mol Biol 215 1990 321 329
    • (1990) J Mol Biol , vol.215 , pp. 321-329
    • Maeda, Y.1    Nunomura, K.2    Ohtsubo, E.3
  • 28
    • 0037026872 scopus 로고    scopus 로고
    • DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel based assay
    • M.T. Bjorndal, and D.K. Fygensan DNA melting in the presence of fluorescent intercalating oxazole yellow dyes measured with a gel based assay Biopolymers 65 2002 40 44
    • (2002) Biopolymers , vol.65 , pp. 40-44
    • Bjorndal, M.T.1    Fygensan, D.K.2
  • 29
    • 0015153612 scopus 로고
    • Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria
    • D.M. Crothers Statistical thermodynamics of nucleic acid melting transitions with coupled binding equilibria Biopolymers 10 1971 2147 2160
    • (1971) Biopolymers , vol.10 , pp. 2147-2160
    • Crothers, D.M.1
  • 30
    • 4143080522 scopus 로고    scopus 로고
    • Energetics of drug-DNA interactions
    • J.B. Chaires Energetics of drug-DNA interactions Biopolymers 44 1997 201 215
    • (1997) Biopolymers , vol.44 , pp. 201-215
    • Chaires, J.B.1
  • 31
    • 34547840328 scopus 로고    scopus 로고
    • Specific binding and self-structure induction to poly (A) by the cytotoxic plant alkaloid sanguinarine
    • P. Giri, and G.S. Kumar Specific binding and self-structure induction to poly (A) by the cytotoxic plant alkaloid sanguinarine Biochim Biophys Acta 1770 2007 1419 1426
    • (2007) Biochim Biophys Acta , vol.1770 , pp. 1419-1426
    • Giri, P.1    Kumar, G.S.2
  • 32
    • 80051675861 scopus 로고    scopus 로고
    • Targeting RNA by small molecules: Comparative structural and thermodynamic aspects of aristolactam-β-D-glucoside and daunomycin binding to t-RNA phe
    • A. Das, K. Bhadra, and G.S. Kumar Targeting RNA by small molecules: comparative structural and thermodynamic aspects of aristolactam-β-D- glucoside and daunomycin binding to t-RNA phe PLos ONE 6 2011 e23186
    • (2011) PLos ONE , vol.6 , pp. 23186
    • Das, A.1    Bhadra, K.2    Kumar, G.S.3
  • 33
    • 70149091049 scopus 로고    scopus 로고
    • Partition of thermodynamic energies of drug-DNA complexation
    • V.V. Kostjukov, N.M. Khomytova, and M.P. Evstigneev Partition of thermodynamic energies of drug-DNA complexation Biopolymers 91 2009 773 790
    • (2009) Biopolymers , vol.91 , pp. 773-790
    • Kostjukov, V.V.1    Khomytova, N.M.2    Evstigneev, M.P.3
  • 34
    • 60649106752 scopus 로고    scopus 로고
    • RNA targeting through binding of small molecules: Studies on t-RNA binding by cytotoxic protoberberine alkaloid coralyne
    • M.M. Islam, P. Pandya, S. Kumar, and G.S. Kumar RNA targeting through binding of small molecules: studies on t-RNA binding by cytotoxic protoberberine alkaloid coralyne Mol Biosyst 5 2009 244 254
    • (2009) Mol Biosyst , vol.5 , pp. 244-254
    • Islam, M.M.1    Pandya, P.2    Kumar, S.3    Kumar, G.S.4
  • 35
    • 62949226596 scopus 로고    scopus 로고
    • DNA binding of benzophenanthridine compounds sanguinarine versus ethidium: Comparative binding and thermodynamic profile of intercalation
    • M. Hossain, and G.S. Kumar DNA binding of benzophenanthridine compounds sanguinarine versus ethidium: comparative binding and thermodynamic profile of intercalation J Chem Thermodyn 41 2009 764 774
    • (2009) J Chem Thermodyn , vol.41 , pp. 764-774
    • Hossain, M.1    Kumar, G.S.2
  • 36
    • 0034713855 scopus 로고    scopus 로고
    • Energetics of DNA intercalation reactions
    • J. Ren, T.C. Jenkins, and J.B. Chaires Energetics of DNA intercalation reactions Biochemistry 39 2000 8439 8447
    • (2000) Biochemistry , vol.39 , pp. 8439-8447
    • Ren, J.1    Jenkins, T.C.2    Chaires, J.B.3
  • 37
    • 33750979299 scopus 로고    scopus 로고
    • Physical and structural basis for the strong interactions of the -ImPy-central pairing motif in the polyamide f-ImPyIm
    • K.L. Buchmueller, S.L. Bailey, D.A. Matthews, Z.T. Taherbhai, J.K. Register, and Z.S. Davis Physical and structural basis for the strong interactions of the -ImPy-central pairing motif in the polyamide f-ImPyIm Biochemistry 45 2006 13551 13565
    • (2006) Biochemistry , vol.45 , pp. 13551-13565
    • Buchmueller, K.L.1    Bailey, S.L.2    Matthews, D.A.3    Taherbhai, Z.T.4    Register, J.K.5    Davis, Z.S.6
  • 38
    • 33645768556 scopus 로고    scopus 로고
    • Binding-linked protonation of a DNA minor-groove agent
    • B. Nguyen, J. Stanek, and W.D. Wilson Binding-linked protonation of a DNA minor-groove agent Biophys J 90 2006 1319 1328
    • (2006) Biophys J , vol.90 , pp. 1319-1328
    • Nguyen, B.1    Stanek, J.2    Wilson, W.D.3
  • 40
    • 84862167444 scopus 로고    scopus 로고
    • Probing the binding of two sugar bearing anticancer agents aristololactam-β-D-glucoside and daunomycin to double stranded RNA polynucleotides: A combined spectroscopic and calorimetric study
    • A. Das, and G.S. Kumar Probing the binding of two sugar bearing anticancer agents aristololactam-β-D-glucoside and daunomycin to double stranded RNA polynucleotides: a combined spectroscopic and calorimetric study Mol BioSyst 8 2012 1958 1969
    • (2012) Mol BioSyst , vol.8 , pp. 1958-1969
    • Das, A.1    Kumar, G.S.2
  • 41
    • 33846599391 scopus 로고    scopus 로고
    • Microcalorimetry of interaction of dihydro-imidazo-phenanthridinium (DIP)-based compounds with duplex DNA
    • K.M. Guthrie, A.D.C. Parenty, L.V. Smith, L. Cronin, and A. Cooper Microcalorimetry of interaction of dihydro-imidazo-phenanthridinium (DIP)-based compounds with duplex DNA Biophys Chem 126 2007 117 123
    • (2007) Biophys Chem , vol.126 , pp. 117-123
    • Guthrie, K.M.1    Parenty, A.D.C.2    Smith, L.V.3    Cronin, L.4    Cooper, A.5
  • 42
    • 0017820499 scopus 로고
    • Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: The roles of ion association or release, screening, and ion effects on water activity
    • M.T. Record Jr., C.F. Anderson, and T.M. Lohman Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity Q Rev Biophys 11 1978 103 178
    • (1978) Q Rev Biophys , vol.11 , pp. 103-178
    • Record, Jr.M.T.1    Anderson, C.F.2    Lohman, T.M.3
  • 43
    • 0034435652 scopus 로고    scopus 로고
    • Structural and thermodynamic strategies for site-specific DNA binding proteins
    • L. Jen-Jacobson, L.E. Engler, and L.A. Jacobson Structural and thermodynamic strategies for site-specific DNA binding proteins Structure 8 2000 1015 1023
    • (2000) Structure , vol.8 , pp. 1015-1023
    • Jen-Jacobson, L.1    Engler, L.E.2    Jacobson, L.A.3
  • 44
    • 33747802145 scopus 로고    scopus 로고
    • A thermodynamic signature for drug-DNA binding mode
    • J.B. Chaires A thermodynamic signature for drug-DNA binding mode Arch Biochem Biophys 453 2006 26 31
    • (2006) Arch Biochem Biophys , vol.453 , pp. 26-31
    • Chaires, J.B.1
  • 45
    • 38349135426 scopus 로고    scopus 로고
    • Enthalpy-entropy compensation: A phantom or something useful?
    • E.V. Starikov, and B. Norden Enthalpy-entropy compensation: a phantom or something useful? J Phys Chem B 111 2007 14431 14435
    • (2007) J Phys Chem B , vol.111 , pp. 14431-14435
    • Starikov, E.V.1    Norden, B.2
  • 46
    • 0030465221 scopus 로고    scopus 로고
    • Dissecting the free energy of drug binding to DNA
    • J.B. Chaires Dissecting the free energy of drug binding to DNA Anti-Cancer Drug Des 11 1996 569 580
    • (1996) Anti-Cancer Drug des , vol.11 , pp. 569-580
    • Chaires, J.B.1


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