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Volumn 39, Issue 22, 2011, Pages 9649-9658

Complexity in the binding of minor groove agents: Netropsin has two thermodynamically different DNA binding modes at a single site

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Indexed keywords

CONGOCIDINE;

EID: 83755205381     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr699     Document Type: Article
Times cited : (31)

References (42)
  • 1
    • 80052225565 scopus 로고    scopus 로고
    • Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers
    • Rahman,K.M., James,C.H. and Thurston,D.E. (2011) Effect of base sequence on the DNA cross-linking properties of pyrrolobenzodiazepine (PBD) dimers. Nucleic Acids Res., 39, 5800-5812.
    • (2011) Nucleic Acids Res. , vol.39 , pp. 5800-5812
    • Rahman, K.M.1    James, C.H.2    Thurston, D.E.3
  • 2
    • 77955505177 scopus 로고    scopus 로고
    • A review of trabectedin (ET-743): A unique mechanism of action
    • D'Incalci,M. and Galmarini,C.M. (2010) A review of trabectedin (ET-743): a unique mechanism of action. Mol. Cancer Ther., 9, 2157-2163.
    • (2010) Mol. Cancer Ther. , vol.9 , pp. 2157-2163
    • D'Incalci, M.1    Galmarini, C.M.2
  • 3
    • 78650264127 scopus 로고    scopus 로고
    • Transcriptional inhibition of progressive renal disease by gene silencing pyrrole-imidazole polyamide targeting of the transforming growth factor-[beta]1 promoter
    • Matsuda,H., Fukuda,N., Ueno,T., Katakawa,M., Wang,X., Watanabe,T., Matsui,S., Aoyama,T., Saito,K., Bando,T. et al. (2011) Transcriptional inhibition of progressive renal disease by gene silencing pyrrole-imidazole polyamide targeting of the transforming growth factor-[beta]1 promoter. Kidney Int., 79, 46-56.
    • (2011) Kidney Int. , vol.79 , pp. 46-56
    • Matsuda, H.1    Fukuda, N.2    Ueno, T.3    Katakawa, M.4    Wang, X.5    Watanabe, T.6    Matsui, S.7    Aoyama, T.8    Saito, K.9    Bando, T.10
  • 4
    • 79955867207 scopus 로고    scopus 로고
    • The development of pyrrolobenzodiazepines as antitumour agents
    • Hartley,J.A. (2011) The development of pyrrolobenzodiazepines as antitumour agents. Expert Opin. Investig. Drugs, 20, 733-744.
    • (2011) Expert Opin. Investig. Drugs , vol.20 , pp. 733-744
    • Hartley, J.A.1
  • 5
    • 70149095918 scopus 로고    scopus 로고
    • Cyclic pyrrole-imidazole polyamides targeted to the androgen response element
    • Chenoweth,D.M., Harki,D.A., Phillips,J.W., Dose,C. and Dervan,P.B. (2009) Cyclic pyrrole-imidazole polyamides targeted to the androgen response element. J. Am. Chem. Soc., 131, 7182-7188.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 7182-7188
    • Chenoweth, D.M.1    Harki, D.A.2    Phillips, J.W.3    Dose, C.4    Dervan, P.B.5
  • 9
    • 79953878855 scopus 로고    scopus 로고
    • Hx, a novel fluorescent, minor groove and sequence specific recognition element: Design, synthesis, and DNA binding properties of p-anisylbenzimidazole- imidazole/pyrrole-containing polyamides
    • Chavda,S., Liu,Y., Babu,B., Davis,R., Sielaff,A., Ruprich,J., Westrate,L., Tronrud,C., Ferguson,A., Franks,A. et al. (2011) Hx, a novel fluorescent, minor groove and sequence specific recognition element: design, synthesis, and DNA binding properties of p-anisylbenzimidazole-imidazole/ pyrrole-containing polyamides. Biochemistry, 50, 3127-3136.
    • (2011) Biochemistry , vol.50 , pp. 3127-3136
    • Chavda, S.1    Liu, Y.2    Babu, B.3    Davis, R.4    Sielaff, A.5    Ruprich, J.6    Westrate, L.7    Tronrud, C.8    Ferguson, A.9    Franks, A.10
  • 10
    • 78651460574 scopus 로고    scopus 로고
    • Labeling Nuclear DNA with Hoechst 33342
    • January 12011 (doi:10.1101/ pdb.prot5557; epub ahead of print)
    • Chazotte,B. (2011) Labeling Nuclear DNA with Hoechst 33342. Cold Spring Harb. Protoc., January 1, 2011 (doi:10.1101/ pdb.prot5557; epub ahead of print).
    • (2011) Cold Spring Harb. Protoc.
    • Chazotte, B.1
  • 11
    • 79952972850 scopus 로고    scopus 로고
    • Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template
    • Stadler,A.L., Renikuntla,B.R., Yaron,D., Fang,A.S. and Armitage,B.A. (2011) Substituent effects on the assembly of helical cyanine dye aggregates in the minor groove of a DNA template. Langmuir, 27, 1472-1479.
    • (2011) Langmuir , vol.27 , pp. 1472-1479
    • Stadler, A.L.1    Renikuntla, B.R.2    Yaron, D.3    Fang, A.S.4    Armitage, B.A.5
  • 13
    • 55249093393 scopus 로고    scopus 로고
    • Quantitating the concentration of Py-Im polyamide-fluorescein conjugates in live cells
    • Hsu,C.F. and Dervan,P.B. (2008) Quantitating the concentration of Py-Im polyamide-fluorescein conjugates in live cells. Bioorg. Med. Chem. Lett., 18, 5851-5855.
    • (2008) Bioorg. Med. Chem. Lett. , vol.18 , pp. 5851-5855
    • Hsu, C.F.1    Dervan, P.B.2
  • 14
    • 64549136640 scopus 로고    scopus 로고
    • A new synthesis of alkene-containing minor-groove binders and essential hydro bonding in binding to DNA and in antibacterial activity
    • Anthony,N.G., Breen,D., Donoghue,G., Khalaf,A.I., Mackay,S.P., Parkinson,J.A. and Suckling,C.J. (2009) A new synthesis of alkene-containing minor-groove binders and essential hydro bonding in binding to DNA and in antibacterial activity. Org. Biomol. Chem., 7, 1843-1850.
    • (2009) Org. Biomol. Chem. , vol.7 , pp. 1843-1850
    • Anthony, N.G.1    Breen, D.2    Donoghue, G.3    Khalaf, A.I.4    MacKay, S.P.5    Parkinson, J.A.6    Suckling, C.J.7
  • 15
    • 79954619907 scopus 로고    scopus 로고
    • The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus
    • Rosado,H., Rahman,K.M., Feuerbaum,E.A., Hinds,J., Thurston,D.E. and Taylor,P.W. (2011) The minor groove-binding agent ELB-21 forms multiple interstrand and intrastrand covalent cross-links with duplex DNA and displays potent bactericidal activity against methicillin-resistant Staphylococcus aureus. J. Antimicrob. Chemother., 66, 985-996.
    • (2011) J. Antimicrob. Chemother. , vol.66 , pp. 985-996
    • Rosado, H.1    Rahman, K.M.2    Feuerbaum, E.A.3    Hinds, J.4    Thurston, D.E.5    Taylor, P.W.6
  • 16
    • 38649134785 scopus 로고    scopus 로고
    • Inhibition of high-mobility-group A2 protein binding to DNA by netropsin: A biosensor-surface plasmon resonance assay
    • Miao,Y., Cui,T., Leng,F. and Wilson,W.D. (2008) Inhibition of high-mobility-group A2 protein binding to DNA by netropsin: a biosensor-surface plasmon resonance assay. Anal. Biochem., 374, 7-15.
    • (2008) Anal. Biochem. , vol.374 , pp. 7-15
    • Miao, Y.1    Cui, T.2    Leng, F.3    Wilson, W.D.4
  • 17
    • 34547157531 scopus 로고    scopus 로고
    • Design and synthesis of a cell-permeable synthetic transcription factor mimic
    • Xiao,X., Yu,P., Lim,H.S., Sikder,D. and Kodadek,T. (2007) Design and synthesis of a cell-permeable synthetic transcription factor mimic. J. Comb. Chem., 9, 592-600.
    • (2007) J. Comb. Chem. , vol.9 , pp. 592-600
    • Xiao, X.1    Yu, P.2    Lim, H.S.3    Sikder, D.4    Kodadek, T.5
  • 18
    • 42249094879 scopus 로고    scopus 로고
    • Small molecules targeting histone H4 as potential therapeutics for chronic myelogenous leukemia
    • DOI 10.1158/1535-7163.MCT-08-0130
    • Chou,C.J., Farkas,M.E., Tsai,S.M., Alvarez,D., Dervan,P.B. and Gottesfeld,J.M. (2008) Small molecules targeting histone H4 as potential therapeutics for chronic myelogenous leukemia. Mol. Cancer Ther., 7, 769-778. (Pubitemid 351551030)
    • (2008) Molecular Cancer Therapeutics , vol.7 , Issue.4 , pp. 769-778
    • Chou, C.J.1    Farkas, M.E.2    Tsai, S.M.3    Alvarez, D.4    Dervan, P.B.5    Gottesfeld, J.M.6
  • 19
    • 0034951136 scopus 로고    scopus 로고
    • DNA minor-groove recognition by small molecules
    • DOI 10.1039/a705982e
    • Neidle,S. (2001) DNA minor-groove recognition by small molecules. Nat. Prod. Rep., 18, 291-309. (Pubitemid 32589165)
    • (2001) Natural Product Reports , vol.18 , Issue.3 , pp. 291-309
    • Neidle, S.1
  • 20
    • 33745422093 scopus 로고    scopus 로고
    • A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: Analysis of a "highly twisted" benzimidazole-diamidine
    • DOI 10.1021/ja0600936
    • Goodwin,K.D., Lewis,M.A., Tanious,F.A., Tidwell,R.R., Wilson,W.D., Georgiadis,M.M. and Long,E.C. (2006) A high-throughput, high-resolution strategy for the study of site-selective DNA binding agents: Analysis of a ''highly twisted'' benzimidazole-diamidine. J. Am. Chem. Soc., 128, 7846-7854. (Pubitemid 43945726)
    • (2006) Journal of the American Chemical Society , vol.128 , Issue.24 , pp. 7846-7854
    • Goodwin, K.D.1    Lewis, M.A.2    Tanious, F.A.3    Tidwell, R.R.4    Wilson, W.D.5    Georgiadis, M.M.6    Long, E.C.7
  • 21
    • 34250156358 scopus 로고    scopus 로고
    • Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: Induced fit and bound water
    • DOI 10.1021/bi700288g
    • Tanious,F.A., Laine,W., Peixoto,P., Bailly,C., Goodwin,K.D., Lewis,M.A., Long,E.C., Georgiadis,M.M., Tidwell,R.R. and Wilson,W.D. (2007) Unusually strong binding to the DNA minor groove by a highly twisted benzimidazole diphenylether: Induced fit and bound water. Biochemistry, 46, 6944-6956. (Pubitemid 46906423)
    • (2007) Biochemistry , vol.46 , Issue.23 , pp. 6944-6956
    • Tanious, F.A.1    Laine, W.2    Peixoto, P.3    Bailly, C.4    Goodwin, K.D.5    Lewis, M.A.6    Long, E.C.7    Georgiadis, M.M.8    Tidwell, R.R.9    Wilson, W.D.10
  • 22
    • 45849127288 scopus 로고    scopus 로고
    • The effects of local DNA sequence on the interaction of ligands with their preferred binding sites
    • Hampshire,A.J. and Fox,K.R. (2008) The effects of local DNA sequence on the interaction of ligands with their preferred binding sites. Biochimie, 90, 988-998.
    • (2008) Biochimie , vol.90 , pp. 988-998
    • Hampshire, A.J.1    Fox, K.R.2
  • 23
    • 61849154273 scopus 로고    scopus 로고
    • A role for water molecules in DNA-ligand minor groove recognition
    • Nguyen,B., Neidle,S. and Wilson,W.D. (2009) A role for water molecules in DNA-ligand minor groove recognition. Acc. Chem. Res., 42, 11-21.
    • (2009) Acc. Chem. Res. , vol.42 , pp. 11-21
    • Nguyen, B.1    Neidle, S.2    Wilson, W.D.3
  • 24
    • 33846621126 scopus 로고    scopus 로고
    • Binding of netropsin to several DNA constructs: Evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand
    • DOI 10.1016/j.bpc.2006.06.009, PII S0301462206002109
    • Freyer,M.W., Buscaglia,R., Cashman,D., Hyslop,S., Wilson,W.D., Chaires,J.B. and Lewis,E.A. (2007) Binding of netropsin to several DNA constructs: evidence for at least two different 1:1 complexes formed from an -AATT-containing ds-DNA construct and a single minor groove binding ligand. Biophys. Chem., 126, 186-196. (Pubitemid 46186646)
    • (2007) Biophysical Chemistry , vol.126 , Issue.1-3 , pp. 186-196
    • Freyer, M.W.1    Buscaglia, R.2    Cashman, D.3    Hyslop, S.4    Wilson, W.D.5    Chaires, J.B.6    Lewis, E.A.7
  • 25
    • 34047211804 scopus 로고    scopus 로고
    • Break in the heat capacity change at 303 K for complex binding of netropsin to AATT containing hairpin DNA constructs
    • DOI 10.1529/biophysj.106.098723
    • Freyer,M.W., Buscaglia,R., Hollingsworth,A., Ramos,J., Blynn,M., Pratt,R., Wilson,W.D. and Lewis,E.A. (2007) Break in the heat capacity change at 303 K for complex binding of netropsin to AATT containing hairpin DNA constructs. Biophys. J., 92, 2516-2522. (Pubitemid 46536433)
    • (2007) Biophysical Journal , vol.92 , Issue.7 , pp. 2516-2522
    • Freyer, M.W.1    Buscaglia, R.2    Hollingsworth, A.3    Ramos, J.4    Blynn, M.5    Pratt, R.6    Wilson, W.D.7    Lewis, E.A.8
  • 26
    • 33746312998 scopus 로고    scopus 로고
    • 2 DNA hairpin: A comparison of biophysical techniques
    • DOI 10.1016/j.ab.2006.04.049, PII S0003269706003289
    • Freyer,M.W., Buscaglia,R., Nguyen,B., Wilson,W.D. and Lewis,E.A. (2006) Binding of netropsin and 4,6-diamidino-2-phenylindole to an A2T2 DNA hairpin: a comparison of biophysical techniques. Anal. Biochem., 355, 259-266. (Pubitemid 44107321)
    • (2006) Analytical Biochemistry , vol.355 , Issue.2 , pp. 259-266
    • Freyer, M.W.1    Buscaglia, R.2    Nguyen, B.3    David Wilson, W.4    Lewis, E.A.5
  • 27
    • 37349062388 scopus 로고    scopus 로고
    • DNA conformational effects on the interaction of netropsin with A-tract sequences
    • DOI 10.1021/bi701722x
    • Degtyareva,N.N., Fresia,M.J. and Petty,J.T. (2007) DNA conformational effects on the interaction of netropsin with A-tract sequences. Biochemistry, 46, 15136-15143. (Pubitemid 350308904)
    • (2007) Biochemistry , vol.46 , Issue.51 , pp. 15136-15143
    • Degtyareva, N.N.1    Fresia, M.J.2    Petty, J.T.3
  • 28
    • 39449092524 scopus 로고    scopus 로고
    • What drives the binding of minor groove-directed ligands to DNA hairpins?
    • DOI 10.1093/nar/gkm1110
    • Lah,J., Drobnak,I., Dolinar,M. and Vesnaver,G. (2008) What drives the binding of minor groove-directed ligands to DNA hairpins. Nucleic Acids Res., 36, 897-904. (Pubitemid 351267245)
    • (2008) Nucleic Acids Research , vol.36 , Issue.3 , pp. 897-904
    • Lah, J.1    Drobnak, I.2    Dolinar, M.3    Vesnaver, G.4
  • 30
    • 4143080522 scopus 로고    scopus 로고
    • Energetics of drug-DNA interactions
    • Chaires,J.B. (1997) Energetics of drug-DNA interactions. Biopolymers, 44, 201-215.
    • (1997) Biopolymers , vol.44 , pp. 201-215
    • Chaires, J.B.1
  • 31
    • 34247540790 scopus 로고    scopus 로고
    • Advances in the analysis of isothermal titration calorimetry data for ligand-DNA interactions
    • DOI 10.1016/j.ymeth.2007.01.010, PII S1046202307000047, Methods Related to DNA Sequence Recognition
    • Buurma,N.J. and Haq,I. (2007) Advances in the analysis of isothermal titration calorimetry data for ligand-DNA interactions. Methods, 42, 162-172. (Pubitemid 46654816)
    • (2007) Methods , vol.42 , Issue.2 , pp. 162-172
    • Buurma, N.J.1    Haq, I.2
  • 32
    • 0033573863 scopus 로고    scopus 로고
    • The thermodynamics of polyamide-DNA recognition: Hairpin polyamide binding the minor groove of duplex DNA
    • Pilch,D.S., Poklar,N., Baird,E.E., Dervan,P.B. and Breslauer,K.J. (1999) The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding the minor groove of duplex DNA. Biochemistry, 38, 2143-2151.
    • (1999) Biochemistry , vol.38 , pp. 2143-2151
    • Pilch, D.S.1    Poklar, N.2    Baird, E.E.3    Dervan, P.B.4    Breslauer, K.J.5
  • 33
    • 0028944342 scopus 로고
    • Interaction of minor groove ligands to an AAATT/AATTT site: Correlation of thermodynamic characterization and solution structure
    • Rentzeperis,D., Dwyer,T.J., Geierstanger,B.H., Pelton,J.G., Wemmer,D.E. and Marky,L.A. (1995) Interaction of minor groove ligands to an AAATT/AATTT site: correlation of thermodynamic characterization and solution structure. Biochemistry, 34, 2937-2945.
    • (1995) Biochemistry , vol.34 , pp. 2937-2945
    • Rentzeperis, D.1    Dwyer, T.J.2    Geierstanger, B.H.3    Pelton, J.G.4    Wemmer, D.E.5    Marky, L.A.6
  • 34
    • 33846899951 scopus 로고    scopus 로고
    • Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides
    • DOI 10.1093/nar/gkl1073
    • Nakano,S., Kirihata,T., Fujii,S., Sakai,H., Kuwahara,M., Sawai,H. and Sugimoto,N. (2007) Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides. Nucleic Acids Res., 35, 486-494. (Pubitemid 46232065)
    • (2007) Nucleic Acids Research , vol.35 , Issue.2 , pp. 486-494
    • Nakano, S.-I.1    Kirihata, T.2    Fujii, S.3    Sakai, H.4    Kuwahara, M.5    Sawai, H.6    Sugimoto, N.7
  • 36
    • 70449719309 scopus 로고    scopus 로고
    • Large, sequence-dependent effects on DNA conformation by minor groove binding compounds
    • Tevis,D.S., Kumar,A., Stephens,C.E., Boykin,D.W. and Wilson,W.D. (2009) Large, sequence-dependent effects on DNA conformation by minor groove binding compounds. Nucleic Acids Res., 37, 5550-5558.
    • (2009) Nucleic Acids Res. , vol.37 , pp. 5550-5558
    • Tevis, D.S.1    Kumar, A.2    Stephens, C.E.3    Boykin, D.W.4    Wilson, W.D.5
  • 37
    • 45949111852 scopus 로고    scopus 로고
    • Electrospray mass spectrometry to study drug-nucleic acids interactions
    • Rosu,F., De Pauw,E. and Gabelica,V. (2008) Electrospray mass spectrometry to study drug-nucleic acids interactions. Biochimie, 90, 1074-1087.
    • (2008) Biochimie , vol.90 , pp. 1074-1087
    • Rosu, F.1    De Pauw, E.2    Gabelica, V.3
  • 38
    • 0037102402 scopus 로고    scopus 로고
    • Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry
    • Rosu,F., Gabelica,V., Houssier,C. and De Pauw,E. (2002) Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. Nucleic Acids Res., 30, e82.
    • (2002) Nucleic Acids Res. , vol.30
    • Rosu, F.1    Gabelica, V.2    Houssier, C.3    De Pauw, E.4
  • 39
    • 0033404871 scopus 로고    scopus 로고
    • Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry
    • DOI 10.1002/(SICI)1096-9888(199912)34:12<1328::AID-JMS889>3.0.CO;2- F
    • Gabelica,V., De Pauw,E. and Rosu,F. (1999) Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry. J. Mass Spectrom., 34, 1328-1337. (Pubitemid 30011534)
    • (1999) Journal of Mass Spectrometry , vol.34 , Issue.12 , pp. 1328-1337
    • Gabelica, V.1    De Pauw, E.2    Rosu, F.3
  • 40
    • 79960107320 scopus 로고    scopus 로고
    • Developments in electrospray ionization mass spectrometry of non-covalent DNA-ligand complexes
    • Beck,J.L. (2011) Developments in electrospray ionization mass spectrometry of non-covalent DNA-ligand complexes. Aust. J. Chem., 64, 705-717.
    • (2011) Aust. J. Chem. , vol.64 , pp. 705-717
    • Beck, J.L.1
  • 41
    • 33846850207 scopus 로고    scopus 로고
    • Hydration changes accompanying the binding of minor groove ligands with DNA
    • DOI 10.1529/biophysj.106.097451
    • Degtyareva,N.N., Wallace,B.D., Bryant,A.R., Loo,K.M. and Petty,J.T. (2007) Hydration changes accompanying the binding of minor groove ligands with DNA. Biophys. J., 92, 959-965. (Pubitemid 46203225)
    • (2007) Biophysical Journal , vol.92 , Issue.3 , pp. 959-965
    • Degtyareva, N.N.1    Wallace, B.D.2    Bryant, A.R.3    Loo, K.M.4    Petty, J.T.5
  • 42
    • 0022398169 scopus 로고
    • Molecular recognition in noncovalent antitumor agent-DNA complexes: NMR studies of the base and sequence dependent recognition of the DNA minor groove by netropsin
    • DOI 10.1016/S0300-9084(85)80181-4
    • Patel,D.J. and Shapiro,L. (1985) Molecular recognition in noncovalent antitumor agent-DNA complexes: NMR studies of the base and sequence dependent recognition of the DNA minor groove by netropsin. Biochimie, 67, 887-915. (Pubitemid 16228281)
    • (1985) Biochimie , vol.67 , Issue.7-8 , pp. 887-915
    • Patel, D.J.1    Shapiro, L.2


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