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Volumn 112, Issue 29, 2008, Pages 8770-8778

Influence of DNA structure on adjacent site cooperative binding

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; NUCLEAR MAGNETIC RESONANCE; NUCLEIC ACIDS; ORGANIC ACIDS;

EID: 49149129740     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp801997v     Document Type: Article
Times cited : (11)

References (44)
  • 1
    • 0028076969 scopus 로고
    • Specific A+T-rich repetitive DNA sequences in maxicircles from wildtype Leishmania mexicana amazonensis and variants with DNA amplification
    • Lee, S. T.; Liu, H. Y.; Chu, T.; Lin, S. Y. Specific A+T-rich repetitive DNA sequences in maxicircles from wildtype Leishmania mexicana amazonensis and variants with DNA amplification. Exp. Parasitol. 1994, 79(1), 29-40.
    • (1994) Exp. Parasitol , vol.79 , Issue.1 , pp. 29-40
    • Lee, S.T.1    Liu, H.Y.2    Chu, T.3    Lin, S.Y.4
  • 2
    • 0028817367 scopus 로고
    • Analysis of functional domains of a GC box-binding protein, BTEB
    • Kobayashi, A.; Sogawa, K.; Imataka, H.; Fujii-Kuriyama, Y. Analysis of functional domains of a GC box-binding protein, BTEB. J. Biochem. 1995, 117 (1), 91-95.
    • (1995) J. Biochem , vol.117 , Issue.1 , pp. 91-95
    • Kobayashi, A.1    Sogawa, K.2    Imataka, H.3    Fujii-Kuriyama, Y.4
  • 3
    • 34250623956 scopus 로고    scopus 로고
    • A population study of the minicircles in Trypanosoma cruzi: Predicting guide RNAs in the absence of empirical RNA editing
    • Thomas, S.; Martinez, L. L.; Westenberger, S. J.; Sturm, N. R. A population study of the minicircles in Trypanosoma cruzi: predicting guide RNAs in the absence of empirical RNA editing. BMC Genomics 2007, 8, 133.
    • (2007) BMC Genomics , vol.8 , pp. 133
    • Thomas, S.1    Martinez, L.L.2    Westenberger, S.J.3    Sturm, N.R.4
  • 4
    • 0242500852 scopus 로고    scopus 로고
    • Treatment perspectives for human African trypanosomiasis
    • Bouteille, B.; Oukem, O.; Bisser, S.; Dumas, M. Treatment perspectives for human African trypanosomiasis. Fundam. Clin. Pharmacol. 2003, 17 (2), 171-181.
    • (2003) Fundam. Clin. Pharmacol , vol.17 , Issue.2 , pp. 171-181
    • Bouteille, B.1    Oukem, O.2    Bisser, S.3    Dumas, M.4
  • 5
    • 0038742717 scopus 로고    scopus 로고
    • Pentamidine uptake and resistance in pathogenic protozoa: Past, present and future
    • Bray, P. G.; Barrett, M. P.; Ward, S. A.; de Koning, H. P. Pentamidine uptake and resistance in pathogenic protozoa: past, present and future. Trends Parasitol. 2003, 19 (5), 232-239.
    • (2003) Trends Parasitol , vol.19 , Issue.5 , pp. 232-239
    • Bray, P.G.1    Barrett, M.P.2    Ward, S.A.3    de Koning, H.P.4
  • 6
    • 22144474782 scopus 로고    scopus 로고
    • Wilson, W. D.; Nguyen, B.; Tanious, F. A.; Mathis, A.; Hall, J. E.; Stephens, G E.; Boykin, D. W. Dications that target the DNA minor groove: compound design and preparation, DNA interactions, cellular distribution and biological activity. Curr. Med. Chem. Anticancer Agents 2005, 5 (4), 389-408.
    • Wilson, W. D.; Nguyen, B.; Tanious, F. A.; Mathis, A.; Hall, J. E.; Stephens, G E.; Boykin, D. W. Dications that target the DNA minor groove: compound design and preparation, DNA interactions, cellular distribution and biological activity. Curr. Med. Chem. Anticancer Agents 2005, 5 (4), 389-408.
  • 8
    • 34249938047 scopus 로고    scopus 로고
    • Pharmacogenomic analyses of targeting the AT-rich malaria parasite genome with AT-specific alkylating drugs
    • Woynarowski, J. M.; Krugliak, M.; Ginsburg, H. Pharmacogenomic analyses of targeting the AT-rich malaria parasite genome with AT-specific alkylating drugs. Mol. Biochem. Parasitol. 2007, 154 (1), 70-81.
    • (2007) Mol. Biochem. Parasitol , vol.154 , Issue.1 , pp. 70-81
    • Woynarowski, J.M.1    Krugliak, M.2    Ginsburg, H.3
  • 9
    • 1542723574 scopus 로고    scopus 로고
    • AT islands-their nature and potential for anticancer strategies
    • Woynarowski, J. M. AT islands-their nature and potential for anticancer strategies. Curr. Cancer Drug Targets 2004, 4 (2), 219-234.
    • (2004) Curr. Cancer Drug Targets , vol.4 , Issue.2 , pp. 219-234
    • Woynarowski, J.M.1
  • 10
    • 0035798704 scopus 로고    scopus 로고
    • AT-rich islands in genomic DNA as a novel target for AT-specific DNA-reactive antitumor drugs
    • Woynarowski, J. M.; Trevino, A. V.; Rodriguez, K. A.; Hardies, S. C.; Benham, C. J. AT-rich islands in genomic DNA as a novel target for AT-specific DNA-reactive antitumor drugs. J. Biol. Chem. 2001, 276 (44), 40555-40566.
    • (2001) J. Biol. Chem , vol.276 , Issue.44 , pp. 40555-40566
    • Woynarowski, J.M.1    Trevino, A.V.2    Rodriguez, K.A.3    Hardies, S.C.4    Benham, C.J.5
  • 11
    • 33845971464 scopus 로고    scopus 로고
    • Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae
    • Lipfert, J.; Das, R.; Chu, V. B.; Kudaravalli, M.; Boyd, N.; Herschlag, D.; Doniach, S. Structural transitions and thermodynamics of a glycine-dependent riboswitch from Vibrio cholerae. J. Mol. Biol. 2007, 365 (5), 1393-1406.
    • (2007) J. Mol. Biol , vol.365 , Issue.5 , pp. 1393-1406
    • Lipfert, J.1    Das, R.2    Chu, V.B.3    Kudaravalli, M.4    Boyd, N.5    Herschlag, D.6    Doniach, S.7
  • 12
    • 0032079564 scopus 로고    scopus 로고
    • Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex
    • Rhee, K. Y.; Senear, D. F.; Hatfield, G. W. Activation of gene expression by a ligand-induced conformational change of a protein-DNA complex. J. Biol. Chem. 1998, 273 (18), 11257-11266.
    • (1998) J. Biol. Chem , vol.273 , Issue.18 , pp. 11257-11266
    • Rhee, K.Y.1    Senear, D.F.2    Hatfield, G.W.3
  • 13
    • 0347720652 scopus 로고    scopus 로고
    • DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives
    • Tanious, F. A.; Hamelberg, D.; Bailly, C.; Czarny, A.; Boykin, D. W.; Wilson, W. D. DNA sequence dependent monomer-dimer binding modulation of asymmetric benzimidazole derivatives. J. Am. Chem. Soc. 2004, 126 (1), 143-153.
    • (2004) J. Am. Chem. Soc , vol.126 , Issue.1 , pp. 143-153
    • Tanious, F.A.1    Hamelberg, D.2    Bailly, C.3    Czarny, A.4    Boykin, D.W.5    Wilson, W.D.6
  • 15
    • 2442528409 scopus 로고    scopus 로고
    • Nonbonded bivalence approach to cell-permeable molecules that target DNA sequences
    • Pang, Y. P. Nonbonded bivalence approach to cell-permeable molecules that target DNA sequences. Bioorg. Med. Chem. 2004, 12 (11), 3063-3068.
    • (2004) Bioorg. Med. Chem , vol.12 , Issue.11 , pp. 3063-3068
    • Pang, Y.P.1
  • 17
    • 84906406700 scopus 로고    scopus 로고
    • Lacy, E. R.; Madsen, E. M.; Lee, M.; Wilson, W. D. Polyamide dimer stacking in the DNA minor groove and recognition of T.G mismatched base pairs in DNA. In DNA and RNA Binders: From Small Molecules to Drugs; Demeunynck, M., Bailly, C., Wilson, W. D., Eds.; Wiley-VCH: Weinheim, Germany, 2003; 2, pp 384-413.
    • Lacy, E. R.; Madsen, E. M.; Lee, M.; Wilson, W. D. Polyamide dimer stacking in the DNA minor groove and recognition of T.G mismatched base pairs in DNA. In DNA and RNA Binders: From Small Molecules to Drugs; Demeunynck, M., Bailly, C., Wilson, W. D., Eds.; Wiley-VCH: Weinheim, Germany, 2003; Vol. 2, pp 384-413.
  • 18
    • 0037070562 scopus 로고    scopus 로고
    • Influence of a terminal formamido group on the sequence recognition of DNA by polyamides
    • Lacy, E. R.; Le, N. M.; Price, G A.; Lee, M.; Wilson, W. D. Influence of a terminal formamido group on the sequence recognition of DNA by polyamides. J. Am. Chem. Soc. 2002, 124 (10), 2153-2163.
    • (2002) J. Am. Chem. Soc , vol.124 , Issue.10 , pp. 2153-2163
    • Lacy, E.R.1    Le, N.M.2    Price, G.A.3    Lee, M.4    Wilson, W.D.5
  • 19
    • 0034830898 scopus 로고    scopus 로고
    • Molecular recognition of DNA by small molecules
    • Dervan, P. B. Molecular recognition of DNA by small molecules. Bioorg. Med. Chem. 2001, 9 (9), 2215-2235.
    • (2001) Bioorg. Med. Chem , vol.9 , Issue.9 , pp. 2215-2235
    • Dervan, P.B.1
  • 20
    • 0037832279 scopus 로고    scopus 로고
    • Recognition of the DNA minor groove by pyrrole-imidazole polyamides
    • Dervan, P. B.; Edelson, B. S. Recognition of the DNA minor groove by pyrrole-imidazole polyamides. Curr. Opin. Struct. Biol. 2003, 13 (3), 284-299.
    • (2003) Curr. Opin. Struct. Biol , vol.13 , Issue.3 , pp. 284-299
    • Dervan, P.B.1    Edelson, B.S.2
  • 21
    • 33746669278 scopus 로고    scopus 로고
    • Spectrophotometric and thermodynamic study on the dimerization equilibrium of ionic dyes in water by chemometrics method
    • Niazi, A.; Yazdanipour, A.; Ghasemi, J.; Kubista, M. Spectrophotometric and thermodynamic study on the dimerization equilibrium of ionic dyes in water by chemometrics method. Spectrochim. Acta, Part A 2006, 65 (1), 73-78.
    • (2006) Spectrochim. Acta, Part A , vol.65 , Issue.1 , pp. 73-78
    • Niazi, A.1    Yazdanipour, A.2    Ghasemi, J.3    Kubista, M.4
  • 22
    • 0242408234 scopus 로고    scopus 로고
    • Selective binding and local photophysics of the fluorescent cyanine dye PicoGreen in double-stranded and single-stranded DNA
    • Schwitzer, C.; Scaiano, J. C. Selective binding and local photophysics of the fluorescent cyanine dye PicoGreen in double-stranded and single-stranded DNA. Phys. Chem. Chem. Phys. 2003, (5), 4911-4917.
    • (2003) Phys. Chem. Chem. Phys , vol.5 , pp. 4911-4917
    • Schwitzer, C.1    Scaiano, J.C.2
  • 23
    • 0035957095 scopus 로고    scopus 로고
    • Evaluation of the influence of compound structure on stacked-dimer formation in the DNA minor groove
    • Wang, L.; Carrasco, C.; Kumar, A.; Stephens, C. E.; Bailly, C.; Boykin, D. W.; Wilson, W. D. Evaluation of the influence of compound structure on stacked-dimer formation in the DNA minor groove. Biochemistry 2001, 40 (8), 2511-2521.
    • (2001) Biochemistry , vol.40 , Issue.8 , pp. 2511-2521
    • Wang, L.1    Carrasco, C.2    Kumar, A.3    Stephens, C.E.4    Bailly, C.5    Boykin, D.W.6    Wilson, W.D.7
  • 24
    • 0345254923 scopus 로고    scopus 로고
    • Cooperative dimerization of a heterocyclic diamidine determines sequence-specific DNA recognition
    • Tanious, F.; Wilson, W. D.; Wang, L.; Kumar, A.; Boykin, D. W.; Marty, C.; Baldeyrou, B.; Bailly, C. Cooperative dimerization of a heterocyclic diamidine determines sequence-specific DNA recognition. Biochemistry 2003, 42 (46), 13576-13586.
    • (2003) Biochemistry , vol.42 , Issue.46 , pp. 13576-13586
    • Tanious, F.1    Wilson, W.D.2    Wang, L.3    Kumar, A.4    Boykin, D.W.5    Marty, C.6    Baldeyrou, B.7    Bailly, C.8
  • 25
    • 0036295082 scopus 로고    scopus 로고
    • Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove
    • Wang, L.; Kumar, A.; Boykin, D. W.; Bailly, C.; Wilson, W. D. Comparative thermodynamics for monomer and dimer sequence-dependent binding of a heterocyclic dication in the DNA minor groove. J. Mol. Biol. 2002, 317 (3), 361-374.
    • (2002) J. Mol. Biol , vol.317 , Issue.3 , pp. 361-374
    • Wang, L.1    Kumar, A.2    Boykin, D.W.3    Bailly, C.4    Wilson, W.D.5
  • 26
    • 9444252283 scopus 로고    scopus 로고
    • DNA-templated assembly of helical cyanine dye aggregates: A supramolecular chain polymerization
    • Hannah, K. C.; Armitage, B. A. DNA-templated assembly of helical cyanine dye aggregates: a supramolecular chain polymerization. Acc. Chem. Res. 2004, 37 (11), 845-853.
    • (2004) Acc. Chem. Res , vol.37 , Issue.11 , pp. 845-853
    • Hannah, K.C.1    Armitage, B.A.2
  • 27
    • 0033531661 scopus 로고    scopus 로고
    • Spontaneous assembly of helical cyanine dye aggregates on DNA nanotemplates
    • Seifert, J. L.; Conner, R. E.; Kushon, S. A.; Wang, M.; Armitage, B. A. Spontaneous assembly of helical cyanine dye aggregates on DNA nanotemplates. J. Am. Chem. Soc. 1999, 121, 2987-2995.
    • (1999) J. Am. Chem. Soc , vol.121 , pp. 2987-2995
    • Seifert, J.L.1    Conner, R.E.2    Kushon, S.A.3    Wang, M.4    Armitage, B.A.5
  • 28
    • 28544433144 scopus 로고    scopus 로고
    • 1H NMR and optical spectroscopic investigation of the sequence-dependent dimerization of a symmetrical cyanine dye in the DNA minor groove
    • Hannah, K. C.; Gil, R. R.; Armitage, B. A. 1H NMR and optical spectroscopic investigation of the sequence-dependent dimerization of a symmetrical cyanine dye in the DNA minor groove. Biochemistry 2005, 44 (48), 15924-15929.
    • (2005) Biochemistry , vol.44 , Issue.48 , pp. 15924-15929
    • Hannah, K.C.1    Gil, R.R.2    Armitage, B.A.3
  • 29
    • 0027535529 scopus 로고
    • Binding of 4′,6-diamidino-2-phenylindole (DAPI) to AT regions of DNA: Evidence for an allosteric conformational change
    • Eriksson, S.; Kim, S. K.; Kubista, M.; Norden, B. Binding of 4′,6-diamidino-2-phenylindole (DAPI) to AT regions of DNA: evidence for an allosteric conformational change. Biochemistry 1993, 32 (12), 2987-2998.
    • (1993) Biochemistry , vol.32 , Issue.12 , pp. 2987-2998
    • Eriksson, S.1    Kim, S.K.2    Kubista, M.3    Norden, B.4
  • 30
    • 0034643815 scopus 로고    scopus 로고
    • The ATT strand of AAT.ATT trinucleotide repeats adopts stable hairpin structures induced by minor groove binding ligands
    • Trotta, E.; Del Grosso, N.; Erba, M.; Paci, M. The ATT strand of AAT.ATT trinucleotide repeats adopts stable hairpin structures induced by minor groove binding ligands. Biochemistry 2000, 39 (23), 6799-6808.
    • (2000) Biochemistry , vol.39 , Issue.23 , pp. 6799-6808
    • Trotta, E.1    Del Grosso, N.2    Erba, M.3    Paci, M.4
  • 31
    • 28544431620 scopus 로고    scopus 로고
    • Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: Insight from thermodynamic integration free energy simulations
    • Marco, E.; Negri, A.; Luque, F. J.; Gago, F. Role of stacking interactions in the binding sequence preferences of DNA bis-intercalators: insight from thermodynamic integration free energy simulations. Nucleic Acids Res. 2005, 33 (19), 6214-6224.
    • (2005) Nucleic Acids Res , vol.33 , Issue.19 , pp. 6214-6224
    • Marco, E.1    Negri, A.2    Luque, F.J.3    Gago, F.4
  • 32
    • 0025295346 scopus 로고
    • Echinomycin binding to the sequence CG(AT)nCG alters the structure of the central AT region
    • Fox, K. R.; Kentebe, E. Echinomycin binding to the sequence CG(AT)nCG alters the structure of the central AT region. Nucleic Acids Res. 1990, 18 (8), 1957-1963.
    • (1990) Nucleic Acids Res , vol.18 , Issue.8 , pp. 1957-1963
    • Fox, K.R.1    Kentebe, E.2
  • 33
    • 0034141784 scopus 로고    scopus 로고
    • Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: Solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2)
    • Gavathiotis, E.; Sharman, G. J.; Searle, M. S. Sequence-dependent variation in DNA minor groove width dictates orientational preference of Hoechst 33258 in A-tract recognition: solution NMR structure of the 2:1 complex with d(CTTTTGCAAAAG)(2). Nucleic Acids Res. 2000, 28 (3), 728-735.
    • (2000) Nucleic Acids Res , vol.28 , Issue.3 , pp. 728-735
    • Gavathiotis, E.1    Sharman, G.J.2    Searle, M.S.3
  • 34
    • 0025316839 scopus 로고
    • Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy
    • Searle, M. S.; Embrey, K. J. Sequence-specific interaction of Hoechst 33258 with the minor groove of an adenine-tract DNA duplex studied in solution by 1H NMR spectroscopy. Nucleic Acids Res. 1990, 18 (13), 3753-3762.
    • (1990) Nucleic Acids Res , vol.18 , Issue.13 , pp. 3753-3762
    • Searle, M.S.1    Embrey, K.J.2
  • 35
  • 36
    • 0001291624 scopus 로고    scopus 로고
    • Synthesis of monocationic and dicationic analogs of Hoechst 33258
    • Czarny, A.; Wilson, W. D.; Boykin, D. W. Synthesis of monocationic and dicationic analogs of Hoechst 33258. J. Heterocycl. Chem. 1996, 33, 1393-1397.
    • (1996) J. Heterocycl. Chem , vol.33 , pp. 1393-1397
    • Czarny, A.1    Wilson, W.D.2    Boykin, D.W.3
  • 37
    • 34247533690 scopus 로고    scopus 로고
    • Biosensor-surface plasmon resonance: Quantitative analysis of small molecule-nucleic acid interactions
    • Nguyen, B.; Tanious, F. A.; Wilson, W. D. Biosensor-surface plasmon resonance: Quantitative analysis of small molecule-nucleic acid interactions. Methods 2007, 42 (2), 150-161.
    • (2007) Methods , vol.42 , Issue.2 , pp. 150-161
    • Nguyen, B.1    Tanious, F.A.2    Wilson, W.D.3
  • 38
    • 0034633281 scopus 로고    scopus 로고
    • Determination of the refractive index increments of small molecules for correction of surface plasmon resonance data
    • Davis, T. M.; Wilson, W. D. Determination of the refractive index increments of small molecules for correction of surface plasmon resonance data. Anal. Biochem. 2000, 284 (2), 348-353.
    • (2000) Anal. Biochem , vol.284 , Issue.2 , pp. 348-353
    • Davis, T.M.1    Wilson, W.D.2
  • 39
    • 0014725117 scopus 로고
    • Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides
    • Cantor, C. R.; Warshaw, M. M.; Shapiro, H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 1970, 9 (9), 1059-1077.
    • (1970) Biopolymers , vol.9 , Issue.9 , pp. 1059-1077
    • Cantor, C.R.1    Warshaw, M.M.2    Shapiro, H.3
  • 41
    • 0034602772 scopus 로고    scopus 로고
    • Specific molecular recognition of mixed nucleic acid sequences: An aromatic dication that binds in the DNA minor groove as a dimer
    • Wang, L.; Bailly, C.; Kumar, A.; Ding, D.; Bajic, M.; Boykin, D. W.; Wilson, W. D. Specific molecular recognition of mixed nucleic acid sequences: an aromatic dication that binds in the DNA minor groove as a dimer. Proc. Natl. Acad. Sci. U.S.A. 2000, 97 (1), 12-16.
    • (2000) Proc. Natl. Acad. Sci. U.S.A , vol.97 , Issue.1 , pp. 12-16
    • Wang, L.1    Bailly, C.2    Kumar, A.3    Ding, D.4    Bajic, M.5    Boykin, D.W.6    Wilson, W.D.7
  • 42
    • 33846850207 scopus 로고    scopus 로고
    • Hydration changes accompanying the binding of minor groove ligands with DNA
    • Degtyareva, N. N.; Wallace, B. D.; Bryant, A. R.; Loo, K. M.; Petty, J. T. Hydration changes accompanying the binding of minor groove ligands with DNA. Biophys. J. 2007, 92 (3), 959-965.
    • (2007) Biophys. J , 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
  • 43
    • 0034846150 scopus 로고    scopus 로고
    • Molecular modelling of ligand-DNA minor groove binding: Role of ligand-water interactions
    • Mikheikin, A. L.; Zhuze, A. L.; Zasedatelev, A. S. Molecular modelling of ligand-DNA minor groove binding: role of ligand-water interactions, J. Biomol. Struct. Dyn. 2001, 79 (1), 175-178.
    • (2001) J. Biomol. Struct. Dyn , vol.79 , Issue.1 , pp. 175-178
    • Mikheikin, A.L.1    Zhuze, A.L.2    Zasedatelev, A.S.3
  • 44
    • 0026899820 scopus 로고    scopus 로고
    • Paner, T. M.; Amaratunga, M.; Benight. A. S. Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14). Biopolymers 1992, 32 (7), 881-892.
    • Paner, T. M.; Amaratunga, M.; Benight. A. S. Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14). Biopolymers 1992, 32 (7), 881-892.


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