메뉴 건너뛰기




Volumn 39, Issue 10, 2011, Pages 4265-4274

Induced topological changes in DNA complexes: Influence of DNA sequences and small molecule structures

Author keywords

[No Author keywords available]

Indexed keywords

DIAMIDINE DERIVATIVE; HETEROCYCLIC DIAMIDINE; UNCLASSIFIED DRUG; AMIDINE; ANTIPARASITIC AGENT; DNA; HETEROCYCLIC COMPOUND;

EID: 79959898511     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkq1362     Document Type: Article
Times cited : (24)

References (42)
  • 5
    • 45549100438 scopus 로고    scopus 로고
    • Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication
    • DOI 10.1093/nar/gkn208
    • Peixoto, P., Liu, Y., Depauw, S., Hildebrand, M.P., Boykin, D.W., Bailly, C., Wilson, W.D. and David-Cordonnier, M.H. (2008) Direct inhibition of the DNA-binding activity of POU transcription factors Pit-1 and Brn-3 by selective binding of a phenyl-furan-benzimidazole dication. Nucleic Acids Res., 36, 3341-3353. (Pubitemid 351859003)
    • (2008) Nucleic Acids Research , vol.36 , Issue.10 , pp. 3341-3353
    • Peixoto, P.1    Liu, Y.2    Depauw, S.3    Hildebrand, M.-P.4    Boykin, D.W.5    Bailly, C.6    Wilson, W.D.7    David-Cordonnier, M.-H.8
  • 6
    • 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
  • 7
    • 22044434857 scopus 로고    scopus 로고
    • Fellowship of the rings: The replication of kinetoplast DNA
    • DOI 10.1016/j.pt.2005.06.008, PII S1471492205001698
    • Liu, B., Liu, Y., Motyka, S.A., Agbo, E.C. and Englund, P.T. (2005) Fellowship of the rings: the replication of kinetoplast DNA. Trends Parasitol., 21, 363-369. (Pubitemid 40968137)
    • (2005) Trends in Parasitology , vol.21 , Issue.8 , pp. 363-369
    • Liu, B.1    Liu, Y.2    Motyka, S.A.3    Agbo, E.E.C.4    Englund, P.T.5
  • 9
    • 0021136538 scopus 로고
    • Physical characterization of a kinetoplast DNA fragment with unusual properties
    • Marini, J.C., Effron, P.N., Goodman, T.C., Singleton, C.K., Wells, R.D., Wartell, R.M. and Englund, P.T. (1984) Physical characterization of a kinetoplast DNA fragment with unusual properties. J. Biol. Chem., 259, 8974-8979. (Pubitemid 14098872)
    • (1984) Journal of Biological Chemistry , vol.259 , Issue.14 , pp. 8974-8979
    • Marini, J.C.1    Effron, P.N.2    Goodman, T.C.3
  • 11
    • 69449087887 scopus 로고    scopus 로고
    • Allosteric modulation of DNA by small molecules
    • Chenoweth, D.M. and Dervan, P.B. (2009) Allosteric modulation of DNA by small molecules. Proc. Natl Acad. Sci. USA, 106, 13175-13179.
    • (2009) Proc. Natl Acad. Sci. USA , vol.106 , pp. 13175-13179
    • Chenoweth, D.M.1    Dervan, P.B.2
  • 13
    • 0026809001 scopus 로고
    • Analyzing DNA curvature in polyacrylamide gels
    • Diekmann, S. (1992) Analyzing DNA curvature in polyacrylamide gels. Methods Enzymol., 212, 30-46.
    • (1992) Methods Enzymol , vol.212 , pp. 30-46
    • Diekmann, S.1
  • 14
    • 0026787523 scopus 로고
    • Global features of DNA structure by comparative gel electrophoresis
    • Crothers, D.M. and Drak, J. (1992) Global features of DNA structure by comparative gel electrophoresis. Methods Enzymol., 212, 46-71.
    • (1992) Methods Enzymol , vol.212 , pp. 46-71
    • Crothers, D.M.1    Drak, J.2
  • 15
    • 0033231411 scopus 로고    scopus 로고
    • Improved quantitation of DNA curvature using ligation ladders
    • DOI 10.1093/nar/27.21.4135
    • Ross, E.D., Den, R.B., Hardwidge, P.R. and Maher, L.J. III. (1999) Improved quantitation of DNA curvature using ligation ladders. Nucleic Acids Res., 27, 4135-4142. (Pubitemid 29500245)
    • (1999) Nucleic Acids Research , vol.27 , Issue.21 , pp. 4135-4142
    • Ross, E.D.1    Den, R.B.2    Hardwidge, P.R.3    Maher III, L.J.4
  • 16
    • 0942279698 scopus 로고    scopus 로고
    • Direct Comparison of A- and T-Strand Minor Groove Interactions in DNA Curvature at A Tracts
    • Maki, A.S., Kim, T. and Kool, E.T. (2004) Direct comparison of A-and T-strand minor groove interactions in DNA curvature at A tracts. Biochemistry, 43, 1102-1110. (Pubitemid 38141510)
    • (2004) Biochemistry , vol.43 , Issue.4 , pp. 1102-1110
    • Maki, A.S.1    Kim, T.2    Kool, E.T.3
  • 17
    • 0033566150 scopus 로고    scopus 로고
    • Ecteinascidin 743: A minor groove alkylator that bends DNA toward the major groove
    • DOI 10.1021/jm990241l
    • Zewail-Foote, M. and Hurley, L.H. (1999) Ecteinascidin 743: a minor groove alkylator that bends DNA toward the major groove. J. Med. Chem., 42, 2493-2497. (Pubitemid 29344290)
    • (1999) Journal of Medicinal Chemistry , vol.42 , Issue.14 , pp. 2493-2497
    • Zewail-Foote, M.1    Hurley, L.H.2
  • 18
    • 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
  • 19
    • 0025002703 scopus 로고
    • Effects of sequence selective drugs on the gel mobility of a bent DNA fragment
    • Cons, B.M. and Fox, K.R. (1990) Effects of sequence selective drugs on the gel mobility of a bent DNA fragment. Biochem. Biophys. Res. Commun., 171, 1064-1070. (Pubitemid 20318058)
    • (1990) Biochemical and Biophysical Research Communications , vol.171 , Issue.3 , pp. 1064-1070
    • Cons, B.M.G.1    Fox, K.R.2
  • 20
    • 3242715653 scopus 로고    scopus 로고
    • Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding
    • DOI 10.1021/ja0492891
    • Persil, O., Santani, C.T., Jain, S.S. and Hud, N.V. (2004) Assembly of an antiparallel homo-adenine DNA duplex by small-molecule binding. J. Am. Chem. Soc., 126, 8644-8645. (Pubitemid 38955716)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.28 , pp. 8644-8645
    • Persil, O.1    Santai, C.T.2    Jain, S.S.3    Hud, N.V.4
  • 21
    • 0017576850 scopus 로고
    • Synthesis and antiprotozoal activity of 2 5-bis(4-guanylphenyl)furans
    • Das, B.P. and Boykin, D.W. (1977) Synthesis and antiprotozoal activity of 2, 5-bis(4-guanylphenyl)furans. J. Med. Chem., 20, 531-536.
    • (1977) J. Med. Chem , vol.20 , pp. 531-536
    • Das, B.P.1    Boykin, D.W.2
  • 23
    • 34247880252 scopus 로고    scopus 로고
    • Induced fit conformational changes of a "reversed amidine" heterocycle: Optimized interactions in a DNA minor groove complex
    • DOI 10.1021/ja069003n
    • Munde, M., Lee, M., Neidle, S., Arafa, R., Boykin, D.W., Liu, Y., Bailly, C. and Wilson, W.D. (2006) Induced fit conformational changes of a "reversed amidine" heterocycle: optimized interactions in a DNA minor groove complex. J. Am. Chem. Soc., 129, 5688-5698. (Pubitemid 46697659)
    • (2007) Journal of the American Chemical Society , vol.129 , Issue.17 , pp. 5688-5698
    • Munde, M.1    Lee, M.2    Neidle, S.3    Arafa, R.4    Boykin, D.W.5    Liu, Y.6    Bailly, C.7    Wilson, W.D.8
  • 25
    • 27644499431 scopus 로고    scopus 로고
    • Dicationic near-linear biphenyl benzimidazole derivatives as DNA-targeted antiprotozoal agents
    • DOI 10.1016/j.bmc.2005.07.024, PII S0968089605006863
    • Ismail, M.A., Batista-Parra, A., Miao, Y., Wilson, W.D., Wenzler, T., Brun, R. and Boykin, D.W. (2005) Dicationic near-linear biphenyl benzimidazole derivatives as DNA-targeted antiprotozoal agents. Bioorg. Med. Chem., 13, 6718-6726. (Pubitemid 41571216)
    • (2005) Bioorganic and Medicinal Chemistry , vol.13 , Issue.24 , pp. 6718-6726
    • Ismail, M.A.1    Batista-Parra, A.2    Miao, Y.3    Wilson, W.D.4    Wenzler, T.5    Brun, R.6    Boykin, D.W.7
  • 26
    • 0001291624 scopus 로고    scopus 로고
    • Synthesis of mono-cationic and dicationic analogs of Hoechst 33258
    • Czarny, A., Wilson, W.D. and Boykin, D.W. (1996) Synthesis of mono-cationic and dicationic analogs of Hoechst 33258. J. Hetero. Chem., 33, 1393-1397. (Pubitemid 126476859)
    • (1996) Journal of Heterocyclic Chemistry , vol.33 , Issue.4 , pp. 1393-1397
    • Czarny, A.1    Wilson, W.D.2    Boykin, D.W.3
  • 27
    • 0035875348 scopus 로고    scopus 로고
    • Experimental evaluation of the Liu-Beveridge dinucleotide step model of DNA structure
    • Hardwidge, P.R. and Maher, L.J. III. (2001) Experimental evaluation of the Liu-Beveridge model of DNA structure. Nucleic Acids Res., 29, 2619-2625. (Pubitemid 32600319)
    • (2001) Nucleic Acids Research , vol.29 , Issue.12 , pp. 2619-2625
    • Hardwidge, P.R.1    Maher, L.J.2
  • 28
    • 0033730618 scopus 로고    scopus 로고
    • Relating independent measures of DNA curvature: Electrophoretic anomaly and cyclization efficiency
    • Hardwidge, P.R., Den, R.B., Ross, E.D. and Maher, L.J. III. (2000) Relating independent measures of DNA curvature: electrophoretic anomaly and cyclization efficiency. J. Biomol. Struct. Dyn., 18, 219-230.
    • (2000) J. Biomol. Struct. Dyn , vol.18 , pp. 219-230
    • Hardwidge, P.R.1    Den, R.B.2    Ross, E.D.3    Maher Iii, L.J.4
  • 29
    • 34247533690 scopus 로고    scopus 로고
    • Biosensor-surface plasmon resonance: Quantitative analysis of small molecule-nucleic acid interactions
    • DOI 10.1016/j.ymeth.2006.09.009, PII S1046202306002453, Methods Related to DNA Sequence Recognition
    • Nguyen, B., Tanious, F.A. and Wilson, W.D. (2007) Biosensor-surface plasmon resonance: quantitative analysis of small molecule-nucleic acid interactions. Methods, 42, 150-161. (Pubitemid 46654814)
    • (2007) Methods , vol.42 , Issue.2 , pp. 150-161
    • Nguyen, B.1    Tanious, F.A.2    Wilson, W.D.3
  • 30
    • 77449098489 scopus 로고    scopus 로고
    • Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection
    • Liu, Y. and Wilson, W.D. (2010) Quantitative analysis of small molecule-nucleic acid interactions with a biosensor surface and surface plasmon resonance detection. Methods Mol. Biol., 613, 1-23.
    • (2010) Methods Mol. Biol. , vol.613 , pp. 1-23
    • Liu, Y.1    Wilson, W.D.2
  • 31
    • 27744550401 scopus 로고    scopus 로고
    • Out-of-shape DNA minor groove binders: Induced fit interactions of heterocyclic dications with the DNA minor groove
    • DOI 10.1021/bi051791q
    • Miao, Y., Lee, M.P., Parkinson, G.N., Batista-Parra, A., Ismail, M.A., Neidle, S., Boykin, D.W. and Wilson, W.D. (2005) Out-of-shape DNA minor groove binders: induced fit interactions of heterocyclic dications with the DNA minor groove. Biochemistry, 44, 14701-14708. (Pubitemid 41612249)
    • (2005) Biochemistry , vol.44 , Issue.45 , pp. 14701-14708
    • Miao, Y.1    Lee, M.P.H.2    Parkinson, G.N.3    Batista-Parra, A.4    Ismail, M.A.5    Neidle, S.6    Boykin, D.W.7    Wilson, W.D.8
  • 34
    • 70350413422 scopus 로고    scopus 로고
    • The effects of hairpin loops on ligand-DNA interactions
    • Nguyen, B. and Wilson, W.D. (2009) The effects of hairpin loops on ligand-DNA interactions. J. Phys. Chem. B, 113, 14329-14335.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 14329-14335
    • Nguyen, B.1    Wilson, W.D.2
  • 35
    • 0035367927 scopus 로고    scopus 로고
    • DNA-cation interactions: The major and minor grooves are flexible ionophores
    • DOI 10.1016/S0959-440X(00)00205-0
    • Hud, N.V. and Polak, M. (2001) DNA-cation interactions: the major and minor grooves are flexible ionophores. Curr. Opin. Struct. Biol., 11, 293-301. (Pubitemid 32568268)
    • (2001) Current Opinion in Structural Biology , vol.11 , Issue.3 , pp. 293-301
    • Hud, N.V.1    Polak, M.2
  • 36
    • 0034802485 scopus 로고    scopus 로고
    • Influence of the dynamic positions of cations on the structure of the DNA minor groove: Sequence-dependent effects
    • DOI 10.1021/ja010341s
    • Hamelberg, D., Williams, L.D. and Wilson, W.D. (2001) Influence of the dynamic positions of cations on the structure of the DNA minor groove: sequence-dependent effects. J. Am. Chem. Soc., 123, 7745-7755. (Pubitemid 32899339)
    • (2001) Journal of the American Chemical Society , vol.123 , Issue.32 , pp. 7745-7755
    • Hamelberg, D.1    Williams, L.D.2    Wilson, W.D.3
  • 37
    • 0027073131 scopus 로고
    • Probing the conformations of eight cloned DNA dodecamers
    • Fox, K.R. (1992) Probing the conformations of eight cloned DNA dodecamers. Nucleic Acids Res., 20, 6487-6493.
    • (1992) Nucleic Acids Res , vol.20 , pp. 6487-6493
    • Fox, K.R.1
  • 38
    • 0029059536 scopus 로고
    • DNA sequence preferences of several AT-selective minor groove binding ligands
    • Abu-Daya, A., Brown, P.M. and Fox, K.R. (1995) DNA sequence preferences of several AT-selective minor groove binding ligands. Nucleic Acids Res., 23, 3385-3392.
    • (1995) Nucleic Acids Res , vol.23 , pp. 3385-3392
    • Abu-Daya, A.1    Brown, P.M.2    Fox, K.R.3
  • 39
    • 0023666166 scopus 로고
    • The unusual conformation adopted by the adenine tracts in kinetoplast DNA
    • Burkhoff, A.M. and Tullius, T.D. (1987) The unusual conformation adopted by the adenine tracts in kinetoplast DNA. Cell, 48, 935-943.
    • (1987) Cell , vol.48 , pp. 935-943
    • Burkhoff, A.M.1    Tullius, T.D.2
  • 40
    • 0037031296 scopus 로고    scopus 로고
    • 1H NMR spectroscopy and manganese(II)
    • DOI 10.1021/bi020159j
    • Hud, N.V. and Feigon, J. (2002) Characterization of divalent cation localization in the minor groove of the A(n)T(n) and T(n)A(n) DNA sequence elements by (1)H NMR spectroscopy and manganese(II). Biochemistry, 41, 9900-9910. (Pubitemid 34839737)
    • (2002) Biochemistry , vol.41 , Issue.31 , pp. 9900-9910
    • Hud, N.V.1    Feigon, J.2
  • 41
    • 0842299592 scopus 로고    scopus 로고
    • DNA A-tract bending in three dimensions: Solving the dA4T4 vs. dT4A4 conundrum
    • Stefl, R., Wu, H., Ravindranathan, S., Sklenar, V. and Feigon, J. (2004) DNA A-tract bending in three dimensions: solving the dA4T4 vs. dT4A4 conundrum. Proc. Natl Acad. Sci. USA, 101, 1177-1182.
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 1177-1182
    • Stefl, R.1    Wu, H.2    Ravindranathan, S.3    Sklenar, V.4    Feigon, J.5
  • 42
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs, R., West, S.M., Sosinsky, A., Liu, P., Mann, R.S. and Honig, B. (2009) The role of DNA shape in protein-DNA recognition. Nature, 461, 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.M.2    Sosinsky, A.3    Liu, P.4    Mann, R.S.5    Honig, B.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.