메뉴 건너뛰기




Volumn 1800, Issue 6, 2010, Pages 599-610

Effect of the bases flanking an abasic site on the recognition of nucleobase by amiloride

Author keywords

Abasic site; Amiloride; Flanking bases; Molecular modeling; Nucleobase recognition; Single nucleotide polymorphism; TDDFT

Indexed keywords

3,5 DIAMINO 6 CHLORO N [1 [N [2 [2 HYDROXY 3 (1 NAPHTHOXY)PROPYLAMINO]ETHYL]CARBAMOYL] 1 METHYLETHYL]PYRAZINE 2 CARBOXAMIDE; AMILORIDE; NUCLEIC ACID BASE; PHOSPHATE; THYMINE;

EID: 77952241888     PISSN: 03044165     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbagen.2010.03.007     Document Type: Article
Times cited : (30)

References (55)
  • 3
    • 14544294087 scopus 로고    scopus 로고
    • Nucleobases as supramolecular motifs
    • Sivakova S., Rowan S.J. Nucleobases as supramolecular motifs. Chem. Soc. Rev. 2005, 34:9-21.
    • (2005) Chem. Soc. Rev. , vol.34 , pp. 9-21
    • Sivakova, S.1    Rowan, S.J.2
  • 4
    • 1542334686 scopus 로고    scopus 로고
    • Zinc-nucleic acid interaction
    • Aoki S., Kimura E. Zinc-nucleic acid interaction. Chem. Rev. 2004, 104:769-788.
    • (2004) Chem. Rev. , vol.104 , pp. 769-788
    • Aoki, S.1    Kimura, E.2
  • 5
    • 0036375907 scopus 로고    scopus 로고
    • Methods of modulating hydrogen bonded interactions in synthetic host-guest systems
    • Cooke G., Rotello V.M. Methods of modulating hydrogen bonded interactions in synthetic host-guest systems. Chem. Soc. Rev. 2002, 31:275-286.
    • (2002) Chem. Soc. Rev. , vol.31 , pp. 275-286
    • Cooke, G.1    Rotello, V.M.2
  • 6
    • 0001270557 scopus 로고
    • Molecular recognition: hydrogen bonding and aromatic stacking converge to bind cytosine derivatives
    • Jeong K.S., Rebek Jr J. Molecular recognition: hydrogen bonding and aromatic stacking converge to bind cytosine derivatives. J. Am. Chem. Soc. 1988, 110:3327-3328.
    • (1988) J. Am. Chem. Soc. , vol.110 , pp. 3327-3328
    • Jeong, K.S.1    Rebek Jr, J.2
  • 7
    • 0024600942 scopus 로고
    • Nucleotide base recognition: a macrocyclic receptor for adenine employing hydrogen bonding and aromatic stacking interactions
    • Goswami S., Engen D.V., Hamilton A.D. Nucleotide base recognition: a macrocyclic receptor for adenine employing hydrogen bonding and aromatic stacking interactions. J. Am. Chem. Soc. 1989, 111:3425-3426.
    • (1989) J. Am. Chem. Soc. , vol.111 , pp. 3425-3426
    • Goswami, S.1    Engen, D.V.2    Hamilton, A.D.3
  • 9
    • 0001128585 scopus 로고
    • Convergent functional groups. 13. High-affinity complexation of adenosine derivatives within induced binding pockets
    • Conn M.M., Deslongchamps G., de.Mendoza J., Jr.Rebek J. Convergent functional groups. 13. High-affinity complexation of adenosine derivatives within induced binding pockets. J. Am. Chem. Soc. 1993, 115:3548-3557.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 3548-3557
    • Conn, M.M.1    Deslongchamps, G.2    de.Mendoza, J.3    Jr.Rebek, J.4
  • 10
    • 0026090414 scopus 로고
    • Convergent functional groups XI. Selective binding of guanosine derivatives
    • Park T.K., Schroeder J., Rebek J. Convergent functional groups XI. Selective binding of guanosine derivatives. Tetrahedron 1991, 47:2507-2518.
    • (1991) Tetrahedron , vol.47 , pp. 2507-2518
    • Park, T.K.1    Schroeder, J.2    Rebek, J.3
  • 11
    • 0032575158 scopus 로고    scopus 로고
    • Thiouronium-thymine conjugate as a new carrier for selective transport of 5′-AMP
    • Yeo W.S., Hong J.I. Thiouronium-thymine conjugate as a new carrier for selective transport of 5′-AMP. Tetrahedron Lett. 1998, 39:3769-3772.
    • (1998) Tetrahedron Lett. , vol.39 , pp. 3769-3772
    • Yeo, W.S.1    Hong, J.I.2
  • 12
    • 0034716346 scopus 로고    scopus 로고
    • Coupling rational design with libraries leads to the production of an ATP selective chemosensor
    • Schneider S.E., O'Neil S.N., Anslyn E.V. Coupling rational design with libraries leads to the production of an ATP selective chemosensor. J. Am. Chem. Soc. 2000, 122:542-543.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 542-543
    • Schneider, S.E.1    O'Neil, S.N.2    Anslyn, E.V.3
  • 13
    • 0000974850 scopus 로고
    • Multiple molecular recognition and catalysis. A multifunctional anion receptor bearing an anion binding site, an intercalating group, and a catalytic site for nucleotide binding and hydrolysis
    • Hosseini M.W., Blacker A.J., Lehn J.M. Multiple molecular recognition and catalysis. A multifunctional anion receptor bearing an anion binding site, an intercalating group, and a catalytic site for nucleotide binding and hydrolysis. J. Am. Chem. Soc. 1990, 112:3896-3904.
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 3896-3904
    • Hosseini, M.W.1    Blacker, A.J.2    Lehn, J.M.3
  • 15
    • 0037130655 scopus 로고    scopus 로고
    • An artificial guanine that binds cytidine through the cooperative interaction of metal coordination and hydrogen bonding
    • Mancin F., Chin J. An artificial guanine that binds cytidine through the cooperative interaction of metal coordination and hydrogen bonding. J. Am. Chem. Soc. 2002, 124:10946-10947.
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 10946-10947
    • Mancin, F.1    Chin, J.2
  • 16
    • 13844311461 scopus 로고    scopus 로고
    • The recognition of nucleotides with model ß-Hairpin receptors: investigation of critical contacts and nucleotide selectivity
    • Butterfield S.M., Sweeney M.M., Waters M.L. The recognition of nucleotides with model ß-Hairpin receptors: investigation of critical contacts and nucleotide selectivity. J. Org. Chem. 2005, 70:1105-1114.
    • (2005) J. Org. Chem. , vol.70 , pp. 1105-1114
    • Butterfield, S.M.1    Sweeney, M.M.2    Waters, M.L.3
  • 17
    • 0035171181 scopus 로고    scopus 로고
    • Scanning of guanine-guanine mismatches in DNA by synthetic ligands using surface plasmon resonance
    • Nakatani K., Sando S., Saito I. Scanning of guanine-guanine mismatches in DNA by synthetic ligands using surface plasmon resonance. Nat. Biotechnol. 2001, 19:51-55.
    • (2001) Nat. Biotechnol. , vol.19 , pp. 51-55
    • Nakatani, K.1    Sando, S.2    Saito, I.3
  • 18
    • 0034654396 scopus 로고    scopus 로고
    • Recognition of a single guanine bulge by 2-acylamino-1, 8-naphthyridine
    • Nakatani K., Sando S., Saito I. Recognition of a single guanine bulge by 2-acylamino-1, 8-naphthyridine. J. Am. Chem. Soc. 2000, 122:2172-2177.
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 2172-2177
    • Nakatani, K.1    Sando, S.2    Saito, I.3
  • 19
    • 0042367663 scopus 로고    scopus 로고
    • Use of abasic site-containing DNA strands for nucleobase recognition in water
    • Yoshimoto K., Nishizawa S., Minagawa M., Teramae N. Use of abasic site-containing DNA strands for nucleobase recognition in water. J. Am. Chem. Soc. 2003, 125:8982-8983.
    • (2003) J. Am. Chem. Soc. , vol.125 , pp. 8982-8983
    • Yoshimoto, K.1    Nishizawa, S.2    Minagawa, M.3    Teramae, N.4
  • 20
    • 0347510983 scopus 로고    scopus 로고
    • Fluorescence detection of guanine-adenine transition by a hydrogen bond forming small compound
    • Yoshimoto K., Xu C.Y., Nishizawa S., Haga T., Satake H., Teramae N. Fluorescence detection of guanine-adenine transition by a hydrogen bond forming small compound. Chem. Commun. 2003, 24:2960-2961.
    • (2003) Chem. Commun. , vol.24 , pp. 2960-2961
    • Yoshimoto, K.1    Xu, C.Y.2    Nishizawa, S.3    Haga, T.4    Satake, H.5    Teramae, N.6
  • 21
    • 57649176767 scopus 로고    scopus 로고
    • Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: a case study with isoxanthopterin and its derivatives
    • Rajendar B., Rajendran A., Sato Y., Nishizawa S., Teramae N. Effect of methyl substitution in a ligand on the selectivity and binding affinity for a nucleobase: a case study with isoxanthopterin and its derivatives. Bioorg. Med. Chem. 2009, 17:351-359.
    • (2009) Bioorg. Med. Chem. , vol.17 , pp. 351-359
    • Rajendar, B.1    Rajendran, A.2    Sato, Y.3    Nishizawa, S.4    Teramae, N.5
  • 22
    • 49749085185 scopus 로고    scopus 로고
    • A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes
    • Zhao C., Rajendran A., Dai Q., Nishizawa S., Teramae N. A pyrazine-based fluorescence-enhancing ligand with a high selectivity for thymine in AP site-containing DNA duplexes. Anal. Sci. 2008, 24:693-695.
    • (2008) Anal. Sci. , vol.24 , pp. 693-695
    • Zhao, C.1    Rajendran, A.2    Dai, Q.3    Nishizawa, S.4    Teramae, N.5
  • 23
    • 0011164114 scopus 로고    scopus 로고
    • Noncovalent interactions: a challenge for experiment and theory
    • Muller-Dethlefs K., Hobza P. Noncovalent interactions: a challenge for experiment and theory. Chem. Rev. 2000, 100:143-168.
    • (2000) Chem. Rev. , vol.100 , pp. 143-168
    • Muller-Dethlefs, K.1    Hobza, P.2
  • 24
    • 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, 13:284-299.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 284-299
    • Dervan, P.B.1    Edelson, B.S.2
  • 25
    • 0000965687 scopus 로고    scopus 로고
    • Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations
    • Hobza P., Sponer J. Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Chem. Rev. 1999, 99:3247-3276.
    • (1999) Chem. Rev. , vol.99 , pp. 3247-3276
    • Hobza, P.1    Sponer, J.2
  • 26
    • 33644777816 scopus 로고    scopus 로고
    • Strong and selective binding of amiloride to thymine base opposite AP sites in DNA duplexes: simultaneous binding to DNA phosphate backbone
    • Zhao C., Dai Q., Seino T., Cui Y.Y., Nishizawa S., Teramae N. Strong and selective binding of amiloride to thymine base opposite AP sites in DNA duplexes: simultaneous binding to DNA phosphate backbone. Chem. Commun. 2006, 11:1185-1187.
    • (2006) Chem. Commun. , vol.11 , pp. 1185-1187
    • Zhao, C.1    Dai, Q.2    Seino, T.3    Cui, Y.Y.4    Nishizawa, S.5    Teramae, N.6
  • 27
    • 34247368602 scopus 로고    scopus 로고
    • Applications of isothermal titration calorimetry in protein folding and molecular recognition
    • Liang Y. Applications of isothermal titration calorimetry in protein folding and molecular recognition. J. Iranian Chem. Soc. 2006, 3:209-219.
    • (2006) J. Iranian Chem. Soc. , vol.3 , pp. 209-219
    • Liang, Y.1
  • 28
    • 17144419278 scopus 로고    scopus 로고
    • Thermodynamics of the interaction of aluminum ions with DNA: implications for the biological function of aluminum
    • Wu J., Du F., Zhang P., Khan I.A., Chen J., Liang Y. Thermodynamics of the interaction of aluminum ions with DNA: implications for the biological function of aluminum. J. Inorg. Biochem. 2005, 99:1145-1154.
    • (2005) J. Inorg. Biochem. , vol.99 , pp. 1145-1154
    • Wu, J.1    Du, F.2    Zhang, P.3    Khan, I.A.4    Chen, J.5    Liang, Y.6
  • 29
    • 58149195262 scopus 로고    scopus 로고
    • Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity
    • Rajendran A., Thiagarajan V., Rajendar B., Nishizawa S., Teramae N. Simultaneous recognition of nucleobase and sites of DNA damage: effect of tethered cation on the binding affinity. Biochim. Biophys. Acta 2009, 1790:95-100.
    • (2009) Biochim. Biophys. Acta , vol.1790 , pp. 95-100
    • Rajendran, A.1    Thiagarajan, V.2    Rajendar, B.3    Nishizawa, S.4    Teramae, N.5
  • 30
    • 0024804759 scopus 로고
    • Absorbance melting curves of RNA
    • Puglisi J.D., Jr Tinoco I. Absorbance melting curves of RNA. Methods Enzymol. 1989, 180:304-325.
    • (1989) Methods Enzymol. , vol.180 , pp. 304-325
    • Puglisi, J.D.1    Jr Tinoco, I.2
  • 31
    • 0024356301 scopus 로고
    • Rapid measurement of binding constants and heats of binding using a new titration calorimeter
    • Wiseman T., Williston S., Brandts J.F., Lin L.N. Rapid measurement of binding constants and heats of binding using a new titration calorimeter. Anal. Biochem. 1989, 179:131-137.
    • (1989) Anal. Biochem. , vol.179 , pp. 131-137
    • Wiseman, T.1    Williston, S.2    Brandts, J.F.3    Lin, L.N.4
  • 33
    • 77952243770 scopus 로고    scopus 로고
    • MacroModel 9.0, Schrödinger, Inc., L. L. C., () New York, NY, USA
    • MacroModel 9.0, Schrödinger, Inc., L. L. C., () New York, NY, USA, 2005. http://www.schrodinger.com.
    • (2005)
  • 35
    • 33750631697 scopus 로고    scopus 로고
    • Unprecedented dual binding behaviour of acridine group of dye: a combined experimental and theoretical investigation for the development of anticancer chemotherapeutic agents
    • Rajendran A., Nair B.U. Unprecedented dual binding behaviour of acridine group of dye: a combined experimental and theoretical investigation for the development of anticancer chemotherapeutic agents. Biochim. Biophys. Acta 2006, 1760:1794-1801.
    • (2006) Biochim. Biophys. Acta , vol.1760 , pp. 1794-1801
    • Rajendran, A.1    Nair, B.U.2
  • 37
    • 0035793105 scopus 로고    scopus 로고
    • 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking
    • Jean J.M., Hall K.B. 2-Aminopurine fluorescence quenching and lifetimes: role of base stacking. Proc. Natl. Acad. Sci. USA 2001, 98:37-41.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 37-41
    • Jean, J.M.1    Hall, K.B.2
  • 38
    • 0037027319 scopus 로고    scopus 로고
    • 2-Aminopurine electronic structure and fluorescence properties in DNA
    • Jean J.M., Hall K.B. 2-Aminopurine electronic structure and fluorescence properties in DNA. Biochemistry 2002, 41:13152-13161.
    • (2002) Biochemistry , vol.41 , pp. 13152-13161
    • Jean, J.M.1    Hall, K.B.2
  • 39
    • 84961985847 scopus 로고    scopus 로고
    • Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model
    • Barone V., Cossi M. Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J. Phys. Chem. A 1998, 102:1995-2001.
    • (1998) J. Phys. Chem. A , vol.102 , pp. 1995-2001
    • Barone, V.1    Cossi, M.2
  • 40
    • 0033963034 scopus 로고    scopus 로고
    • Molden: a pre- and post-processing program for molecular and electronic structures
    • Schaftenaar G., Noordik J.H. Molden: a pre- and post-processing program for molecular and electronic structures. J. Comput.-Aided Mol. Des. 2000, 14:123-134.
    • (2000) J. Comput.-Aided Mol. Des. , vol.14 , pp. 123-134
    • Schaftenaar, G.1    Noordik, J.H.2
  • 41
    • 0025156960 scopus 로고
    • Temperature dependence of enthalpy changes for ehtidium and propidium binding to DNA: effect of alkylamine chains
    • Jr H.P., Hopkins J.Fumero, Wilson W.D. Temperature dependence of enthalpy changes for ehtidium and propidium binding to DNA: effect of alkylamine chains. Biopolymers 1990, 29:449-459.
    • (1990) Biopolymers , vol.29 , pp. 449-459
    • Jr, H.P.1    Hopkins, J.F.2    Wilson, W.D.3
  • 42
    • 0033552270 scopus 로고    scopus 로고
    • Fluorescence sensing of anions via intramolecular excimer formation in a pyrophosphate-induced self-assembly of a pyrene-functionalized guanidinium receptor
    • Nishizawa S., Kato Y., Teramae N. Fluorescence sensing of anions via intramolecular excimer formation in a pyrophosphate-induced self-assembly of a pyrene-functionalized guanidinium receptor. J. Am. Chem. Soc. 1999, 121:9463-9464.
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 9463-9464
    • Nishizawa, S.1    Kato, Y.2    Teramae, N.3
  • 43
    • 2442687873 scopus 로고    scopus 로고
    • Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-Π interactions
    • Biot C., Wintjens R., Rooman M. Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-Π interactions. J. Am. Chem. Soc. 2004, 126:6220-6221.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 6220-6221
    • Biot, C.1    Wintjens, R.2    Rooman, M.3
  • 44
    • 0028904989 scopus 로고
    • Origins of the large differences in stability of DNA and RNA helixes: C-5 methyl and 2′-hydroxyl effects
    • Wang S., Kool E.T. Origins of the large differences in stability of DNA and RNA helixes: C-5 methyl and 2′-hydroxyl effects. Biochemistry 1995, 34:4125-4132.
    • (1995) Biochemistry , vol.34 , pp. 4125-4132
    • Wang, S.1    Kool, E.T.2
  • 47
    • 0018791736 scopus 로고
    • A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein
    • Klug A., Jack A., Viswamitra M.A., Kennard O., Shakked Z., Steitz T.A. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J. Mol. Biol. 1979, 131:669-680.
    • (1979) J. Mol. Biol. , vol.131 , pp. 669-680
    • Klug, A.1    Jack, A.2    Viswamitra, M.A.3    Kennard, O.4    Shakked, Z.5    Steitz, T.A.6
  • 50
    • 0041887202 scopus 로고    scopus 로고
    • Basis set and electron correlation effects on ab initio calculations of cation-π/H-bond stair motifs
    • Wintjens R., Biot C., Rooman M., Lievin J. Basis set and electron correlation effects on ab initio calculations of cation-π/H-bond stair motifs. J. Phys. Chem. A 2003, 107:6249-6258.
    • (2003) J. Phys. Chem. A , vol.107 , pp. 6249-6258
    • Wintjens, R.1    Biot, C.2    Rooman, M.3    Lievin, J.4
  • 51
    • 0036308878 scopus 로고    scopus 로고
    • Cation-π/H-bond stair motifs at protein-DNA interfaces
    • Rooman M., Lievin J., Buisine E., Wintjens R. Cation-π/H-bond stair motifs at protein-DNA interfaces. J. Mol. Biol. 2002, 319:67-76.
    • (2002) J. Mol. Biol. , vol.319 , pp. 67-76
    • Rooman, M.1    Lievin, J.2    Buisine, E.3    Wintjens, R.4
  • 52
    • 0001684847 scopus 로고    scopus 로고
    • A density functional study of the optical spectra and nonlinear optical properties of heteroleptic tetrapyrrole sandwich complexes: the porphyrinato-porphyrazinato-zirconium(IV) complex as a case study
    • Ricciardi G., Rosa A., van Gisbergen S.J.A., Baerends E.J. A density functional study of the optical spectra and nonlinear optical properties of heteroleptic tetrapyrrole sandwich complexes: the porphyrinato-porphyrazinato-zirconium(IV) complex as a case study. J. Phys. Chem. A 2000, 104:635-643.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 635-643
    • Ricciardi, G.1    Rosa, A.2    van Gisbergen, S.J.A.3    Baerends, E.J.4
  • 53
    • 33746601044 scopus 로고    scopus 로고
    • Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids
    • Hardman S.J.O., Thompson K.C. Influence of base stacking and hydrogen bonding on the fluorescence of 2-aminopurine and pyrrolocytosine in nucleic acids. Biochemistry 2006, 45:9145-9155.
    • (2006) Biochemistry , vol.45 , pp. 9145-9155
    • Hardman, S.J.O.1    Thompson, K.C.2
  • 54
    • 33748595282 scopus 로고    scopus 로고
    • Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies
    • Seidel C.A.M., Schulz A., Sauer M.H.M. Nucleobase-specific quenching of fluorescent dyes. 1. Nucleobase one-electron redox potentials and their correlation with static and dynamic quenching efficiencies. J. Phys. Chem. 1996, 100:5541-5553.
    • (1996) J. Phys. Chem. , vol.100 , pp. 5541-5553
    • Seidel, C.A.M.1    Schulz, A.2    Sauer, M.H.M.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.