메뉴 건너뛰기




Volumn 40, Issue 8, 2012, Pages 3732-3740

Structural changes of an abasic site in duplex DNA affect noncovalent binding of the spin label Ç

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; TETRAHYDROFURAN DERIVATIVE;

EID: 84860363149     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr1210     Document Type: Article
Times cited : (20)

References (47)
  • 1
    • 0000962446 scopus 로고
    • Spin-magnetic resonance in paramagnetics
    • Zavoisky, E.K. (1945) Spin-magnetic resonance in paramagnetics. J. Phys. USSR, 9, 211-245.
    • (1945) J. Phys. USSR , vol.9 , pp. 211-245
    • Zavoisky, E.K.1
  • 2
    • 84909509457 scopus 로고
    • Interaction of the radical ion of chlorpromazine with deoxyribonucleic acid
    • Ohnishi, S.I. and McConnell, H.M. (1965) Interaction of the radical ion of chlorpromazine with deoxyribonucleic acid. J. Am. Chem. Soc., 87, 2293.
    • (1965) J. Am. Chem. Soc. , vol.87 , pp. 2293
    • Ohnishi, S.I.1    McConnell, H.M.2
  • 3
    • 0034743154 scopus 로고    scopus 로고
    • Pulsed EPR spectroscopy: Biological applications
    • Prisner, T., Rohrer, M. and MacMillan, F. (2001) Pulsed EPR spectroscopy: biological applications. Annu. Rev. Phys. Chem., 52, 279-313.
    • (2001) Annu. Rev. Phys. Chem. , vol.52 , pp. 279-313
    • Prisner, T.1    Rohrer, M.2    MacMillan, F.3
  • 5
    • 34548317408 scopus 로고    scopus 로고
    • Long-range distance determinations in biomacromolecules by EPR spectroscopy
    • Schiemann, O. and Prisner, T.F. (2007) Long-range distance determinations in biomacromolecules by EPR spectroscopy. Q. Rev. Biophys., 40, 1-53.
    • (2007) Q. Rev. Biophys. , vol.40 , pp. 1-53
    • Schiemann, O.1    Prisner, T.F.2
  • 8
    • 70349847622 scopus 로고    scopus 로고
    • Techniques for EPR spectroscopy of pulsed electron double resonance (PELDOR): A review
    • Tsvetkov, Y.D. and Grishin, Y.A. (2009) Techniques for EPR spectroscopy of pulsed electron double resonance (PELDOR): a review. Instrum. Exp. Tech., 52, 615-636.
    • (2009) Instrum. Exp. Tech. , vol.52 , pp. 615-636
    • Tsvetkov, Y.D.1    Grishin, Y.A.2
  • 9
    • 79551492492 scopus 로고    scopus 로고
    • Studying bimolecular complexes with pulsed electron-electron double resonance spectroscopy
    • Schiemann, O. and Reginsson, G.W. (2011) Studying bimolecular complexes with pulsed electron-electron double resonance spectroscopy. Biochem. Soc. Trans., 39, 128-139.
    • (2011) Biochem. Soc. Trans. , vol.39 , pp. 128-139
    • Schiemann, O.1    Reginsson, G.W.2
  • 13
    • 79951848597 scopus 로고    scopus 로고
    • Nitroxides and nucleic acids: Chemistry and electron paramagnetic resonance (EPR) spectroscopy
    • Sigurdsson, S.T. (2011) Nitroxides and nucleic acids: chemistry and electron paramagnetic resonance (EPR) spectroscopy. Pure. Appl. Chem., 83, 677-686.
    • (2011) Pure. Appl. Chem. , vol.83 , pp. 677-686
    • Sigurdsson, S.T.1
  • 14
    • 84859586717 scopus 로고    scopus 로고
    • Site-directed spin labeling of nucleic acids
    • Shelke, S.A. and Sigurdsson, S.T. (2012) Site-directed spin labeling of nucleic acids. Eur. J. Org. Chem., 2012, 2291-2301.
    • (2012) Eur. J. Org. Chem. , vol.2012 , pp. 2291-2301
    • Shelke, S.A.1    Sigurdsson, S.T.2
  • 15
    • 84973622043 scopus 로고    scopus 로고
    • Site-directed nitroxide spin labeling of biopolymers
    • Springer-Berlin Heidelberg, (in press) doi:10.1007/430-2011-62
    • Shelke, S.A. and Sigurdsson, S.T. (2011) Site-directed nitroxide spin labeling of biopolymers. In: Struct. Bond., Springer-Berlin Heidelberg, (in press) doi:10.1007/430-2011-62.
    • (2011) Struct. Bond.
    • Shelke, S.A.1    Sigurdsson, S.T.2
  • 18
    • 54549092772 scopus 로고    scopus 로고
    • Rigid spin-labeled nucleoside C: A nonperturbing EPR probe of nucleic acid conformation
    • Cekan, P., Smith, A.L., Barhate, N., Robinson, B.H. and Sigurdsson, S.T. (2008) Rigid spin-labeled nucleoside C: a nonperturbing EPR probe of nucleic acid conformation. Nucleic Acids Res., 36, 5946-5954.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 5946-5954
    • Cekan, P.1    Smith, A.L.2    Barhate, N.3    Robinson, B.H.4    Sigurdsson, S.T.5
  • 19
    • 0017231707 scopus 로고
    • Electron-spin resonance spin-label studies of intercalation of ethidium-bromide and aromatic amine carcinogens in DNA
    • Hong, S.J. and Piette, L.H. (1976) Electron-spin resonance spin-label studies of intercalation of ethidium-bromide and aromatic amine carcinogens in DNA. Cancer Res., 36, 1159-1171.
    • (1976) Cancer Res. , vol.36 , pp. 1159-1171
    • Hong, S.J.1    Piette, L.H.2
  • 20
    • 0020492988 scopus 로고
    • Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes
    • Hurley, I., Osei-Gyimah, P., Archer, S., Scholes, C.P. and Lerman, L.S. (1982) Torsional motion and elasticity of the deoxyribonucleic acid double helix and its nucleosomal complexes. Biochemistry, 21, 4999-4509.
    • (1982) Biochemistry , vol.21 , pp. 4999-4509
    • Hurley, I.1    Osei-Gyimah, P.2    Archer, S.3    Scholes, C.P.4    Lerman, L.S.5
  • 21
    • 0016729068 scopus 로고
    • Acridine spin labels as probes for nucleic-acids
    • Sinha, B.K. and Chignell, C.F. (1975) Acridine spin labels as probes for nucleic-acids. Life Sci., 17, 1829-1836.
    • (1975) Life Sci. , vol.17 , pp. 1829-1836
    • Sinha, B.K.1    Chignell, C.F.2
  • 22
    • 0017810216 scopus 로고
    • Electron-spin resonance spin label studies of intercalation of nitrobenzene in DNA
    • Hong, S.J. and Piette, L.H. (1978) Electron-spin resonance spin label studies of intercalation of nitrobenzene in DNA. Arch. Biochem. Biophys., 185, 307-315.
    • (1978) Arch. Biochem. Biophys. , vol.185 , pp. 307-315
    • Hong, S.J.1    Piette, L.H.2
  • 23
    • 0032539782 scopus 로고    scopus 로고
    • Introduction of a nitroxide group on position 2 of 9-phenoxyacridine: Easy access to spin labelled DNA-binding conjugates
    • Belmont, P., Chapelle, C., Demeunynck, M., Michon, J., Michon, P. and Lhomme, J. (1998) Introduction of a nitroxide group on position 2 of 9-phenoxyacridine: easy access to spin labelled DNA-binding conjugates. Bioorg. Med. Chem. Lett., 8, 669-674.
    • (1998) Bioorg. Med. Chem. Lett. , vol.8 , pp. 669-674
    • Belmont, P.1    Chapelle, C.2    Demeunynck, M.3    Michon, J.4    Michon, P.5    Lhomme, J.6
  • 24
    • 0033044713 scopus 로고    scopus 로고
    • Interaction of a spin-labeled adenine-acridine conjugate with a DNA duplex containing an abasic site model
    • Thomas, F., Michon, J. and Lhomme, J. (1999) Interaction of a spin-labeled adenine-acridine conjugate with a DNA duplex containing an abasic site model. Biochemistry, 38, 1930-1937.
    • (1999) Biochemistry , vol.38 , pp. 1930-1937
    • Thomas, F.1    Michon, J.2    Lhomme, J.3
  • 25
    • 78349285157 scopus 로고    scopus 로고
    • Noncovalent and site-directed spin labeling of nucleic acids
    • Shelke, S.A. and Sigurdsson, S.T. (2010) Noncovalent and site-directed spin labeling of nucleic acids. Angew. Chem. Int. Ed., 49, 7984-7986.
    • (2010) Angew. Chem. Int. Ed. , vol.49 , pp. 7984-7986
    • Shelke, S.A.1    Sigurdsson, S.T.2
  • 26
    • 70349786387 scopus 로고    scopus 로고
    • Relative orientation of rigid nitroxides by PELDOR: Beyond distance measurements in nucleic acids
    • Schiemann, O., Cekan, P., Margraf, D., Prisner, T.F. and Sigurdsson, S.T. (2009) Relative orientation of rigid nitroxides by PELDOR: beyond distance measurements in nucleic acids. Angew. Chem. Int. Ed., 48, 3292-3295.
    • (2009) Angew. Chem. Int. Ed. , vol.48 , pp. 3292-3295
    • Schiemann, O.1    Cekan, P.2    Margraf, D.3    Prisner, T.F.4    Sigurdsson, S.T.5
  • 27
    • 34248598957 scopus 로고    scopus 로고
    • A nucleoside that contains a rigid nitroxide spin label: A fluorophore in disguise
    • Barhate, N., Cekan, P., Massey, A.P. and Sigurdsson, S.T. (2007) A nucleoside that contains a rigid nitroxide spin label: a fluorophore in disguise. Angew. Chem. Int. Ed., 46, 2655-2658.
    • (2007) Angew. Chem. Int. Ed. , vol.46 , pp. 2655-2658
    • Barhate, N.1    Cekan, P.2    Massey, A.P.3    Sigurdsson, S.T.4
  • 28
    • 0023649630 scopus 로고
    • Oligodeoxyribonucleotides containing 1, 3-propanediol as nucleoside substitute
    • Seela, F. and Kaiser, K. (1987) Oligodeoxyribonucleotides containing 1, 3-propanediol as nucleoside substitute. Nucleic Acids Res., 15, 3113-3129.
    • (1987) Nucleic Acids Res. , vol.15 , pp. 3113-3129
    • Seela, F.1    Kaiser, K.2
  • 29
    • 0025941506 scopus 로고
    • DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities
    • Ono, A., Chen, C.N. and Kan, L.S. (1991) DNA triplex formation of oligonucleotide analogues consisting of linker groups and octamer segments that have opposite sugar-phosphate backbone polarities. Biochemistry, 30, 9914-9912.
    • (1991) Biochemistry , vol.30 , pp. 9914-9912
    • Ono, A.1    Chen, C.N.2    Kan, L.S.3
  • 30
    • 77951514908 scopus 로고
    • Integration of EPR-spectra
    • Schick, A. and Rager, H. (1993) Integration of EPR-Spectra. Appl. Magn. Reson., 4, 367-375.
    • (1993) Appl. Magn. Reson. , vol.4 , pp. 367-375
    • Schick, A.1    Rager, H.2
  • 31
    • 0029859191 scopus 로고    scopus 로고
    • Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases
    • Peracchi, A., Beigelman, L., Usman, N. and Herschlag, D. (1996) Rescue of abasic hammerhead ribozymes by exogenous addition of specific bases. Proc. Natl Acad. Sci. USA, 93, 11522-11527.
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 11522-11527
    • Peracchi, A.1    Beigelman, L.2    Usman, N.3    Herschlag, D.4
  • 32
    • 0002125735 scopus 로고    scopus 로고
    • Abasic DNA structure, reactivity, and recognition
    • Lhomme, J., Constant, J. and Demeunynck, M. (1999) Abasic DNA structure, reactivity, and recognition. Biopolymers, 52, 65-83.
    • (1999) Biopolymers , vol.52 , pp. 65-83
    • Lhomme, J.1    Constant, J.2    Demeunynck, M.3
  • 33
    • 38949136324 scopus 로고    scopus 로고
    • Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms
    • Rajendar, B., Nishizawa, S. and Teramae, N. (2008) Alloxazine as a ligand for selective binding to adenine opposite AP sites in DNA duplexes and analysis of single-nucleotide polymorphisms. Org. Biomol. Chem., 6, 670-673.
    • (2008) Org. Biomol. Chem. , vol.6 , pp. 670-673
    • Rajendar, B.1    Nishizawa, S.2    Teramae, N.3
  • 34
    • 57249086260 scopus 로고    scopus 로고
    • 6, 7-Dimethyllumazine as a potential ligand for selective recognition of adenine opposite an abasic site in DNA duplexes
    • Ye, Z., Rajendar, B., Qing, D., Nishizawa, S. and Teramae, N. (2008) 6, 7-Dimethyllumazine as a potential ligand for selective recognition of adenine opposite an abasic site in DNA duplexes. Chem. Commun., 6588-6590.
    • (2008) Chem. Commun. , pp. 6588-6590
    • Ye, Z.1    Rajendar, B.2    Qing, D.3    Nishizawa, S.4    Teramae, N.5
  • 35
    • 61949165909 scopus 로고    scopus 로고
    • Small-molecule binding at an abasic site of DNA: Strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms
    • Sankaran, N., Sato, Y., Sato, F., Rajendar, B., Morita, K., Seino, T., Nishizawa, S. and Teramae, N. (2009) Small-molecule binding at an abasic site of DNA: strong binding of lumiflavin for improved recognition of thymine-related single nucleotide polymorphisms. J. Phys. Chem. B, 113, 1522-1529.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 1522-1529
    • Sankaran, N.1    Sato, Y.2    Sato, F.3    Rajendar, B.4    Morita, K.5    Seino, T.6    Nishizawa, S.7    Teramae, N.8
  • 36
    • 75649110462 scopus 로고    scopus 로고
    • NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA
    • Thiagarajan, V., Rajendran, A., Satake, H., Nishizawa, S. and Teramae, N. (2010) NBD-based green fluorescent ligands for typing of thymine-related SNPs by using an abasic site-containing probe DNA. Chembiochem, 11, 94-100.
    • (2010) Chembiochem , vol.11 , pp. 94-100
    • Thiagarajan, V.1    Rajendran, A.2    Satake, H.3    Nishizawa, S.4    Teramae, N.5
  • 37
    • 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. and Teramae, N. (2009) 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., 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
  • 39
    • 34248515424 scopus 로고    scopus 로고
    • Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances
    • Schiemann, O., Piton, N., Plackmeyer, J., Bode, B., Prisner, T. and Engels, J. (2007) Spin labeling of oligonucleotides with the nitroxide TPA and use of PELDOR, a pulse EPR method, to measure intramolecular distances. Nat. Protoc., 2, 904-923.
    • (2007) Nat. Protoc. , vol.2 , pp. 904-923
    • Schiemann, O.1    Piton, N.2    Plackmeyer, J.3    Bode, B.4    Prisner, T.5    Engels, J.6
  • 40
    • 0000965687 scopus 로고    scopus 로고
    • Structure energetics, and dynamics of the nucleic acid base pairs: Nonempirical ab initio calculations
    • Hobza, P. and Sponer, J. (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations. Appl. Magn. Reson., 99, 3247-3276.
    • (1999) Appl. Magn. Reson. , vol.99 , pp. 3247-3276
    • Hobza, P.1    Sponer, J.2
  • 41
    • 0034194135 scopus 로고    scopus 로고
    • Thermodynamic parameters for DNA sequences with dangling ends
    • Bommarito, S., Peyret, N. and SantaLucia, J. Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res., 28, 1929-1934.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 1929-1934
    • Bommarito, S.1    Peyret, N.2    SantaLucia Jr., J.3
  • 42
    • 0025285869 scopus 로고
    • The abasic site as a challenge to DNA polymerase. A nuclear magnetic resonance study of G, C and T opposite a model abasic site
    • Cuniasse, P., Fazakerley, G.V., Guschlbauer, W., Kaplan, B.E. and Sowers, L.C. (1990) The abasic site as a challenge to DNA polymerase. A nuclear magnetic resonance study of G, C and T opposite a model abasic site. J. Mol. Biol., 213, 303-314.
    • (1990) J. Mol. Biol. , vol.213 , pp. 303-314
    • Cuniasse, P.1    Fazakerley, G.V.2    Guschlbauer, W.3    Kaplan, B.E.4    Sowers, L.C.5
  • 43
    • 0030964066 scopus 로고    scopus 로고
    • Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC) x d(GCGTGTGTGCG): The unpaired thymine stacks inside the helix
    • Coppel, Y., Berthet, N., Coulombeau, C., Garcia, J. and Lhomme, J. (1997) Solution conformation of an abasic DNA undecamer duplex d(CGCACXCACGC) x d(GCGTGTGTGCG): the unpaired thymine stacks inside the helix. Biochemistry, 36, 4817-4830.
    • (1997) Biochemistry , vol.36 , pp. 4817-4830
    • Coppel, Y.1    Berthet, N.2    Coulombeau, C.3    Garcia, J.4    Lhomme, J.5
  • 44
    • 38349188454 scopus 로고    scopus 로고
    • DNA oligonucleotides with A, T, G or C opposite an abasic site: Structure and dynamics
    • Chen, J., Dupradeau, F., Case, D., Turner, C. and Stubbe, J. (2008) DNA oligonucleotides with A, T, G or C opposite an abasic site: structure and dynamics. Nucleic Acids Res., 36, 253-262.
    • (2008) Nucleic Acids Res. , vol.36 , pp. 253-262
    • Chen, J.1    Dupradeau, F.2    Case, D.3    Turner, C.4    Stubbe, J.5
  • 45
    • 0021166273 scopus 로고
    • Local mobility of nucleic acids as determined from crystallographic data. I. RNA and B form DNA
    • Holbrook, S.R. and Kim, S.H. (1984) Local mobility of nucleic acids as determined from crystallographic data. I. RNA and B form DNA. J. Mol. Biol., 173, 361-388.
    • (1984) J. Mol. Biol. , vol.173 , pp. 361-388
    • Holbrook, S.R.1    Kim, S.H.2
  • 47
    • 0037078836 scopus 로고    scopus 로고
    • Synthesis of amino-and guanidino-G-clamp PNA monomers
    • Ausin, C., Ortega, J.A., Robles, J., Grandas, A. and Pedroso, E. (2002) Synthesis of amino-and guanidino-G-clamp PNA monomers. Org. Lett., 4, 4073-4075.
    • (2002) Org. Lett. , vol.4 , pp. 4073-4075
    • Ausin, C.1    Ortega, J.A.2    Robles, J.3    Grandas, A.4    Pedroso, E.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.