메뉴 건너뛰기




Volumn 41, Issue 3, 2013, Pages 2034-2046

Guanine base stacking in G-quadruplex nucleic acids

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE QUADRUPLEX;

EID: 84873654205     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1110     Document Type: Article
Times cited : (121)

References (89)
  • 1
    • 38049030699 scopus 로고    scopus 로고
    • Human telomere, oncogenic promoter and 50-UTR G-quadruplexes: Diverse higher order DNA and RNA targets for cancer therapeutics
    • Patel,D.J., Phan,A.T. and Kuryavyi,V. (2007) Human telomere, oncogenic promoter and 50-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res., 35, 7429-7455.
    • (2007) Nucleic Acids Res , vol.35 , pp. 7429-7455
    • Patel, D.J.1    Phan, A.T.2    Kuryavyi, V.3
  • 3
    • 79953313413 scopus 로고    scopus 로고
    • Targeting G-quadruplexes in gene promoters: A novel anticancer strategy?
    • Balasubramanian,S., Hurley,L.H. and Neidle,S. (2011) Targeting G-quadruplexes in gene promoters: A novel anticancer strategy? Nat. Rev. Drug Discov., 10, 261-275.
    • (2011) Nat. Rev. Drug Discov , vol.10 , pp. 261-275
    • Balasubramanian, S.1    Hurley, L.H.2    Neidle, S.3
  • 5
    • 77955253773 scopus 로고    scopus 로고
    • Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae
    • Piazza,A., Boule,J.B., Lopes,J., Mingo,K., Largy,E., Teulade-Fichou,M.P. and Nicolas,A. (2010) Genetic instability triggered by G-quadruplex interacting Phen-DC compounds in Saccharomyces cerevisiae. Nucleic Acids Res., 38, 4337-4348.
    • (2010) Nucleic Acids Res , vol.38 , pp. 4337-4348
    • Piazza, A.1    Boule, J.B.2    Lopes, J.3    Mingo, K.4    Largy, E.5    Teulade-Fichou, M.P.6    Nicolas, A.7
  • 6
    • 65649129343 scopus 로고    scopus 로고
    • Nucleic acid aptamers based on the G-quadruplex structure: Therapeutic and diagnostic potential
    • Gatto,B., Palumbo,M. and Sissi,C. (2009) Nucleic acid aptamers based on the G-quadruplex structure: Therapeutic and diagnostic potential. Curr. Med. Chem., 16, 1248-1265.
    • (2009) Curr. Med. Chem , vol.16 , pp. 1248-1265
    • Gatto, B.1    Palumbo, M.2    Sissi, C.3
  • 7
    • 81455140677 scopus 로고    scopus 로고
    • The application of DNA and RNA G-quadruplexes to therapeutic medicines
    • Collie,G.W. and Parkinson,G.N. (2011) The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem. Soc. Rev., 40, 5867-5892.
    • (2011) Chem. Soc. Rev , vol.40 , pp. 5867-5892
    • Collie, G.W.1    Parkinson, G.N.2
  • 8
    • 0030905954 scopus 로고    scopus 로고
    • Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: A quantum-chemical study
    • Sponer,J., Gabb,H.A., Leszczynski,J. and Hobza,P. (1997) Base-base and deoxyribose-base stacking interactions in B-DNA and Z-DNA: A quantum-chemical study. Biophys. J., 73, 76-87.
    • (1997) Biophys. J. , vol.73 , pp. 76-87
    • Sponer, J.1    Gabb, H.A.2    Leszczynski, J.3    Hobza, P.4
  • 9
    • 0037010001 scopus 로고    scopus 로고
    • Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations
    • Hobza,P. and Sponer,J. (2002) Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations. J. Am. Chem. Soc., 124, 11802-11808.
    • (2002) J. Am. Chem. Soc , vol.124 , pp. 11802-11808
    • Hobza, P.1    Sponer, J.2
  • 10
    • 14544274054 scopus 로고    scopus 로고
    • Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG,i AT, and AC DNA steps and in the NMR geometry of the 50-d(GCGAAGC)-30 hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels
    • Dabkowska,I., Gonzalez,H.V., Jurecka,P. and Hobza,P. (2005) Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 50-d(GCGAAGC)-30 hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels. J. Phys. Chem. A, 109, 1131-1136.
    • (2005) J. Phys. Chem. A , vol.109 , pp. 1131-1136
    • Dabkowska, I.1    Gonzalez, H.V.2    Jurecka, P.3    Hobza, P.4
  • 11
    • 33645326510 scopus 로고    scopus 로고
    • Nature of base stacking: Reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps
    • Sponer,J., Jurecka,P., Marchan,I., Luque,F.J., Orozco,M. and Hobza,P. (2006) Nature of base stacking: reference quantum-chemical stacking energies in ten unique B-DNA base-pair steps. Chem. Eur. J., 12, 2854-2865.
    • (2006) Chem. Eur. J. , vol.12 , pp. 2854-2865
    • Sponer, J.1    Jurecka, P.2    Marchan, I.3    Luque, F.J.4    Orozco, M.5    Hobza, P.6
  • 12
    • 43449137856 scopus 로고    scopus 로고
    • Nature and magnitude of aromatic stacking of nucleic acid bases
    • Sponer,J., Riley,K.E. and Hobza,P. (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys., 10, 2595-2610.
    • (2008) Phys. Chem. Chem. Phys , vol.10 , pp. 2595-2610
    • Sponer, J.1    Riley, K.E.2    Hobza, P.3
  • 13
    • 75649121122 scopus 로고    scopus 로고
    • Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations?
    • Svozil,D., Hobza,P. and Sponer,J. (2010) Comparison of intrinsic stacking energies of ten unique dinucleotide steps in A-RNA and B-DNA duplexes. Can we determine correct order of stability by quantum-chemical calculations? J. Phys. Chem. B, 114, 1191-1203.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 1191-1203
    • Svozil, D.1    Hobza, P.2    Sponer, J.3
  • 14
    • 0034227603 scopus 로고    scopus 로고
    • A remarkable alteration in the bonding pattern: An HF and DFT study of the interactions between the metal cations and the Hoogsteen hydrogen-bonded G-tetrad
    • Gu,J.D. and Leszczynski,J. (2000) A remarkable alteration in the bonding pattern: An HF and DFT study of the interactions between the metal cations and the Hoogsteen hydrogen-bonded G-tetrad. J. Phys. Chem. A, 104, 6308-6313.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 6308-6313
    • Gu, J.D.1    Leszczynski, J.2
  • 15
    • 0037165458 scopus 로고    scopus 로고
    • Origin of Na+/K+ selectivity of the guanine tetraplexes in water: The theoretical rationale
    • Gu,J.D. and Leszczynski,J. (2002) Origin of Na+/K+ selectivity of the guanine tetraplexes in water: The theoretical rationale. J. Phys. Chem. A, 106, 529-532.
    • (2002) J. Phys. Chem. A , vol.106 , pp. 529-532
    • Gu, J.D.1    Leszczynski, J.2
  • 16
    • 14744279716 scopus 로고    scopus 로고
    • Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads
    • Meyer,M., Hocquet,A. and Suhnel,J. (2005) Interaction of sodium and potassium ions with sandwiched cytosine-, guanine-, thymine-, and uracil-base tetrads. J. Comput. Chem., 26, 352-364.
    • (2005) J. Comput. Chem , vol.26 , pp. 352-364
    • Meyer, M.1    Hocquet, A.2    Suhnel, J.3
  • 18
    • 0031576353 scopus 로고    scopus 로고
    • The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution
    • Phillips,K., Dauter,Z., Murchie,A.I.H., Lilley,D.M.J. and Luisi,B. (1997) The crystal structure of a parallel-stranded guanine tetraplex at 0.95 angstrom resolution. J. Mol. Biol., 273, 171-182.
    • (1997) J. Mol. Biol , vol.273 , pp. 171-182
    • Phillips, K.1    Dauter, Z.2    Murchie, A.I.H.3    Lilley, D.M.J.4    Luisi, B.5
  • 19
    • 0035923718 scopus 로고    scopus 로고
    • X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61 angstrom
    • Deng,J.P., Xiong,Y. and Sundaralingam,M. (2001) X-ray analysis of an RNA tetraplex (UGGGGU)4 with divalent Sr2+ ions at subatomic resolution (0.61 angstrom). Proc. Natl Acad. Sci. USA, 98, 13665-13670.
    • (2001) Proc. Natl Acad. Sci. USA , vol.98 , pp. 13665-13670
    • Deng, J.P.1    Xiong, Y.2    Sundaralingam, M.3
  • 20
    • 0037142071 scopus 로고    scopus 로고
    • Crystal structure of parallel quadruplexes from human telomeric DNA
    • Parkinson,G.N., Lee,M.P.H. and Neidle,S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature, 417, 876-880.
    • (2002) Nature , vol.417 , pp. 876-880
    • Parkinson, G.N.1    Lee, M.P.H.2    Neidle, S.3
  • 22
    • 2442657982 scopus 로고    scopus 로고
    • Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats
    • Kondo,J., Adachi,W., Umeda,S., Sunami,T. and Takenaka,A. (2004) Crystal structures of a DNA octaplex with I-motif of G-quartets and its splitting into two quadruplexes suggest a folding mechanism of eight tandem repeats. Nucleic Acids Res., 32, 2541-2549.
    • (2004) Nucleic Acids Res , vol.32 , pp. 2541-2549
    • Kondo, J.1    Adachi, W.2    Umeda, S.3    Sunami, T.4    Takenaka, A.5
  • 23
    • 33646465719 scopus 로고    scopus 로고
    • Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex
    • Hazel,P., Parkinson,G.N. and Neidle,S. (2006) Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex. J. Am. Chem. Soc., 128, 5480-5487.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 5480-5487
    • Hazel, P.1    Parkinson, G.N.2    Neidle, S.3
  • 24
    • 34548172421 scopus 로고    scopus 로고
    • Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel
    • Lee,M.P.H., Parkinson,G.N., Hazel,P. and Neidle,S. (2007) Observation of the coexistence of sodium and calcium ions in a DNA G-quadruplex ion channel. J. Am. Chem. Soc., 129, 10106-10107.
    • (2007) J. Am. Chem. Soc , vol.129 , pp. 10106-10107
    • Lee, M.P.H.1    Parkinson, G.N.2    Hazel, P.3    Neidle, S.4
  • 26
    • 33847675742 scopus 로고    scopus 로고
    • Structural basis for binding of porphyrin to human telomeres
    • Parkinson,G.N., Ghosh,R. and Neidle,S. (2007) Structural basis for binding of porphyrin to human telomeres. Biochemistry, 46, 2390-2397.
    • (2007) Biochemistry , vol.46 , pp. 2390-2397
    • Parkinson, G.N.1    Ghosh, R.2    Neidle, S.3
  • 27
    • 48749109524 scopus 로고    scopus 로고
    • Topology conservation and loop flexibility in quadruplex-drug recognition: Crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes
    • Parkinson,G.N., Cuenca,F. and Neidle,S. (2008) Topology conservation and loop flexibility in quadruplex-drug recognition: Crystal structures of inter- and intramolecular telomeric DNA quadruplex-drug complexes. J. Mol. Biol., 381, 1145-1156.
    • (2008) J. Mol. Biol , vol.381 , pp. 1145-1156
    • Parkinson, G.N.1    Cuenca, F.2    Neidle, S.3
  • 28
    • 0035914469 scopus 로고    scopus 로고
    • An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a (:A):G(:A):G(:A):G heptad, and its dimeric interaction
    • Matsugami,A., Ouhashi,K., Kanagawa,M., Liu,H., Kanagawa,S., Uesugi,S. and Katahira,M. (2001) An intramolecular quadruplex of (GGA)4 triplet repeat DNA with a G:G:G:G tetrad and a (:A):G(:A):G(:A):G heptad, and its dimeric interaction. J. Mol. Biol., 313, 255-269.
    • (2001) J. Mol. Biol , vol.313 , pp. 255-269
    • Matsugami, A.1    Ouhashi, K.2    Kanagawa, M.3    Liu, H.4    Kanagawa, S.5    Uesugi, S.6    Katahira, M.7
  • 29
    • 0035979714 scopus 로고    scopus 로고
    • V-shaped scaffold: A new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads
    • Zhang,N., Gorin,A., Majumdar,A., Kettani,A., Chernichenko,N., Skripkin,E. and Patel,D.J. (2001) V-shaped scaffold: A new architectural motif identified in an A x (G x G x G x G) pentad-containing dimeric DNA quadruplex involving stacked G(anti) x G(anti) x G(anti) x G(syn) tetrads. J. Mol. Biol., 311, 1063-1079.
    • (2001) J. Mol. Biol , vol.311 , pp. 1063-1079
    • Zhang, N.1    Gorin, A.2    Majumdar, A.3    Kettani, A.4    Chernichenko, N.5    Skripkin, E.6    Patel, D.J.7
  • 30
    • 0036411968 scopus 로고    scopus 로고
    • A dimeric RNA quadruplex architecture comprised of two G:G(:A):G:G(:A) hexads, G:G:G: G tetrads and UUUU loops
    • Liu,H., Matsugami,A., Katahira,M. and Uesugi,S. (2002) A dimeric RNA quadruplex architecture comprised of two G:G(:A):G:G(:A) hexads, G:G:G:G tetrads and UUUU loops. J. Mol. Biol., 322, 955-970.
    • (2002) J. Mol. Biol , vol.322 , pp. 955-970
    • Liu, H.1    Matsugami, A.2    Katahira, M.3    Uesugi, S.4
  • 31
    • 0042847316 scopus 로고    scopus 로고
    • Intramolecular higher order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA
    • Matsugami,A., Okuizumi,T., Uesugi,S. and Katahira,M. (2003) Intramolecular higher order packing of parallel quadruplexes comprising a G:G:G:G tetrad and a G(:A):G(:A):G(:A):G heptad of GGA triplet repeat DNA. J. Biol. Chem., 278, 28147-28153.
    • (2003) J. Biol. Chem , vol.278 , pp. 28147-28153
    • Matsugami, A.1    Okuizumi, T.2    Uesugi, S.3    Katahira, M.4
  • 32
    • 14144254793 scopus 로고    scopus 로고
    • An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase
    • Phan,A.T., Kuryavyi,V., Ma,J.B., Faure,A., Andreola,M.L. and Patel,D.J. (2005) An interlocked dimeric parallel-stranded DNA quadruplex: A potent inhibitor of HIV-1 integrase. Proc. Natl Acad. Sci. USA, 102, 634-639.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 634-639
    • Phan, A.T.1    Kuryavyi, V.2    Ma, J.B.3    Faure, A.4    Andreola, M.L.5    Patel, D.J.6
  • 33
    • 70350674192 scopus 로고    scopus 로고
    • Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein
    • Mashima,T., Matsugami,A., Nishikawa,F., Nishikawa,S. and Katahira,M. (2009) Unique quadruplex structure and interaction of an RNA aptamer against bovine prion protein. Nucleic Acids Res., 37, 6249-6258.
    • (2009) Nucleic Acids Res , vol.37 , pp. 6249-6258
    • Mashima, T.1    Matsugami, A.2    Nishikawa, F.3    Nishikawa, S.4    Katahira, M.5
  • 34
    • 80455170603 scopus 로고    scopus 로고
    • Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity
    • Do,N.Q., Lim,K.W., Teo,M.H., Heddi,B. and Phan,A.T. (2011) Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity. Nucleic Acids Res., 39, 9448-9457.
    • (2011) Nucleic Acids Res , vol.39 , pp. 9448-9457
    • Do, N.Q.1    Lim, K.W.2    Teo, M.H.3    Heddi, B.4    Phan, A.T.5
  • 35
    • 67749143935 scopus 로고    scopus 로고
    • Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution
    • Martadinata,H. and Phan,A.T. (2009) Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution. J. Am. Chem. Soc., 131, 2570-2578.
    • (2009) J. Am. Chem. Soc , vol.131 , pp. 2570-2578
    • Martadinata, H.1    Phan, A.T.2
  • 36
    • 77956539976 scopus 로고    scopus 로고
    • A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex
    • Collie,G.W., Haider,S.M., Neidle,S. and Parkinson,G.N. (2010) A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res., 38, 5569-5580.
    • (2010) Nucleic Acids Res , Issue.38 , pp. 5569-5580
    • Collie, G.W.1    Haider, S.M.2    Neidle, S.3    Parkinson, G.N.4
  • 37
    • 80455129678 scopus 로고    scopus 로고
    • HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges
    • Mukundan,V.T., Do,N.Q. and Phan,A.T. (2011) HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges. Nucleic Acids Res., 39, 8984-8991.
    • (2011) Nucleic Acids Res , vol.39 , pp. 8984-8991
    • Mukundan, V.T.1    Do, N.Q.2    Phan, A.T.3
  • 38
    • 35448946080 scopus 로고    scopus 로고
    • Molecular dynamics simulations and their application to four-stranded DNA
    • Sponer,J. and Spackova,N. (2007) Molecular dynamics simulations and their application to four-stranded DNA. Methods, 43, 278-290.
    • (2007) Methods , vol.43 , pp. 278-290
    • Sponer, J.1    Spackova, N.2
  • 39
    • 79961199372 scopus 로고    scopus 로고
    • Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes
    • Cang,X.H., Sponer,J. and Cheatham,T.E. (2011) Explaining the varied glycosidic conformational, G-tract length and sequence preferences for anti-parallel G-quadruplexes. Nucleic Acids Res., 39, 4499-4512.
    • (2011) Nucleic Acids Res , vol.39 , pp. 4499-4512
    • Cang, X.H.1    Sponer, J.2    Cheatham, T.E.3
  • 40
    • 80052569980 scopus 로고    scopus 로고
    • Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis
    • Cang,X.H., Sponer,J. and Cheatham,T.E. (2011) Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. J. Am. Chem. Soc., 133, 14270-14279.
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 14270-14279
    • Cang, X.H.1    Sponer, J.2    Cheatham, T.E.3
  • 41
    • 37249066753 scopus 로고    scopus 로고
    • Geometric formalism for DNA quadruplex folding
    • Webba da Silva,M. (2007) Geometric formalism for DNA quadruplex folding. Chem. Eur. J., 13, 9738-9745.
    • (2007) Chem. Eur. J. , vol.13 , pp. 9738-9745
    • Webba Da Silva, M.1
  • 42
    • 0026759706 scopus 로고
    • A comprehensive classification of nucleic-acid structural families based on strand direction and base-pairing
    • Lavery,R., Zakrzewska,K., Sun,J.S. and Harvey,S.C. (1992) A comprehensive classification of nucleic-acid structural families based on strand direction and base-pairing. Nucleic Acids Res., 20, 5011-5016.
    • (1992) Nucleic Acids Res , vol.20 , pp. 5011-5016
    • Lavery, R.1    Zakrzewska, K.2    Sun, J.S.3    Harvey, S.C.4
  • 43
    • 84890021933 scopus 로고
    • Calculation of small molecular interactions by differences of separate total energies - Some procedures with reduced errors
    • Boys,S.F. and Bernardi,F. (1970) Calculation of small molecular interactions by differences of separate total energies - some procedures with reduced errors. Mol. Phys., 19, 553-566.
    • (1970) Mol. Phys , vol.19 , pp. 553-566
    • Boys, S.F.1    Bernardi, F.2
  • 44
    • 6944251055 scopus 로고
    • Note on an approximation treatment for many-electron systems
    • Moller,C. and Plesset,M.S. (1934) Note on an approximation treatment for many-electron systems. Phys. Rev., 46, 618-622.
    • (1934) Phys. Rev , vol.46 , pp. 618-622
    • Moller, C.1    Plesset, M.S.2
  • 47
    • 0002026077 scopus 로고
    • The superposition error problem - The (HF)2 and (H2O)2 complexes at the SCF and MP2 levels
    • Hobza,P., Schneider,B., Carsky,P. and Zahradnik,R. (1986) The superposition error problem - the (HF)2 and (H2O)2 complexes at the SCF and MP2 levels. J. Mol. Struc., 31, 377-385.
    • (1986) J. Mol. Struc , vol.31 , pp. 377-385
    • Hobza, P.1    Schneider, B.2    Carsky, P.3    Zahradnik, R.4
  • 50
    • 34250318638 scopus 로고    scopus 로고
    • Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers
    • Perez,A., Marchan,I., Svozil,D., Sponer,J., Cheatham,T.E., Laughton,C.A. and Orozco,M. (2007) Refinenement of the AMBER force field for nucleic acids: Improving the description of alpha/gamma conformers. Biophys. J., 92, 3817-3829.
    • (2007) Biophys. J. , vol.92 , pp. 3817-3829
    • Perez, A.1    Marchan, I.2    Svozil, D.3    Sponer, J.4    Cheatham, T.E.5    Laughton, C.A.6    Orozco, M.7
  • 52
    • 84868672305 scopus 로고    scopus 로고
    • Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study
    • Do,N.Q. and Phan,A.T. (2012) Monomer-dimer equilibrium for the 5'-5' stacking of propeller-type parallel-stranded G-quadruplexes: NMR structural study. Chem. Eur. J., 18, 14752-14759.
    • (2012) Chem. Eur. J. , vol.18 , pp. 14752-14759
    • Do, N.Q.1    Phan, A.T.2
  • 55
    • 84946450438 scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • Vangunsteren,W.F. and Berendsen,H.J.C. (1977) Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys., 34, 1311-1327.
    • (1977) Mol. Phys , vol.34 , pp. 1311-1327
    • Vangunsteren, W.F.1    Berendsen, H.J.C.2
  • 56
    • 33846823909 scopus 로고
    • Particle mesh Ewald -an N.Log(N) method for Ewald sums in large systems
    • Darden,T., York,D. and Pedersen,L. (1993) Particle mesh Ewald -an N.Log(N) method for Ewald sums in large systems. J. Chem. Phys., 98, 10089-10092.
    • (1993) J. Chem. Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 57
    • 44349142304 scopus 로고    scopus 로고
    • Structural basis of DNA quadruplex recognition by an acridine drug
    • Campbell,N.H., Parkinson,G.N., Reszka,A.P. and Neidle,S. (2008) Structural basis of DNA quadruplex recognition by an acridine drug. J. Am. Chem. Soc., 130, 6722-6724.
    • (2008) J. Am. Chem. Soc , vol.130 , pp. 6722-6724
    • Campbell, N.H.1    Parkinson, G.N.2    Reszka, A.P.3    Neidle, S.4
  • 58
    • 79952269800 scopus 로고    scopus 로고
    • Structural basis of telomeric RNA quadruplex-acridine ligand recognition
    • Collie,G.W., Sparapani,S., Parkinson,G.N. and Neidle,S. (2011) Structural basis of telomeric RNA quadruplex-acridine ligand recognition. J. Am. Chem. Soc., 133, 2721-2728.
    • (2011) J. Am. Chem. Soc , vol.133 , pp. 2721-2728
    • Collie, G.W.1    Sparapani, S.2    Parkinson, G.N.3    Neidle, S.4
  • 59
    • 0037427245 scopus 로고    scopus 로고
    • Structure of the first parallel DNA quadruplex-drug complex
    • Clark,G.R., Pytel,P.D., Squire,C.J. and Neidle,S. (2003) Structure of the first parallel DNA quadruplex-drug complex. J. Am. Chem. Soc., 125, 4066-4067.
    • (2003) J. Am. Chem. Soc , vol.125 , pp. 4066-4067
    • Clark, G.R.1    Pytel, P.D.2    Squire, C.J.3    Neidle, S.4
  • 60
    • 0242710951 scopus 로고    scopus 로고
    • Crystal structure of a bulged RNA tetraplex at 1.1 angstrom resolution: Implications for a novel binding site in RNA tetraplex
    • Pan,B.C., Xiong,Y., Shi,K. and Sundaralingam,M. (2003) Crystal structure of a bulged RNA tetraplex at 1.1 angstrom resolution: Implications for a novel binding site in RNA tetraplex. Structure, 11, 1423-1430.
    • (2003) Structure , vol.11 , pp. 1423-1430
    • Pan, B.C.1    Xiong, Y.2    Shi, K.3    Sundaralingam, M.4
  • 61
    • 0038681084 scopus 로고    scopus 로고
    • Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes
    • Pan,B.C., Xiong,Y., Shi,K., Deng,J.P. and Sundaralingam,M. (2003) Crystal structure of an RNA purine-rich tetraplex containing adenine tetrads: Implications for specific binding in RNA tetraplexes. Structure, 11, 815-823.
    • (2003) Structure , vol.11 , pp. 815-823
    • Pan, B.C.1    Xiong, Y.2    Shi, K.3    Deng, J.P.4    Sundaralingam, M.5
  • 62
    • 0037970596 scopus 로고    scopus 로고
    • An eight-stranded helical fragment in RNA crystal structure: Implications for tetraplex interaction
    • Pan,B.C., Xiong,Y., Shi,K. and Sundaralingam,M. (2003) An eight-stranded helical fragment in RNA crystal structure: Implications for tetraplex interaction. Structure, 11, 825-831.
    • (2003) Structure , vol.11 , pp. 825-831
    • Pan, B.C.1    Xiong, Y.2    Shi, K.3    Sundaralingam, M.4
  • 63
    • 33749168652 scopus 로고    scopus 로고
    • Crystal structure of an RNA quadruplex containing inosine tetrad: Implications for the roles of NH2 group in purine tetrads
    • Pan,B.C., Shi,K. and Sundaralingam,M. (2006) Crystal structure of an RNA quadruplex containing inosine tetrad: Implications for the roles of NH2 group in purine tetrads. J. Mol. Biol., 363, 451-459.
    • (2006) J. Mol. Biol , vol.363 , pp. 451-459
    • Pan, B.C.1    Shi, K.2    Sundaralingam, M.3
  • 64
    • 0035816210 scopus 로고    scopus 로고
    • DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex
    • Horvath,M.P. and Schultz,S.C. (2001) DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex. J. Mol. Biol., 310, 367-377.
    • (2001) J. Mol. Biol , vol.310 , pp. 367-377
    • Horvath, M.P.1    Schultz, S.C.2
  • 65
    • 0036290781 scopus 로고    scopus 로고
    • Crystal structure of the potassium form of an Oxytricha nova G-quadruplex
    • Haider,S., Parkinson,G.N. and Neidle,S. (2002) Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. J. Mol. Biol., 320, 189-200.
    • (2002) J. Mol. Biol , vol.320 , pp. 189-200
    • Haider, S.1    Parkinson, G.N.2    Neidle, S.3
  • 66
    • 0037423728 scopus 로고    scopus 로고
    • Structure of a G-quadruplex-ligand complex
    • Haider,S.M., Parkinson,G.N. and Neidle,S. (2003) Structure of a G-quadruplex-ligand complex. J. Mol. Biol., 326, 117-125.
    • (2003) J. Mol. Biol , vol.326 , pp. 117-125
    • Haider, S.M.1    Parkinson, G.N.2    Neidle, S.3
  • 67
    • 33750031344 scopus 로고    scopus 로고
    • Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex
    • Gill,M.L., Strobel,S.A. and Loria,J.P. (2006) Crystallization and characterization of the thallium form of the Oxytricha nova G-quadruplex. Nucleic Acids Res., 34, 4506-4514.
    • (2006) Nucleic Acids Res , vol.34 , pp. 4506-4514
    • Gill, M.L.1    Strobel, S.A.2    Loria, J.P.3
  • 69
    • 79951657834 scopus 로고    scopus 로고
    • Fluorine in medicinal chemistry: Beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA
    • Campbell,N.H., Smith,D.L., Reszka,A.P., Neidle,S. and O'Hagan,D. (2011) Fluorine in medicinal chemistry: beta-fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G-quadruplex DNA. Org. Biomol. Chem., 9, 1328-1331.
    • (2011) Org. Biomol. Chem , vol.9 , pp. 1328-1331
    • Campbell, N.H.1    Smith, D.L.2    Reszka, A.P.3    Neidle, S.4    O'Hagan, D.5
  • 70
    • 33644778701 scopus 로고    scopus 로고
    • Base-tetrad swapping results in dimerization of RNA quadruplexes: Implications for formation of the i-motif RNA octaplex
    • Pan,B., Shi,K. and Sundaralingam,M. (2006) Base-tetrad swapping results in dimerization of RNA quadruplexes: Implications for formation of the i-motif RNA octaplex. Proc. Natl Acad. Sci. USA, 103, 3130-3134.
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , pp. 3130-3134
    • Pan, B.1    Shi, K.2    Sundaralingam, M.3
  • 71
    • 0028774726 scopus 로고
    • Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G-tetraplex
    • Wang,Y. and Patel,D.J. (1994) Solution structure of the Tetrahymena telomeric repeat d(T2G4)4 G-tetraplex. Structure, 2, 1141-1156.
    • (1994) Structure , vol.2 , pp. 1141-1156
    • Wang, Y.1    Patel, D.J.2
  • 72
    • 33746600695 scopus 로고    scopus 로고
    • Structure of the human telomere in K+ solution: An intramolecular (3+1) G-quadruplex scaffold
    • Luu,K.N., Phan,A.T., Kuryavyi,V., Lacroix,L. and Patel,D.J. (2006) Structure of the human telomere in K+ solution: An intramolecular (3+1) G-quadruplex scaffold. J. Am. Chem. Soc., 128, 9963-9970.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 9963-9970
    • Luu, K.N.1    Phan, A.T.2    Kuryavyi, V.3    Lacroix, L.4    Patel, D.J.5
  • 73
    • 58549102895 scopus 로고    scopus 로고
    • Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop
    • Balkwill,G.D., Garner,T.P., Williams,H.E. and Searle,M.S. (2009) Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop. J. Mol. Biol., 385, 1600-1615.
    • (2009) J. Mol. Biol , vol.385 , pp. 1600-1615
    • Balkwill, G.D.1    Garner, T.P.2    Williams, H.E.3    Searle, M.S.4
  • 74
    • 77956252000 scopus 로고    scopus 로고
    • Coexistence of two distinct G-quadruplex conformations in the hTERT promoter
    • Lim,K.W., Lacroix,L., Yue,D.J., Lim,J.K., Lim,J.M. and Phan,A.T. (2010) Coexistence of two distinct G-quadruplex conformations in the hTERT promoter. J. Am. Chem. Soc., 132, 12331-12342.
    • (2010) J. Am. Chem. Soc , vol.132 , pp. 12331-12342
    • Lim, K.W.1    Lacroix, L.2    Yue, D.J.3    Lim, J.K.4    Lim, J.M.5    Phan, A.T.6
  • 75
    • 70349785011 scopus 로고    scopus 로고
    • Solution structure of a locked nucleic a0cid modified quadruplex: Introducing the V4 folding topology
    • Nielsen,J.T., Arar,K. and Petersen,M. (2009) Solution structure of a locked nucleic a0cid modified quadruplex: Introducing the V4 folding topology. Angew. Chem. Int. Ed. Engl., 48, 3099-3103.
    • (2009) Angew. Chem. Int. Ed. Engl , vol.48 , pp. 3099-3103
    • Nielsen, J.T.1    Arar, K.2    Petersen, M.3
  • 76
    • 79960516726 scopus 로고    scopus 로고
    • Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks
    • Martadinata,H., Heddi,B., Lim,K.W. and Phan,A.T. (2011) Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks. Biochemistry, 50, 6455-6461.
    • (2011) Biochemistry , vol.50 , pp. 6455-6461
    • Martadinata, H.1    Heddi, B.2    Lim, K.W.3    Phan, A.T.4
  • 77
    • 22244464285 scopus 로고    scopus 로고
    • Dynamics and thermodynamics of dimerization of parallel G-quadruplexed DNA formed from d(TTAGn) (n=3-5)
    • Kato,Y., Ohyama,T., Mita,H. and Yamamoto,Y. (2005) Dynamics and thermodynamics of dimerization of parallel G-quadruplexed DNA formed from d(TTAGn) (n=3-5). J. Am. Chem. Soc., 127, 9980-9981.
    • (2005) J. Am. Chem. Soc , vol.127 , pp. 9980-9981
    • Kato, Y.1    Ohyama, T.2    Mita, H.3    Yamamoto, Y.4
  • 78
    • 33845294453 scopus 로고    scopus 로고
    • Characterization of structure and stability of long telomeric DNA G-quadruplexes
    • Yu,H.Q., Miyoshi,D. and Sugimoto,N. (2006) Characterization of structure and stability of long telomeric DNA G-quadruplexes. J. Am. Chem. Soc., 128, 15461-15468.
    • (2006) J. Am. Chem. Soc , vol.128 , pp. 15461-15468
    • Yu, H.Q.1    Miyoshi, D.2    Sugimoto, N.3
  • 79
    • 67649756727 scopus 로고    scopus 로고
    • Structure of long telomeric RNA transcripts: The G-rich RNA forms a compact repeating structure containing G-quartets
    • Randall,A. and Griffith,J.D. (2009) Structure of long telomeric RNA transcripts: The G-rich RNA forms a compact repeating structure containing G-quartets. J. Biol. Chem., 284, 13980-13986.
    • (2009) J. Biol. Chem , vol.284 , pp. 13980-13986
    • Randall, A.1    Griffith, J.D.2
  • 80
    • 70349661733 scopus 로고    scopus 로고
    • Consecutive formation of G-quadruplexes in human telomeric-overhang DNA: A protective capping structure for telomere ends
    • Xu,Y., Ishizuka,T., Kurabayashi,K. and Komiyama,M. (2009) Consecutive formation of G-quadruplexes in human telomeric-overhang DNA: A protective capping structure for telomere ends. Angew. Chem. Int. Ed. Engl., 48, 7833-7836.
    • (2009) Angew. Chem. Int. Ed. Engl , vol.48 , pp. 7833-7836
    • Xu, Y.1    Ishizuka, T.2    Kurabayashi, K.3    Komiyama, M.4
  • 81
    • 77955791968 scopus 로고    scopus 로고
    • Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures
    • Collie,G.W., Parkinson,G.N., Neidle,S., Rosu,F., De Pauw,E. and Gabelica,V. (2010) Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures. J. Am. Chem. Soc., 132, 9328-9334.
    • (2010) J. Am. Chem. Soc , vol.132 , pp. 9328-9334
    • Collie, G.W.1    Parkinson, G.N.2    Neidle, S.3    Rosu, F.4    De Pauw, E.5    Gabelica, V.6
  • 82
    • 0027750779 scopus 로고
    • Solution structure of a parallel-stranded G-quadruplex DNA
    • Wang,Y. and Patel,D.J. (1993) Solution structure of a parallel-stranded G-quadruplex DNA. J. Mol. Biol., 234, 1171-1183.
    • (1993) J. Mol. Biol , vol.234 , pp. 1171-1183
    • Wang, Y.1    Patel, D.J.2
  • 83
    • 0027918585 scopus 로고
    • Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex
    • Wang,Y. and Patel,D.J. (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3] G-tetraplex. Structure, 1, 263-282.
    • (1993) Structure , vol.1 , pp. 263-282
    • Wang, Y.1    Patel, D.J.2
  • 84
    • 0028318093 scopus 로고
    • Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGT TGGTGTGGTTGG)
    • Schultze,P., Macaya,R.F. and Feigon,J. (1994) Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGT TGGTGTGGTTGG). J. Mol. Biol., 235, 1532-1547.
    • (1994) J. Mol. Biol , vol.235 , pp. 1532-1547
    • Schultze, P.1    MacAya, R.F.2    Feigon, J.3
  • 85
    • 0028773155 scopus 로고
    • Refined solution structure of the dimeric quadruplex formed from the oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG
    • Schultze,P., Smith,F.W. and Feigon,J. (1994) Refined solution structure of the dimeric quadruplex formed from the oxytricha telomeric oligonucleotide d(GGGGTTTTGGGG). Structure, 2, 221-233.
    • (1994) Structure , vol.2 , pp. 221-233
    • Schultze, P.1    Smith, F.W.2    Feigon, J.3
  • 86
    • 0032566629 scopus 로고    scopus 로고
    • Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA
    • Kettani,A., Bouaziz,S., Gorin,A., Zhao,H., Jones,R.A. and Patel,D.J. (1998) Solution structure of a Na cation stabilized DNA quadruplex containing G.G.G.G and G.C.G.C tetrads formed by G-G-G-C repeats observed in adeno-associated viral DNA. J. Mol. Biol., 282, 619-636.
    • (1998) J. Mol. Biol , vol.282 , pp. 619-636
    • Kettani, A.1    Bouaziz, S.2    Gorin, A.3    Zhao, H.4    Jones, R.A.5    Patel, D.J.6
  • 87
    • 0032566709 scopus 로고    scopus 로고
    • A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats
    • Bouaziz,S., Kettani,A. and Patel,D.J. (1998) A K cation-induced conformational switch within a loop spanning segment of a DNA quadruplex containing G-G-G-C repeats. J. Mol. Biol., 282, 637-652.
    • (1998) J. Mol. Biol , vol.282 , pp. 637-652
    • Bouaziz, S.1    Kettani, A.2    Patel, D.J.3
  • 88
    • 0030993474 scopus 로고    scopus 로고
    • Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads
    • Kettani,A., Bouaziz,S., Wang,W., Jones,R.A. and Patel,D.J. (1997) Bombyx mori single repeat telomeric DNA sequence forms a G-quadruplex capped by base triads. Nat. Struct. Biol., 4, 382-389.
    • (1997) Nat. Struct. Biol , vol.4 , pp. 382-389
    • Kettani, A.1    Bouaziz, S.2    Wang, W.3    Jones, R.A.4    Patel, D.J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.