203
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
70. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence,
topology and structure. Nucleic Acids Res 34:5402–5415
71. Dai J, Carver M, Yang D (2008) Polymorphism of human telomeric quadruplex structures.
Biochimie 90:1172–1183
72. Yang D, Okamoto K (2010) Structural insights into G-quadruplexes: towards new anticancer
drugs. Future Med Chem 2:619–646
73. Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D (2006) Human telomeric sequence
forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel
strands in potassium solution. Nucleic Acids Res 34:2723–2735
74. Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3]
G-tetraplex. Structure 1:263–282
75. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
76. Jain AK, Bhattacharya S (2011) Interaction of G-quadruplexes with nonintercalating duplexDNA minor groove binding ligands. Bioconjugate Chem 22:2355–2368
77. Trotta R, De Tito S, Lauri I, La Pietra V, Marinelli L, Cosconati S, Martino L, Conte MR,
Mayol L, Novellino E, Randazzo A (2011) A more detailed picture of the interactions between
virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and
ITC studies. Biochimie 93:1280–1287
78. Williamson JR (1994) G-quartet structures in telomeric DNA. Annu Rev Biophys Biomol
Struct 23:703–730
79. Davies JT (2004) G-quartets 40 years later: from 5’-GMP to molecular biology and supramolecular chemistry. Angew. Chem Int Ed 43:668–698
80. Riley KE, Hobza P (2011) Noncovalent interactions in biochemistry. Wiley Interdisc. Revs
Comput Mol Sci 1:3–17
81. Bryan TM, Baumann P (2011) G-Quadruplexes: from guanine gels to chemotherapeutics.
Mol. Biotechnol 49:198–208
82. Chong DP (ed) (1995) Recent advances in density functional methods. V. 1. recent advances
in density functional methods (Part I). World Scientific Publishing, Singapore
83. Wesolowski TA, Wang YA (eds) (2013) Recent advances in computational chemistry. V. 6.
recent progress in orbital-free density functional theory. World Scientific Publishing, Singapore
84. Jissy AK, Ashik UPM, Datta A (2011) Nucleic acid G-quartets: insights into diverse patterns
and optical properties. J Phys Chem C 115:12530–12546
85. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J
Chem Phys 98:5648–5652
86. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789
87. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the
method of constraint satisfaction with parametrization for thermochemistry, thermochemical
kinetics, and noncovalent interactions. J Chem Theory Comput 2:364–382
88. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition
elements: two new functionals and systematic testing of four M06-class functionals and 12
other functionals. Theor Chem Acc 120:215–241
89. Jissy AK, Datta A (2010) Designing molecular switches based on DNA-base mispairing. J
Phys Chem B 114:15311–15318
90. Kendall RA, Fruchtl HA (1997) The impact of the resolution of the identity approximate
integral method on modern ab initio algorithm development. Theor Chem Acc 97:158–163
91. Vahtras O, Almlof J, Feyereisen MW (1993) Integral approximations for LCAO-SCF calculations. Chem Phys Lett 213:514–518
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
70. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence,
topology and structure. Nucleic Acids Res 34:5402–5415
71. Dai J, Carver M, Yang D (2008) Polymorphism of human telomeric quadruplex structures.
Biochimie 90:1172–1183
72. Yang D, Okamoto K (2010) Structural insights into G-quadruplexes: towards new anticancer
drugs. Future Med Chem 2:619–646
73. Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D (2006) Human telomeric sequence
forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel
strands in potassium solution. Nucleic Acids Res 34:2723–2735
74. Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG3(T2AG3)3]
G-tetraplex. Structure 1:263–282
75. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE
(2004) UCSF Chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612
76. Jain AK, Bhattacharya S (2011) Interaction of G-quadruplexes with nonintercalating duplexDNA minor groove binding ligands. Bioconjugate Chem 22:2355–2368
77. Trotta R, De Tito S, Lauri I, La Pietra V, Marinelli L, Cosconati S, Martino L, Conte MR,
Mayol L, Novellino E, Randazzo A (2011) A more detailed picture of the interactions between
virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and
ITC studies. Biochimie 93:1280–1287
78. Williamson JR (1994) G-quartet structures in telomeric DNA. Annu Rev Biophys Biomol
Struct 23:703–730
79. Davies JT (2004) G-quartets 40 years later: from 5’-GMP to molecular biology and supramolecular chemistry. Angew. Chem Int Ed 43:668–698
80. Riley KE, Hobza P (2011) Noncovalent interactions in biochemistry. Wiley Interdisc. Revs
Comput Mol Sci 1:3–17
81. Bryan TM, Baumann P (2011) G-Quadruplexes: from guanine gels to chemotherapeutics.
Mol. Biotechnol 49:198–208
82. Chong DP (ed) (1995) Recent advances in density functional methods. V. 1. recent advances
in density functional methods (Part I). World Scientific Publishing, Singapore
83. Wesolowski TA, Wang YA (eds) (2013) Recent advances in computational chemistry. V. 6.
recent progress in orbital-free density functional theory. World Scientific Publishing, Singapore
84. Jissy AK, Ashik UPM, Datta A (2011) Nucleic acid G-quartets: insights into diverse patterns
and optical properties. J Phys Chem C 115:12530–12546
85. Becke AD (1993) Density-functional thermochemistry. III. The role of exact exchange. J
Chem Phys 98:5648–5652
86. Lee C, Yang W, Parr RG (1988) Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys Rev B 37:785–789
87. Zhao Y, Schultz NE, Truhlar DG (2006) Design of density functionals by combining the
method of constraint satisfaction with parametrization for thermochemistry, thermochemical
kinetics, and noncovalent interactions. J Chem Theory Comput 2:364–382
88. Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition
elements: two new functionals and systematic testing of four M06-class functionals and 12
other functionals. Theor Chem Acc 120:215–241
89. Jissy AK, Datta A (2010) Designing molecular switches based on DNA-base mispairing. J
Phys Chem B 114:15311–15318
90. Kendall RA, Fruchtl HA (1997) The impact of the resolution of the identity approximate
integral method on modern ab initio algorithm development. Theor Chem Acc 97:158–163
91. Vahtras O, Almlof J, Feyereisen MW (1993) Integral approximations for LCAO-SCF calculations. Chem Phys Lett 213:514–518