202
M. Ilchenko and I. Dubey
48. McCammon JA, Harvey SC (1987) Dynamics of Proteins and Nucleic Acids. Cambridge
University Press, New York
49. Špačková N, Berger I, Šponer J (2001) Structural dynamics and cation interactions of DNA
quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale
MD simulations. J Am Chem Soc 123:3295–3307
50. Šponer J, Špačková N (2007) Molecular dynamics simulations and their application to fourstranded DNA. Methods 43:278–290
51. Haider S, Parkinson GN, Neidle S (2008) Molecular dynamics and principal components
analysis of human telomeric quadruplex multimers. Biophys J 95:296–311
52. Šponer J, Cang X, Cheatham TE III (2012) Molecular dynamics simulations of G-DNA and
perspectives on the simulation of nucleic acid structures. Methods 57:25–39
53. Chowdhury S, Bansal M (2000) Effect of coordinated ions on structure and flexibility of
parallel G-quandruplexes: a molecular dynamics study. J Biomol Struct Dyn 18:11–28
54. Cavallari M, Calzolari A, Garbesi A., DiFelice R (2006) Stability and migration of metal ions
in G4-wires by molecular dynamics simulations. J Phys Chem B 110:26337–26348
55. Akhshi P, Acton G, Wu G (2012) Molecular dynamics simulations to provide new insights
into the asymmetrical ammonium ion movement inside of the [d(G 3 T 4 G 4 )] 2 G-quadruplex
DNA structure. J Phys Chem B 116:9363–9370
56. Novotny J, Kulhanek P, Marek R (2012) Biocompatible xanthine-quadruplex scaffold for iontransporting DNA channels. J Phys Chem Lett 3:1788–1792
57. Read MA, Wood AA, Harrison JR, Gowan SM, Kelland LR, Dosanjh HS, Neidle S (1999)
Molecular modelling studies on G-quadruplex complexes of telomerase inhibitors: structureactivity relationships. J Med Chem 42, 4538–4546
58. Gavathiotis E, Heald RA, Stevens MFG, Searle MS (2003) Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT) 4 containing the human telomeric
repeat. J Mol Biol 334:25–36
59. Agrawal S, Ojha RP, Maiti S (2008) Energetics of the human Tel-22 quadruplex-telomestatin
interaction: a molecular dynamics study. J Phys Chem B 112:6828–6836
60. Hou J-Q, Chen S-B, Tan J-H, Ou T-M, Luo H-B, Li D, Xu J, Gu L-Q, Huaang Z-S (2010)
New insights into the structures of ligand-quadruplex complexes from molecular dynamics
simulations. J Phys Chem B 114:15301–15310
61. Li M-H, Luo Q, Li Z-S (2010) Molecular dynamics study on the interactions of porphyrin
with two antiparallel human telomeric quadruplexes. J Phys Chem B 114:6216–6224.
62. Li J, Jin X, Hu L, Wang J, Su Z (2011) Identification of nonplanar small molecule for Gquadruplex grooves: molecular docking and molecular dynamic study. Bioorg Med Chem
Lett 21:6969–6972
63. Hou J-Q, Chen S-B, Tan J-H, Luo H-B, Li D, Gu L-Q, Huaang Z-S. (2012) New insights
from molecular dynamic simulation studies of the multiple binding sodes of a ligand with
G-quadruplex DNA. J Comput Aided Mol Des 26:1355–1368
64. Holt PA, Chaires JB, Trent JO (2008) Molecular docking of intercalators and groove-binders
to nucleic acids using Autodock and Surflex. J Chem Inf Model 48:1602–1615
65. Ma D-L, Chan DS-H, Lee P, Kwan MH-T, Leung C-H (2011) Molecular modeling of drugDNA interactions: virtual screening to structure-based design. Biochimie 93:1252–1266
66. Ma D-L, Ma VP-Y, Chan DS-H, Leung K-H, Zhong H-J, Leung C-H. (2012) In silico screening of quadruplex-binding ligands. Methods 57:106–114
67. Alcaro S, Musetti C, Distinto S, Casatti M, Zagotto G, Artese A, Parrotta L, Moraca F, Costa
G, Ortuso F, Maccioni E, Sissi C (2013).Identification and characterization of new DNA Gquadruplex binders selected by a combination of ligand and structure-based virtual screening
approaches. J Med Chem 56:843–855
68. Haider S, Neidle S (2010) Molecular modeling and simulation of G-quadruplexes and quadruplex-ligand complexes. In: Baumann P. (ed.). G-Quadruplex DNA: Methods and Protocols. Methods Mol Biol, vol 608. Humana Press, New York, p. 17–37
69. Lee JY, Okumus B, Kim DS, Ha T (2005) Extreme conformational diversity in human telomeric DNA. Proc Natl Acad Sci USA 102:18938–18943
M. Ilchenko and I. Dubey
48. McCammon JA, Harvey SC (1987) Dynamics of Proteins and Nucleic Acids. Cambridge
University Press, New York
49. Špačková N, Berger I, Šponer J (2001) Structural dynamics and cation interactions of DNA
quadruplex molecules containing mixed guanine/cytosine quartets revealed by large-scale
MD simulations. J Am Chem Soc 123:3295–3307
50. Šponer J, Špačková N (2007) Molecular dynamics simulations and their application to fourstranded DNA. Methods 43:278–290
51. Haider S, Parkinson GN, Neidle S (2008) Molecular dynamics and principal components
analysis of human telomeric quadruplex multimers. Biophys J 95:296–311
52. Šponer J, Cang X, Cheatham TE III (2012) Molecular dynamics simulations of G-DNA and
perspectives on the simulation of nucleic acid structures. Methods 57:25–39
53. Chowdhury S, Bansal M (2000) Effect of coordinated ions on structure and flexibility of
parallel G-quandruplexes: a molecular dynamics study. J Biomol Struct Dyn 18:11–28
54. Cavallari M, Calzolari A, Garbesi A., DiFelice R (2006) Stability and migration of metal ions
in G4-wires by molecular dynamics simulations. J Phys Chem B 110:26337–26348
55. Akhshi P, Acton G, Wu G (2012) Molecular dynamics simulations to provide new insights
into the asymmetrical ammonium ion movement inside of the [d(G 3 T 4 G 4 )] 2 G-quadruplex
DNA structure. J Phys Chem B 116:9363–9370
56. Novotny J, Kulhanek P, Marek R (2012) Biocompatible xanthine-quadruplex scaffold for iontransporting DNA channels. J Phys Chem Lett 3:1788–1792
57. Read MA, Wood AA, Harrison JR, Gowan SM, Kelland LR, Dosanjh HS, Neidle S (1999)
Molecular modelling studies on G-quadruplex complexes of telomerase inhibitors: structureactivity relationships. J Med Chem 42, 4538–4546
58. Gavathiotis E, Heald RA, Stevens MFG, Searle MS (2003) Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT) 4 containing the human telomeric
repeat. J Mol Biol 334:25–36
59. Agrawal S, Ojha RP, Maiti S (2008) Energetics of the human Tel-22 quadruplex-telomestatin
interaction: a molecular dynamics study. J Phys Chem B 112:6828–6836
60. Hou J-Q, Chen S-B, Tan J-H, Ou T-M, Luo H-B, Li D, Xu J, Gu L-Q, Huaang Z-S (2010)
New insights into the structures of ligand-quadruplex complexes from molecular dynamics
simulations. J Phys Chem B 114:15301–15310
61. Li M-H, Luo Q, Li Z-S (2010) Molecular dynamics study on the interactions of porphyrin
with two antiparallel human telomeric quadruplexes. J Phys Chem B 114:6216–6224.
62. Li J, Jin X, Hu L, Wang J, Su Z (2011) Identification of nonplanar small molecule for Gquadruplex grooves: molecular docking and molecular dynamic study. Bioorg Med Chem
Lett 21:6969–6972
63. Hou J-Q, Chen S-B, Tan J-H, Luo H-B, Li D, Gu L-Q, Huaang Z-S. (2012) New insights
from molecular dynamic simulation studies of the multiple binding sodes of a ligand with
G-quadruplex DNA. J Comput Aided Mol Des 26:1355–1368
64. Holt PA, Chaires JB, Trent JO (2008) Molecular docking of intercalators and groove-binders
to nucleic acids using Autodock and Surflex. J Chem Inf Model 48:1602–1615
65. Ma D-L, Chan DS-H, Lee P, Kwan MH-T, Leung C-H (2011) Molecular modeling of drugDNA interactions: virtual screening to structure-based design. Biochimie 93:1252–1266
66. Ma D-L, Ma VP-Y, Chan DS-H, Leung K-H, Zhong H-J, Leung C-H. (2012) In silico screening of quadruplex-binding ligands. Methods 57:106–114
67. Alcaro S, Musetti C, Distinto S, Casatti M, Zagotto G, Artese A, Parrotta L, Moraca F, Costa
G, Ortuso F, Maccioni E, Sissi C (2013).Identification and characterization of new DNA Gquadruplex binders selected by a combination of ligand and structure-based virtual screening
approaches. J Med Chem 56:843–855
68. Haider S, Neidle S (2010) Molecular modeling and simulation of G-quadruplexes and quadruplex-ligand complexes. In: Baumann P. (ed.). G-Quadruplex DNA: Methods and Protocols. Methods Mol Biol, vol 608. Humana Press, New York, p. 17–37
69. Lee JY, Okumus B, Kim DS, Ha T (2005) Extreme conformational diversity in human telomeric DNA. Proc Natl Acad Sci USA 102:18938–18943