Experimental methods for studying the interactions between G-quadruplex structures and ligands

Current Pharmaceutical Design

Volumn 18, Issue 14, 2012, Pages 1900-1916

  Jaumot, Joaquim ^a   Gargallo, Raimundo ^a  

^a UNIVERSITY OF BARCELONA   (Spain)

Author keywords

G quadruplex; Instrumental techniques; Ligand; Review

Indexed keywords

GUANINE QUADRUPLEX; LIGAND;

CIRCULAR DICHROISM; DNA BINDING; DNA STRUCTURE; FLUORESCENCE; HUMAN; ISOTHERMAL TITRATION CALORIMETRY; MASS SPECTROMETRY; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS; REVIEW; SPECTROSCOPY; SURFACE PLASMON RESONANCE;

CALORIMETRY; CIRCULAR DICHROISM; G-QUADRUPLEXES; HUMANS; LIGANDS; MAGNETIC RESONANCE SPECTROSCOPY; SPECTROMETRY, FLUORESCENCE; SPECTROMETRY, MASS, ELECTROSPRAY IONIZATION; SPECTROPHOTOMETRY, ULTRAVIOLET; SURFACE PLASMON RESONANCE;

EID: 84860116133     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/138161212799958486     Document Type: Review

References (182)

1. Neidle S, Balasubramanian S, Eds. Quadruplex Nucleic Acids. Cambridge, UK: Royal Society of Chemistry 2006.
2. Bloomfield VA, Crothers DM, Tinoco Jr I, Eds. Nucleic Acids: Structures, Properties and Functions. Sausalito, US: University Science Books 2000.
3. Huppert JL, Balasubramanian S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res 2007; 35: 406- 413.
4. Wu Y, Brosh RM. G-quadruplex nucleic acids and human disease. FEBS J. 2010; 277: 3470-3488.
5. Baumann P, Ed. G-Quadruplex DNA. New York, US: Humana Press 2010.
6. Fox KR, Ed. Drug-DNA Interaction Protocols. New York, US: Humana Press 2010.
7. Neidle S. Methods for studying quadruplex nucleic acids. Methods 2007; 43: 245-245.
8. Ho PS. Methods to study nucleic acid structure. Methods 2009; 47: 141-141.
9. Rachwal PA, Fox KR. Quadruplex melting. Methods 2007; 43: 291-301.
10. Paramasivan S, Rujan I, Bolton PH. Circular dichroism of quadruplex DNAs: Applications to structure, cation effects and ligand binding. Methods 2007; 43: 324-331.
11. Webba da Silva M. NMR methods for studying quadruplex nucleic acids. Methods 2007; 43: 264-277.
12. Redman JE. Surface plasmon resonance for probing quadruplex folding and interactions with proteins and small molecules. Methods 2007; 43: 302-312.
13. Ragazzon P, Chaires JB. Use of competition dialysis in the discovery of G-quadruplex selective ligands. Methods 2007; 43: 313-323.
14. Lee H-T, Olsen CM, Waters L, Sukup H, Marky LA. Thermodynamic contributions of the reactions of DNA intramolecular structures with their complementary strands. Biochimie 2008; 90: 1052-1063.
15. Rosu F, De Pauw E, Gabelica V. Electrospray mass spectrometry to study drug-nucleic acids interactions. Biochimie 2008; 90: 1074-1087.
16. Monchaud D, Allain C, Bertrand H, et al. Ligands playing musical chairs with G-quadruplex DNA: A rapid and simple displacement assay for identifying selective G-quadruplex binders. Biochimie 2008; 90: 1207-1223.
17. Shirude PS, Balasubramanian S. Single molecule conformational analysis of DNA G-quadruplexes. Biochimie 2008; 90: 1197-1206.
18. Neidle S, Parkinson GN. Quadruplex DNA crystal structures and drug design. Biochimie 2008; 90: 1184-1196.
19. Murat P, Singh Y, Defrancq E. Methods for investigating G-quadruplex DNA/ligand interactions. Chem Soc Rev 2011; 40: 5293-5307.
20. Sun H, Xiang J, Zhang Y, Xu G, Xu L, Tang Y. Spectroscopic studies of the interaction between methylene blue and G-quadruplex. Chinese Science Bulletin 2006; 51: 1687-1692.
21. Sun H, Tang Y, Xiang J, et al. Spectroscopic studies of the interaction between quercetin and G-quadruplex DNA. Bioorg Med Chem Lett 2006; 16: 3586-3589.
22. Wei C, Jia G, Yuan J, Feng Z, Li C. A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs. Biochemistry 2006; 45: 6681-6691.
23. Dincalp H, Avcibasi N, Icli S. Spectral properties and G-quadruplex DNA binding selectivities of a series of unsymmetrical perylene diimides. Journal of Photochemistry and Photobiology A: Chemistry 2007; 185: 1-12.
24. Barbieri CM, Srinivasan AR, Rzuczek SG, Rice JE, LaVoie EJ, Pilch DS. Defining the mode, energetics and specificity with which a macrocyclic hexaoxazole binds to human telomeric G-quadruplex DNA. Nucleic Acids Res 2007; 35: 3272-3286.
25. Galezowska E, Masternak A, Rubis B, et al. Spectroscopic study and G-quadruplex DNA binding affinity of two bioactive papaverine-derived ligands. International Journal of Biological Macromolecules 2007; 41: 558-563.
26. Arora A, Maiti S. Effect of loop orientation on quadruplex -TMPyP4 interaction. J Phys Chem B 2008; 112: 8151-8159.
27. Fu B, Zhang D, Weng X, et al. Cationic metal-corrole complexes: Design, synthesis, and properties of guanine-quadruplex stabilizers. Chemistry 2008; 14: 9431-9441.
28. Mei WJ, Wei XY, Liu YJ, Wang B. Studies on the interactions of a novel ruthenium(II) complex with G-quadruplex DNA. Transition Metal Chemistry 2008; 33: 907-910.
29. Wei C, Han G, Jia G, Zhou J, Li C. Study on the interaction of porphyrin with G-quadruplex DNAs. Biophys Chem 2008; 137: 19-23.
30. del Toro M, Bucek P, Aviñó A, et al. Targeting the G-quadruplex-forming region near the P1 promoter in the human BCL-2 gene with the cationic porphyrin TMPyP4 and with the complementary C-rich strand. Biochimie 2009; 91: 894-902.
31. del Toro M, Gargallo R, Eritja R, Jaumot J. Study of the interaction between the G-quadruplex-forming thrombin-binding aptamer and the porphyrin 5,10,15,20-tetrakis-(N-methyl-4-pyridyl)-21,23H-porphyrin tetratosylate. Anal Biochem 2008; 379: 8-15.
32. Dik-Lung M, Che CM, Yan SC. Platinum(II) complexes with dipyridophenazine ligands as human telomerase inhibitors and luminescent probes for G-quadruplex DNA. J Am Chem Soc 2009; 131: 1835-1846.
33. Chen M, Song G, Wang C, Hu D, Ren J, Qu X. Small-molecule selectively recognizes human telomeric G-quadruplex DNA and regulates its conformational switch. Biophys J 2009; 97: 2014-2023.
34. Zhang H, Xiao X, Wang P, et al. Conformational conversion of DNA G-quadruplex induced by a cationic porphyrin. Spectrochim Acta A Mol Biomol Spectrosc 2009; 74: 243-247.
35. Arora A, Maiti S. Stability and molecular recognition of quadruplexes with different loop length in the absence and presence of molecular crowding agents. J Phys Chem B 2009; 113: 8784-8792.
36. Wei C, Jia G, Zhou J, Han G, Li C. Evidence for the binding mode of porphyrins to G-quadruplex DNA. Phys Chem Chem Phys 2009; 11: 4025-4032.
37. Bhattacharya S, Chaudhuri P, Jain AK, Paul A. Symmetrical bisbenzimidazoles with benzenediyl spacer: The role of the shape of the ligand on the stabilization and structural alterations in telomeric g-quadruplex dna and telomerase inhibition. Bioconjug Chem 2010; 21: 1148-1159.
38. Dutikova YV, Borisova OF, Shchyolkina AK, et al. 5,10,15,20-Tetra-(N-methyl-3-pyridyl)porphyrin destabilizes the antiparallel telomeric quadruplex d(TTAGGG)4. Mol Biol 2010; 44: 823-831.
39. Nagesh N, Buscaglia R, Dettler JM, Lewis EA. Studies on the site and mode of TMPyP4 interactions with Bcl-2 promoter sequence G-quadruplexes. Biophys J 2010; 98: 2628-2633.
40. Wei C, Wang J, Zhang M. Spectroscopic study on the binding of porphyrins to (G4T4G4)4 parallel G-quadruplex. Biophys Chem 2010; 148: 51-55.
41. Shi S, Geng X, Zhao J, et al. Interaction of [Ru(bpy)2(dppz)]2+ with human telomeric DNA: Preferential binding to G-quadruplexes over i-motif. Biochimie 2010; 92: 370-377.
42. Lee HM, Chan DSH, Yang F, et al. Identification of natural product Fonsecin B as a stabilizing ligand of c-myc G-quadruplex DNA by high-throughput virtual screening. Chem Commun 2010; 46: 4680-4682.
43. Wang P, Leung CH, Ma DL, Yan SC, Che CM. Structure-based design of platinum(II) Complexes as c-myc oncogene Down-regulators and luminescent probes for G-quadruplex DNA. Chemistry 2010; 16: 6900-6911.
44. Yaku H, Murashima T, Miyoshi D, Sugimoto N. Anionic phthalocyanines targeting G-quadruplexes and inhibiting telomerase activity in the presence of excessive DNA duplexes. Chem Commun 2010; 46: 5740-5742.
45. Petraccone L, Fotticchia I, Cummaro A, et al. The triazatruxene derivative azatrux binds to the parallel form of the human telomeric G-quadruplex under molecular crowding conditions: Biophysical and molecular modeling studies. Biochimie 2011; 93: 1318-1327
46. Bhadra K, Kumar GS. Interaction of berberine, palmatine, coralyne, and sanguinarine to quadruplex DNA: A comparative spectroscopic and calorimetric study. BiochimBiophys Acta 2011; 1810: 485-496.
47. Jaumot J, Eritja R, Gargallo R. Chemical equilibria studies using multivariate analysis methods. Anal Bioanal Chem 2011; 399: 1983-1997.
48. Bhattacharjee AJ, Ahluwalia K, Taylor S, et al. Induction of G-quadruplex DNA structure by Zn(II) 5,10,15,20-tetrakis(N-methyl-4-pyridyl)porphyrin. Biochimie 2011; 93: 1297-1309.
49. Cummaro A, Fotticchia I, Franceschin M, Giancola C, Petraccone L. Binding properties of human telomeric quadruplex multimers: A new route for drug design. Biochimie 2011; 93: 1392-1400.
50. Dash J, Waller ZAE, Pantos GD, Balasubramanian S. Synthesis and binding studies of novel diethynyl-pyridine amides with genomic promoter DNA G-quadruplexes. Chemistry 2011; 17: 4571-4581.
51. Cian AD, Mergny JL. Quadruplex ligands may act as molecular chaperones for tetramolecular quadruplex formation. Nucleic Acids Res 2007; 35: 2483-2493.
52. Sun H, Xiang J, Liu Y, Li L, Li Q, Xu G, Tang Y. A stabilizing and denaturing dual-effect for natural polyamines interacting with G-quadruplexes depending on concentration. Biochimie 2011; 93: 1351-1356.
53. Sun J, An Y, Zhang L, Chen HY, Han Y, Wang YJ, Mao ZW, Ji LN. Studies on synthesis, characterization, and G-quadruplex binding of Ru(II) complexes containing two dppz ligands. J Inorg Biochem 2011; 105: 149-154.
54. Cogoi S, Xodo LE. Enhanced G4-DNA binding of 5,10,15,20 (N-propyl-4-pyridyl) porphyrin (TPrPyP4): A comparative study with TMPyP4. Chem Commun 2010; 46: 7364-7366.
55. Xu W, Tan JH, Chen SB, Hou JQ, Li D, Huang ZS, Gu LQ. Studies on the binding of 5-N-methylated quindoline derivative to human telomeric G-quadruplex. Biochem Biophys Res Commun 2011; 406: 454-458.
56. Mergny JL, Lacroix L. Analysis of Thermal Melting Curves. Oligonucleotides 2003; 13: 515-537.
57. Agarwal T, Roy S, Chakraborty TK, Maiti S. Selective targeting of G-quadruplex using furan-based cyclic homooligopeptides: Effect on c-MYC expression. Biochemistry 2010; 49: 8388-8397.
58. Pilch DS, Barbieri CM, Rzuczek SG, LaVoie EJ, Rice JE. Targeting human telomeric G-quadruplex DNA with oxazole-containing macrocyclic compounds. Biochimie 2008; 90: 1233-1249.
59. Cheng X, Liu X, Bing T, Cao Z, Shangguan D. General peroxidase activity of G-quadruplex-hemin complexes and its application in ligand screening. Biochemistry 2009; 48: 7817-7823.
60. Li H, Liu Y, Lin S, Yuan G. Spectroscopy probing of the formation, recognition, and conversion of a G-quadruplex in the promoter region of the bcl-2 oncogene. Chemistry 2009; 15: 2445-2452.
61. Ren L, Zhang A, Huang J, et al. Quaternary ammonium zinc phthalocyanine: Inhibiting telomerase by stabilizing G quadruplexes and inducing G-quadruplex structure transition and formation. ChemBioChem 2007; 8: 775-780.
62. Xue L, Ranjan N, Arya DP. Synthesis and spectroscopic studies of the aminoglycoside (Neomycin)-perylene conjugate binding to human telomeric DNA. Biochemistry 2011; 50: 2838-2849.
63. Masiero S, Trotta R, Pieraccini S, et al. A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures. Org Biomol Chem 2010; 8: 2683-2692.
64. Nadai M, Doria F, Di Antonio M, et al. Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex. Biochimie 2011; 93: 1328-1340.
65. Micheli E, Martufi M, Cacchione S, De Santis P, Savino M. Self-organization of G-quadruplex structures in the hTERT core promoter stabilized by polyaminic side chain perylene derivatives. Biophys Chem 2010; 153: 43-53.
66. Linder J, Garner TP, Williams HEL, Searle MS, Moody CJ. Telomestatin: Formal total synthesis and cation-mediated interaction of its seco-derivatives with G-quadruplexes. J Am Chem Soc 2010; 133: 1044-1051.
67. Garner TP, Williams HEL, Gluszyk KI, et al. Selectivity of small molecule ligands for parallel and anti-parallel DNA G-quadruplex structures. Org Biomol Chem 2009; 7: 4194-4200.
68. Palumbo SL, Ebbinghaus SW, Hurley LH. Formation of a unique end-to-end stacked pair of G-quadruplexes in the hTERT core promoter with implications for inhibition of telomerase by G-quadruplex-interactive ligands. J Am Chem Soc 2009; 131: 10878-10891.
69. White EW, Tanious F, Ismail MA, et al. Structure-specific recognition of quadruplex DNA by organic cations: Influence of shape, substituents and charge. Biophys Chem 2007; 126: 140-153.
70. Jantos K, Rodriguez R, Ladame S, Shirude PS, Balasubramanian S. Oxazole-based peptide macrocycles: A new class of G-quadruplex binding ligands. J Am Chem Soc 2006; 128: 13662-13663.
71. Wu WB, Chen SH, Hou JQ, et al. Disubstituted 2-phenyl-benzopyranopyrimidine derivatives as a new type of highly selective ligands for telomeric G-quadruplex DNA. Org Biomol Chem 2011; 9: 2975-2986.
72. Li Q, Xiang J, Li X, et al. Stabilizing parallel G-quadruplex DNA by a new class of ligands: Two non-planar alkaloids through interaction in lateral grooves. Biochimie 2009; 91: 811-819.
73. Wang L, Wen Y, Liu J, Zhou J, Li C, Wei C. Promoting the formation and stabilization of human telomeric G-quadruplex DNA, inhibition of telomerase and cytotoxicity by phenanthroline derivatives. Org Biomol Chem 2011; 9: 2648-2653.
74. Romera C, Bombarde O, Bonnet R, et al. Improvement of porphyrins for G-quadruplex DNA targeting. Biochimie 2011; 93: 1310-1317.
75. Keating LR, Szalai VA. Parallel-stranded guanine quadruplex interactions with a copper cationic porphyrin. Biochemistry 2004; 43: 15891-15900.
76. Shinohara KI, Sannohe Y, Kaieda S, et al. A chiral wedge molecule inhibits telomerase activity. J Am Chem Soc 2010; 132: 3778-3782.
77. Waller ZAE, Sewitz SA, Hsu STD, Balasubramanian S. A small molecule that disrupts G-quadruplex DNA structure and enhances gene expression. J Am Chem Soc 2009; 131: 12628-12633.
78. Ma Y, Ou TM, Tan JH, et al. Quinolino-benzo-[5, 6]-dihydroisoquindolium compounds derived from berberine: A new class of highly selective ligands for G-quadruplex DNA in c-myc oncogene. Eur J Med Chem 2011; 46: 1906-1913.
79. Sun D, Liu WJ, Guo K, et al. The proximal promoter region of the human vascular endothelial growth factor gene has a G-quadruplex structure that can be targeted by G-quadruplex-interactive agents. Mol Cancer Ther 2008; 7: 880-889.
80. Cogoi S, Xodo LE. G-quadruplex formation within the promoter of the KRAS proto-oncogene and its effect on transcription. Nucleic Acids Res 2006; 34: 2536-2549.
81. Owen EA, Keniry MA. Exploring the binding of calothrixin A to the G-quadruplex from the c-myc oncogene promotor. Aust J Chem 2009; 62: 1544-1549.
82. Alzeer J, Luedtke NW. PH-mediated fluorescence and G-quadruplex binding of amido phthalocyanines. Biochemistry 2010; 49: 4339-4348.
83. Dembska A, Juskowiak B. The fluorescence properties and lifetime study of G-quadruplexes single- and double-labeled with pyrene. J Fluoresc 2010; 20: 1029-1035.
84. Wei C, Wang L, Jia G, Zhou J, Han G, Li C. The binding mode of porphyrins with cation side arms to (TG4T)4 G-quadruplex: Spectroscopic evidence. Biophys Chem 2009; 143: 79-84.
85. Largy E, Hamon F, Teulade-Fichou MP. Development of a high-throughput G4-FID assay for screening and evaluation of small molecules binding quadruplex nucleic acid structures. Anal Bioanal Chem 2011: 400: 3419-3427.
86. Tran PLT, Largy E, Hamon F, Teulade-Fichou MP, Mergny JL. Fluorescence intercalator displacement assay for screening G4 ligands towards a variety of G-quadruplex structures. Biochimie 2011; 93: 1288-1296.
87. Chan DSH, Yang H, Kwan MHT, et al. Structure-based optimization of FDA-approved drug methylene blue as a c-myc G-quadruplex DNA stabilizer. Biochimie 2011; 93: 1055-1064.
88. De Cian A, Guittat L, Kaiser M, et al. Fluorescence-based melting assays for studying quadruplex ligands. Methods 2007; 42: 183-195.
89. Bertrand H, Bombard S, Monchaud D, Teulade-Fichou MP. A platinum-quinacridine hybrid as a G-quadruplex ligand. J Biol Inorg Chem 2007; 12: 1003-1014.
90. Sparapani S, Bellini S, Gunaratnam M, et al. Bis-guanylhydrazone diimidazo[1,2-a:1,2-c]pyrimidine as a novel and specific G-quadruplex binding motif. Chem Commun 2010; 46: 5680-5682.
91. Laronze-Cochard M, Kim YM, Brassart B, Riou JF, Laronze JY, Sapi J. Synthesis and biological evaluation of novel 4,5- bis(dialkylaminoalkyl)-substituted acridines as potent telomeric G-quadruplex ligands. Eur J Med Chem 2009; 44: 3880-3888.
92. Musetti C, Lucatello L, Bianco S, Krapcho AP, Cadamuro SA, Palumbo M, Sissi C. Metal ion-mediated assembly of effective phenanthroline-based G-quadruplex ligands. Dalton Trans 2009: 3657-3660.
93. Chen Z, Zheng KW, Hao YH, Tan Z. Reduced or diminished stabilization of the telomere G-quadruplex and inhibition of telomerase by small chemical ligands under molecular crowding condition. J Am Chem Soc 2009; 131: 10430-10438.
94. Ma Y, Ou TM, Tan JH, et al. Synthesis and evaluation of 9-O-substituted berberine derivatives containing aza-aromatic terminal group as highly selective telomeric G-quadruplex stabilizing ligands. Bioorg Med Chem Lett 2009; 19: 3414-3417.
95. Peng D, Tan JH, Chen SB, Ou TM, Gu LQ, Huang ZS. Bisaryldiketene derivatives: A new class of selective ligands for c-myc G-quadruplex DNA. Bioorg Med Chem 2010; 18: 8235-8242.
96. Stefan L, Guedin A, Amrane S, et al. DOTASQ as a prototype of nature-inspired G-quadruplex ligand. Chem Commun 2011; 47: 4992-4994.
97. Wang XD, Ou TM, Lu YJ, et al. Turning off transcription of the bcl-2 gene by stabilizing the bcl-2 promoter quadruplex with quindoline derivatives. J Med Chem 2010; 53: 4390-4398.
98. Bejugam M, Gunaratnam M, Müller S, Sanders DA, Sewitz S, Fletcher JA, Neidle S, Balasubramanian S. Targeting the c-Kit promoter g-quadruplexes with 6-substituted indenoisoquinolines. ACS Med Chem Lett 2010; 1: 306-310.
99. Green JJ, Ladame S, Ying L, Klenerman D, Balasubramanian S. Investigating a quadruplex - Ligand interaction by unfolding kinetics. J Am Chem Soc 2006; 128: 9809-9812.
100. Jena PV, Shirude PS, Okumus B, et al. G-quadruplex DNA bound by a synthetic ligand is highly dynamic. J Am Chem Soc 2009; 131: 12522-12523.
101. Pothukuchy A, Mazzitelli CL, Rodriguez ML, et al. Duplex and quadruplex DNA binding and photocleavage by trioxatriangulenium ion. Biochemistry 2005; 44: 2163-2172.
102. Zhang XF, Zhang HJ, Xiang JF, et al. The binding modes of carbazole derivatives with telomere G-quadruplex. J Mol Struct 2010; 982: 133-138.
103. Bieri M, Kwan AH, Mobli M, King GF, MacKay JP, Gooley PR. Macromolecular NMR spectroscopy for the non-spectroscopist: Beyond macromolecular solution structure determination. FEBS J 2011; 278: 704-715.
104. Kwan AH, Mobli M, Gooley PR, King GF, MacKay JP. Macromolecular NMR spectroscopy for the non-spectroscopist. FEBS J 2011; 278: 687-703.
105. Fedoroff OY, Salazar M, Han H, Chemeris VV, Kerwin SM, Hurley LH. NMR-Based model of a telomerase-inhibiting compound bound to G-quadruplex DNA. Biochemistry 1998; 37: 12367-12374.
106. Rangan A, Fedoroff OY, Hurley LH. Induction of duplex to G-quadruplex transition in the c-myc promoter region by a small molecule. J Biol Chem 2001; 276: 4640-4646.
107. Kern JT, Thomas PW, Kerwin SM. The relationship between ligand aggregation and G-quadruplex DNA selectivity in a series of 3,4,9,10-perylenetetracarboxylic acid diimides. Biochemistry 2002; 41: 11379-11389.
108. Gavathiotis E, Heald RA, Stevens MFG, Searle MS. Drug recognition and stabilisation of the parallel-stranded DNA quadruplex d(TTAGGGT)4 containing the human telomeric repeat. J Mol Biol 2003; 334: 25-36.
109. [109] Pagano B, Virno A, Mattia CA, Mayol L, Randazzo A, Giancola C. Targeting DNA quadruplexes with distamycin A and its derivatives: An ITC and NMR study. Biochimie 2008; 90: 1224-1232.
110. Ferreira R, Artali R, Farrera-Sinfreu J, et al. Acridine and quindoline oligomers linked through a 4-aminoproline backbone prefer G-quadruplex structures. Biochim Biophys Acta 2011; 1810: 769-776.
111. Shang Q, Xiang JF, Zhang XF, Sun HX, Li L, Tang YL. Fishing potential antitumor agents from natural plant extracts pool by dialysis and G-quadruplex recognition. Talanta 2011; 85: 820-823.
112. Dash J, Shirude PS, Hsu STD, Balasubramanian S. Diarylethynyl amides that recognize the parallel conformation of genomic promoter DNA G-quadruplexes. J Am Chem Soc 2008; 130: 15950-15956.
113. Haider SM, Neidle S, Parkinson GN. A structural analysis of G-quadruplex/ligand interactions. Biochimie 2011; 93: 1239-1251.
114. Martino L, Virno A, Pagano B, et al. Structural and thermodynamic studies of the interaction of distamycin A with the parallel quadruplex structure [d(TGGGGT)]4. J Am Chem Soc 2007; 129: 16048-16056.
115. Hounsou C, Guittat L, Monchaud D, et al. G-quadruplex recognition by quinacridines: A SAR, NMR, and biological study. ChemMedChem 2007; 2: 655-666.
116. Trotta R, De Tito S, Lauri I, et al. A more detailed picture of the interactions between virtual screening-derived hits and the DNA G-quadruplex: NMR, molecular modelling and ITC studies. Biochimie 2011; 93: 1280-1287.
117. Beck JL, Colgrave ML, Ralph SF, Sheil MM. Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. Mass Spectrom Rev 2001; 20: 61-87.
118. Brodbelt JS. Evaluation of DNA/Ligand Interactions by Electrospray Ionization Mass Spectrometry. Annu Rev Anal Chem 2010; 3: 67-87.
119. [119] Yuan G, Zhang Q, Zhou J, Li H. Mass spectrometry of G-quadruplex DNA: Formation, recognition, property, conversion, and conformation. Mass Spectrom Rev, in press (DOI: 10.1002/mas.20315).
120. Nagesh N, Krishnaiah A, Dhople VM, Sundaram CS, Jagannadham MV. Noncovalent interaction of G-quadruplex DNA with acridine at low concentration monitored by MALDI-TOF mass spectrometry. Nucleosides Nucleotides Nucleic Acids 2007; 26: 303-315.
121. Gabelica V. Determination of equilibrium association constants of ligand-DNA complexes by electrospray mass spectrometry. Methods Mol Biol 2010; 613: 89-101.
122. Gabelica V, Baker ES, Teulade-Fichou MP, De Pauw E, Bowers MT. Stabilization and structure of telomeric and c-myc region intramolecular G-quadruplexes: The role of central cations and small planar ligands. J Am Chem Soc 2007; 129: 895-904.
123. Rosu F, De Pauw E, Guittat L, et al. Selective interaction of ethidium derivatives with quadruplexes: An equilibrium dialysis and electrospray ionization mass spectrometry analysis. Biochemistry 2003; 42: 10361-10371.
124. Casagrande V, Alvino A, Bianco A, Ortaggi G, Franceschin M. Study of binding affinity and selectivity of perylene and coronene derivatives towards duplex and quadruplex dma by ESI-MS. J Mass Spectrom 2009; 44: 530-540.
125. Li H, Zhang Q, Yuan G. Investigation of the formation and recognition of a dimeric G-quadruplex in the promoter of Bcl-2 proto-oncogene by electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2010; 24: 393-395.
126. Li H, Yuan G. Electrospray ionization mass spectrometry probing of formation and recognition of the g-quadruplex in the proximal promoter of the human vascular endothelial growth factor gene. Rapid Commun Mass Spectrom 2010; 24: 2030-2034.
127. Amato J, Oliviero G, Borbone N, et al. Ligand binding to tetra-end-linked (TGGGGT)4 G-quadruplexes: an electrospray mass spectroscopy study. Nucleic Acids Symp Ser (Oxf) 2008; 52: 165-166.
128. Gornall KC, Samosorn S, Tanwirat B, et al. A mass spectrometric investigation of novel quadruplex DNA-selective berberine derivatives. Chem Commun 2010; 46: 6602-6604.
129. Gornall KC, Samosorn S, Talib J, Bremner JB, Beck JL. Selectivity of an indolyl berberine derivative for tetrameric G-quadruplex DNA. Rapid Commun Mass Spectrom 2007; 21: 1759-1766.
130. Mazzitelli CL, Brodbelt JS, Kern JT, Rodriguez M, Kerwin SM. Evaluation of binding of perylene diimide and benzannulated perylene diimide ligands to DNA by electrospray ionization mass spectrometry. J Am Soc Mass Spectrom 2006; 17: 593-604.
131. Zhou J, Yuan G. Specific recognition of human telomeric G-Quadruplex DNA with small molecules and the conformational analysis by ESI mass spectrometry and circular dichroism spectropolarimetry. Chemistry 2007; 13: 5018-5023.
132. Tera M, Iida K, Ikebukuro K, Seimiya H, Shin-Ya K, Nagasawa K. Visualization of G-quadruplexes by using a BODIPY-labeled macrocyclic heptaoxazole. Org Biomol Chem 2010; 8: 2749-2755.
133. Moses JE, Ritson DJ, Zhang F, et al. A click chemistry approach to C3 symmetric, G-quadruplex stabilising ligands. Org Biomol Chem 2010; 8: 2926-2930.
134. David WM, Brodbelt J, Kerwin SM, Wang Thomas P. Investigation of quadruplex oligonucleotide - Drug interactions by electrospray ionization mass spectrometry. Anal Chem 2002; 74: 2029-2033.
135. Rosu F, Gabelica V, Shin-Ya K, De Pauw E. Telomestatin-induced stabilization of the human telomeric DNA quadruplex monitored by electrospray mass spectrometry. Chem Commun 2003; 9: 2702-2703.
136. Bianco S, Musetti C, Waldeck A, Sparapani S, Seitz JD, Krapcho AP, Palumbo M, Sissi C. Bis-phenanthroline derivatives as suitable scaffolds for effective G-quadruplex recognition. Dalton Trans 2010; 39: 5833-5841.
137. Homola J, Yee SS, Gauglitz G. Surface plasmon resonance sensors: review. Sensor Actuat B-Chem 1999; 54: 3-15.
138. Karlsson R. SPR for molecular interaction analysis: A review of emerging application areas. J Mol Recognit 2004; 17: 151-161.
139. Murat P, Bonnet R, Van Der Heyden A, et al. Template-Assembled Synthetic G-Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies. Chemistry 2010; 16: 6106-6114.
140. Waller ZAE, Shirude PS, Rodriguez R, Balasubramanian S. Triarylpyridines: A versatile small molecule scaffold for G-quadruplex recognition. Chem Commun 2008: 1467-1469.
141. Drewe WC, Nanjunda R, Gunaratnam M, et al. Rational design of substituted diarylureas: A scaffold for binding to G-quadruplex motifs. J Med Chem 2008; 51: 7751-7767.
142. Li G, Huang J, Zhang M, et al. Bis(benzimidazole)pyridine derivative as a new class of G-quadruplex inducing and stabilizing ligand. Chem Commun 2008: 4564-4566.
143. Dixon IM, Lopez F, Tejera AM, et al. A G-quadruplex ligand with 10000-fold selectivity over duplex DNA. J Am Chem Soc 2007; 129: 1502-3.
144. Nielsen MC, Borch J, Ulven T. Design, synthesis and evaluation of 4,7-diamino-1,10-phenanthroline G-quadruplex ligands. Bioorg Med Chem 2009; 17: 8241-8246.
145. Halder K, Chowdhury S. Quadruplex-coupled kinetics distinguishes ligand binding between G4 DNA motifs. Biochemistry 2007; 46: 14762-14770.
146. Pillet F, Romera C, Trevisiol E, et al. Surface plasmon resonance imaging (SPRi) as an alternative technique for rapid and quantitative screening of small molecules, useful in drug discovery. Sensor Actuat B-Chem 2011; 157: 304-309.
147. Salim NN, Feig AL. Isothermal titration calorimetry of RNA. Methods 2009; 47: 198-205.
148. Erra E, Petraccone L, Esposito V, et al. Interaction of porphyrin with G-quadruplex structures. Nucleosides Nucleotides Nucleic Acids 2005; 24: 753-756.
149. Pagano B, Mattia CA, Virno A, Randazzo A, Mayol L, Giancola C. Thermodynamic analysis of quadruplex DNA-drug interaction. Nucleosides Nucleotides Nucleic Acids 2007; 26: 761-765.
150. Hudson JS, Brooks SC, Graves DE. Interactions of actinomycin D with human telomeric G-quadruplex DNA. Biochemistry 2009; 48: 4440-4447.
151. Ren J, Chaires JB. Rapid screening of structurally selective ligand binding to nucleic acids. Methods Enzymol. 2001; 340: 99-108.
152. Ragazzon PA, Garbett NC, Chaires JB. Competition dialysis: A method for the study of structural selective nucleic acid binding. Methods 2007; 42: 173-182.
153. Zhang WJ, Ou TM, Lu YJ, et al. 9-Substituted berberine derivatives as G-quadruplex stabilizing ligands in telomeric DNA. Bioorg Med Chem 2007; 15: 5493-5501.
154. Alcaro S, Artese A, Iley JN, et al. Rational design, synthesis, biophysical and antiproliferative evaluation of fluorenone derivatives with DNA G-quadruplex binding properties. ChemMedChem 2010; 5: 575-583.
155. Granotier C, Pennarun G, Riou L, et al. Preferential binding of a G-quadruplex ligand to human chromosome ends. Nucleic Acids Res 2005; 33: 4182-4190.
156. Martin R. Gel Electrophoresis: Nucleic Acids. Oxford, UK: Garland Science 1996.
157. Araya F, Skellern GG, Waigh RD. Quantification of binding data using capillary electrophoresis. Methods Mol Biol 2010; 613: 71-88.
158. Araya F, Huchet G, McGroarty I, Skellern GG, Waigh RD. Capillary electrophoresis for studying drug-DNA interactions. Methods 2007; 42: 141-149.
159. Hamdan II, Skellern GG, Waigh RD. Use of capillary electrophoresis in the study of ligand-DNA interactions. Nucleic Acids Res 1998; 26: 3053-3058.
160. McGroarty I, Hamdan II, Skellern GG, Waigh RD. Determination of sequence binding preference of ligands with DNA using free solution capillary electrophoresis. J Pharm Pharmacol 2000; 52: 144.
161. Smith JS, Johnson FB. Isolation of G-quadruplex DNA using NMM-sepharose affinity chromatography. Methods Mol Biol 2010; 608: 207-221.
162. Jin Y, Li H, Liu P. Label-free electrochemical selection of G-quadruplex-binding ligands based on structure switching. Biosens Bioelectron 2010; 25: 2669-2674.
163. Liu XQ, Jin Y, Wang Y, Qiao Y. Electrochemical selection of G-quadruplex-binding ligands based on structure-switching of telomeric DNA. Anal Methods 2011; 3: 1270-1273.
164. Yang Q, Nie Y, Zhu X, Liu X, Li G. Study on the electrocatalytic activity of human telomere G-quadruplex-hemin complex and its interaction with small molecular ligands. Electrochim Acta 2009; 55: 276-280.
165. Zhang KJ, Liu WY. Electrochemical and spectroscopic study on the interaction between G-quadruplex DNA and (R)-/(S)-2-(5-fluorouracil-1-acetyl) amido-1, 5-dimethyl glutarate. Int J Electrochem Sc 2011; 6: 4006-4015.
166. Jin Y, Qiao Y. A label-free method for identifying electroactive G-quadruplex-binding ligand. Electrochem Commun 2010; 12: 966-969.
167. Jennerwein MM, Eastman A. A polymerase chain reaction-based method to detect cisplatin adducts in specific genes. Nucleic Acids Res 1991; 19: 6209-6214.
168. Gomez D, Lamarteleur T, Lacroix L, Mailliet P, Mergny JL, Riou JF. Telomerase downregulation induced by the G-quadruplex ligand 12459 in A549 cells is mediated by hTERT RNA alternative splicing. Nucleic Acids Research 2004; 32: 371-379.
169. Lemarteleur T, Gomez D, Paterski R, Mandine E, Mailliet P, Riou JF. Stabilization of the c-myc gene promoter quadruplex by specific ligands' inhibitors of telomerase. Biochem Biophys Res Commun 2004; 323: 802-808.
170. Wang JT, Zheng XH, Xia Q, Mao ZW, Ji LN, Wang K. 1,10-Phenanthroline platinum(II) complex: A simple molecule for efficient G-quadruplex stabilization. Dalton Trans 2010; 39: 7214-7216.
171. Evison BJ, Phillips DR, Cutts SM. In vitro transcription assay for resolution of drug-DNA interactions at defined DNA sequences. Methods Mol Biol 2010; 613: 207-222.
172. Kim NW, Piatyszek MA, Prowse KR, et al. Specific association of human telomerase activity with immortal cells and cancer. Science 1994; 266: 2011-2015.
173. Reed J, Gunaratnam M, Beltran M, Reszka AP, Vilar R, Neidle S. TRAP-LIG, a modified telomere repeat amplification protocol assay to quantitate telomerase inhibition by small molecules. Anal Biochem 2008; 380: 99-105.
174. Gunaratnam M, Greciano O, Martins C, et al. Mechanism of acridine-based telomerase inhibition and telomere shortening. Biochem Pharmacol 2007; 74: 679-689.
175. De Cian A, DeLemos E, Mergny JL, Teulade-Fichou MP, Monchaud D. Highly efficient G-quadruplex recognition by bisquinolinium compounds. J Am Chem Soc 2007; 129: 1856-1857.
176. Moorhouse AD, Haider S, Gunaratnam M, Munnur D, Neidle S, Moses JE. Targeting telomerase and telomeres: A click chemistry approach towards highly selective G-quadruplex ligands. Mol BioSyst 2008; 4: 629-642.
177. Guittat L, De Cian A, Rosu F, et al. Ascididemin and meridine stabilise G-quadruplexes and inhibit telomerase in vitro. Biochim Biophys Acta 2005; 1724: 375-384.
178. Han H, Hurley LH, Salazar M. A DNA polymerase stop assay for G-quadruplex-interactive compounds. Nucleic Acids Res 1999; 27: 537-542.
179. Rubis B, Kaczmarek M, Szymanowska N, et al. The biological activity of G-quadruplex DNA binding papaverine-derived ligand in breast cancer cells. Invest New Drugs 2009; 27: 289-296.
180. Rezler EM, Seenisamy J, Bashyam S, et al. Telomestatin and diseleno sapphyrin bind selectively to two different forms of the human telomeric G-quadruplex structure. J Am Chem Soc 2005; 127: 9439-9447.
181. Hampshire AJ, Rusling DA, Broughton-Head VJ, Fox KR. Footprinting: A method for determining the sequence selectivity, affinity and kinetics of DNA-binding ligands. Methods 2007; 42: 128-140.
182. Hampshire AJ, Fox KR. The effects of local DNA sequence on the interaction of ligands with their preferred binding sites. Biochimie 2008; 90: 988-998.