Luminescent G-quadruplex probes

Current Pharmaceutical Design

Volumn 18, Issue 14, 2012, Pages 2058-2075

  Ma, Dik Lung ^a   Chan, Daniel Shiu Hin ^a   Yang, Hui ^a   He, Hong Zhang ^a   Leung, Chung Hang ^b,c  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b UNIVERSITY OF MACAU   (Macao)

^c University of Macau   (Macao)

Author keywords

Detection; DNA; G quadruplex; Luminescent probes; Small molecules

Indexed keywords

ACRIDINE; BERBERINE; CARBAZOLE DERIVATIVE; CARBOCYANINE; ENZYME INHIBITOR; ETHIDIUM; FLUORESCENT DYE; GUANINE QUADRUPLEX; LUMINESCENT AGENT; METAL COMPLEX; PORPHYRIN; PROTOPORPHYRIN; RUTHENIUM COMPLEX; SINGLE STRANDED DNA; TELOMERASE INHIBITOR; TELOMESTATIN; THIAZOLE ORANGE; TRIPHENYLMETHANE; URACIL DNA GLYCOSIDASE;

BIOSENSOR; CANCER CELL; CELL STRAIN MCF 7; CHROMATOGRAPHY; CIRCULAR DICHROISM; CONFOCAL MICROSCOPY; CRYSTAL STRUCTURE; CYTOTOXICITY; DNA PROBE; DNA SEQUENCE; DNA STRUCTURE; FLUORESCENCE SPECTROSCOPY; GEL ELECTROPHORESIS; HIGH THROUGHPUT SCREENING; HUMAN; IMAGING; MOLECULAR BEACON; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; QUANTUM YIELD; REVIEW; SENSITIVITY ANALYSIS; SPECTROSCOPY; TELOMERE SHORTENING;

EID: 84860131858     PISSN: 13816128     EISSN: 18734286     Source Type: Journal    
DOI: 10.2174/138161212799958314     Document Type: Review

References (85)

1. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 2006; 34: 5402-5415.
2. Ambrus A, Chen D, Dai J, Bialis T, Jones RA, Yang D. Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res 2006; 34: 2723-2735.
3. Collie GW, Parkinson GN. The application of DNA and RNA G-quadruplexes to therapeutic medicines. Chem Soc Rev 2011.
4. Todd AK, Johnston M, Neidle S. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res 2005; 33: 2901-2907.
5. Huppert JL, Balasubramanian S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res 2005; 33: 2908-2916.
6. Rawal P, Kummarasetti VB, Ravindran J, et al. Genome-wide prediction of G4 DNA as regulatory motifs: role in Escherichia coli global regulation. Genome Res 2006; 16: 644-655.
7. Huppert JL, Balasubramanian S. G-quadruplexes in promoters throughout the human genome. Nucleic Acids Res 2007; 35: 406-413.
8. Gonzalez V, Hurley LH. The c-MYC NHE III1: function and regulation. Annu Rev Pharmacol Toxicol 2010; 50: 1111-29.
9. Dai J, Dexheimer TS, Chen D, et al. An Intramolecular G-Quadruplex Structure with Mixed Parallel/Antiparallel G-Strands Formed in the Human BCL-2 Promoter Region in Solution. J Am Chem Soc 2006; 128: 1096-1098.
10. 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.
11. Rankin S, Reszka AP, Huppert J, et al. Putative DNA Quadruplex Formation within the Human c-kit Oncogene. J Am Chem Soc 2005; 127: 10584-10589.
12. Eddy J, Maizels N. Conserved elements with potential to form polymorphic G-quadruplex structures in the first intron of human genes. Nucleic Acids Res 2008; 36: 1321-1333.
13. Balasubramanian S, Hurley LH, Neidle S. Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov 2011; 10: 261-275.
14. Zahler AM, Williamson JR, Cech TR, Prescott DM. Inhibition of telomerase by G-quartet DNA structures. Nature 1991; 350: 718-720.
15. Neidle S, Parkinson G. Telomere maintenance as a target for anti-cancer drug discovery. Nat Rev Drug Discov 2002; 1: 383-393.
16. Mergny JL, Riou JF, Maillieet P, Teulade-Fichou MP, Gilson E. Natural and pharmacological regulation of telomerase. Nucleic Acids Res 2002; 30: 839-865.
17. Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40: 2719-2740.
18. Neidle S. Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS Journal 2010; 277: 1118-1125.
19. Paeschke K, Simonsson T, Postberg J, Rhodes D, Lipps HJ. Te-lomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat Struct Mol Biol 2005; 12: 847-854.
20. Tang J, Kan Zy, Yao Y, Wang Q, Hao Yh, Tan Z. G-quadruplex preferentially forms at the very 3' end of vertebrate telomeric DNA. Nucleic Acids Res 2008; 36: 1200-1208.
21. Neidle S. The structures of quadruplex nucleic acids and their drug complexes. Curr Opin Struct Biol 2009; 19: 239-250.
22. Webba da Silva M. Geometric Formalism for DNA Quadruplex Folding. Chem - Eur J 2007; 13: 9738-9745.
23. Monchaud D, Teulade-Fichou MP. A hitchhiker's guide to G-quadruplex ligands. Org Biomol Chem 2008; 6: 627-636.
24. Haider SM, Neidle S, Parkinson GN. A structural analysis of G-quadruplex/ligand interactions. Biochimie 2011; 93: 1239-1251.
25. Chen Q, Kuntz ID, Shafer RH. Spectroscopic recognition of gua-nine dimeric hairpin quadruplexes by a carbocyanine dye. Proc Natl Acad Sci USA 1996; 93: 2635-2639.
26. Lubitz I, Zikich D, Kotlyar A. Specific High-Affinity Binding of Thiazole Orange to Triplex and G-Quadruplex DNA. Biochemistry 2010; 49: 3567-3574.
27. Monchaud D, Allain C, Teulade-Fichou M-P. Development of a fluorescent intercalator displacement assay (G4-FID) for establishing quadruplex-DNA affinity and selectivity of putative ligands. Bioorg Med Chem Lett 2006; 16: 4842-4845.
28. 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.
29. Largy E, Hamon F, Teulade-Fichou M-P. 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.
30. Allain C, Monchaud D, Teulade-Fichou M-P. FRET Templated by G-Quadruplex DNA: A Specific Ternary Interaction Using an Original Pair of Donor/Acceptor Partners. J Am Chem Soc 2006; 128: 11890-11893.
31. Nakayama S, Kelsey I, Wang J, et al. Thiazole Orange-Induced c-di-GMP Quadruplex Formation Facilitates a Simple Fluorescent Detection of This Ubiquitous Biofilm Regulating Molecule. J Am Chem Soc 2011; 133: 4856-4864.
32. Hengge R. Principles of c-di-GMP signalling in bacteria. Nat Rev Microbiol 2009; 7: 263-273.
33. Römling U, Gomelsky M, Galperin MY. C-di-GMP: the dawning of a novel bacterial signalling system. Mol Microbiol 2005; 57: 629-639.
34. Yang P, De Cian A, Teulade-Fichou M-P, Mergny JL, Monchaud D. Engineering Bisquinolinium/Thiazole Orange Conjugates for Fluorescent Sensing of G-Quadruplex DNA. Angew Chem Int Ed 2009; 48: 2188-2191.
35. Yang Q, Xiang J, Yang S, Li Q, et al. Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism. Nucleic Acids Res 2010; 38: 1022-1033.
36. Yang Q, Xiang J, Yang S, et al. Recognizing Hybrid/Mixed G-quadruplex in Human Telomeres by Using a Cyanine Dye Su-pramolecule with Confocal Laser Scanning Microscopy. Chin J Chem 2010; 28: 1126-1132.
37. Kovalska V, Losytskyy M, Yarmoluk S, Lubitz I, Kotlyar A. Mono and Trimethine Cyanines Cyan 40 and Cyan 2 as Probes for Highly Selective Fluorescent Detection of Non-canonical DNA Structures. J Fluoresc 2011; 21: 223-230.
38. Meguellati K, Koripelly G, Ladame S. DNA-Templated Synthesis of Trimethine Cyanine Dyes: A Versatile Fluorogenic Reaction for Sensing G-Quadruplex Formation. Angew Chem Int Ed 2010; 49: 2738-2742.
39. Arthanari H, Basu S, Kawano TL, Bolton PH. Fluorescent dyes specific for quadruplex DNA. Nucleic Acids Res 1998; 26: 3724-3728.
40. 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.
41. Parkinson GN, Ghosh R, Neidle S. Structural Basis for Binding of Porphyrin to Human Telomeres. Biochemistry 2007; 46: 2390-2997.
42. Hu D, Pu F, Huang Z, Ren J, Qu X. A Quadruplex-Based, Label-Free, and Real-Time Fluorescence Assay for RNase H Activity and Inhibition. Chem - Eur J 2010; 16: 2605-2610.
43. Hu D, Huang Z, Pu F, Ren J, Qu X. A Label-Free, Quadruplex-Based Functional Molecular Beacon (LFG4-MB) for Fluorescence Turn-On Detection of DNA and Nuclease. Chem - Eur J 2011; 17: 1635-1641.
44. Li T, Wang E, Dong S. Parallel G-Quadruplex-Specific Fluorescent Probe for Monitoring DNA Structural Changes and Label-Free Detection of Potassium Ion. Anal Chem 2010; 82: 7576-7580.
45. Zhao P, Xu LC, Huang JW, Fu B, Yu HC, Ji LN. Cationic porphy-rin-anthraquinone dyads: Modes of interaction with G-quadruplex DNA. Dyes Pigm 2009; 83: 81-87.
46. Koeppel F, Riou JF, Laoui A, et al. Ethidium derivatives bind to G-quartets, inhibit telomerase and act as fluorescent probes for quad-ruplexes. Nucleic Acids Res 2001; 29: 1087-1096.
47. 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.
48. Chang CC, Wu JY, Chien CW, et al. A fluorescent carbazole derivative: high sensitivity for quadruplex DNA. Anal Chem 2003; 75: 6177-6183.
49. Yang D-Y, Sheu S-Y. Interaction between Human Telomere and a Carbazole Derivative: A Molecular Dynamics Simulation of a Quadruplex Stabilizer and Telomerase Inhibitor. J Phys Chem A. 2007; 111: 9224-9232.
50. Chang CC, Kuo IC, Ling IF, et al. Detection of quadruplex DNA structures in human telomeres by a fluorescent carbazole derivative. Anal Chem 2004; 76: 4490-4494.
51. Huang FC, Chang CC, Lou PJ, et al. G-Quadruplex Stabilizer 3,6-Bis(1-Methyl-4-Vinylpyridinium)Carbazole Diiodide Induces Accelerated Senescence and Inhibits Tumorigenic Properties in Cancer Cells. Mol Cancer Res 2008; 6: 955-964.
52. Tsai YL, Wang ZF, Chen WW, Chang TC. Emulsified BMVC derivative induced filtration for G-quadruplex DNA structural separation. Nucleic Acids Res 2011.
53. Chang CC, Chu JF, Kao FJ, et al. Verification of Antiparallel G-Quadruplex Structure in Human Telomeres by Using Two-Photon Excitation Fluorescence Lifetime Imaging Microscopy of the 3,6-Bis(1-methyl-4-vinylpyridinium)carbazole Diiodide Molecule. Anal Chem 2006; 78: 2810-2815.
54. Chang CC, Chien CW, Lin YH, Kang CC, Chang TC. Investigation of spectral conversion of d(TTAGGG)4 and d(TTAGGG)13 upon potassium titration by a G-quadruplex recognizer BMVC molecule. Nucleic Acids Res 2007; 35: 2846-2860.
55. Dumat B, Bordeau G, Faurel-Paul E, et al. N-phenyl-carbazole-based two-photon fluorescent probes: Strong sequence dependence of the duplex vs quadruplex selectivity. Biochimie 2011; 93: 1209-1218.
56. Bhasikuttan AC, Mohanty J, Pal H. Interaction of malachite green with guanine-rich single-stranded DNA: preferential binding to a G-quadruplex. Angew Chem Int Ed 2007; 46: 9305-9307.
57. Kong DM, Ma YE, Wu J, Shen HX. Discrimination of G-quadruplexes from duplex and single-stranded DNAs with fluorescence and energy-transfer fluorescence spectra of crystal violet. Chem - Eur J 2009; 15: 901-909.
58. Guo JH, Zhu LN, Kong DM, Shen HX. Triphenylmethane dyes as fluorescent probes for G-quadruplex recognition. Talanta 2009; 80: 607-613.
59. Kong DM, Guo JH, Yang W, Ma YE, Shen HX. Crystal violet-G-quadruplex complexes as fluorescent sensors for homogeneous detection of potassium ion. Biosens Bioelectron 2009; 25: 88-93.
60. Guo JH, Kong DM, Shen HX. Design of a fluorescent DNA IMPLICATION logic gate and detection of Ag+ and cysteine with triphenylmethane dye/G-quadruplex complexes. Biosens Bioelectron 2010; 26: 327-332.
61. Leung CH, Chan DSH, Man BYW, et al. Simple and Convenient G-Quadruplex-Based Turn-On Fluorescence Assay for 3' -> 5' Ex-onuclease Activity. Anal Chem 2010; 83: 463-466.
62. Ma DL, Kwan MHT, Chan DSH, et al. Crystal violet as a fluorescent switch-on probe for i-motif: label-free DNA-based logic gate. Analyst 2011; 136: 2692-6.
63. He HZ, Ma VPY, Leung KH, et al. A label-free G-quadruplex-based switch-on fluorescence assay for the selective detection of ATP. Analyst 2012, DOI: 101039/c2an15999f.
64. Hong Y, Häussler M, Lam JWY, et al. Label-Free Fluorescent Probing of G-Quadruplex Formation and Real-Time Monitoring of DNA Folding by a Quaternized Tetraphenylethene Salt with Aggregation-Induced Emission Characteristics. Chem - Eur J 2008; 14: 6428-6437.
65. Huang J, Wang M, Zhou Y, et al. Visual observation of G-quadruplex DNA with the label-free fluorescent probe silole with aggregation-induced emission. Bioorg Med Chem 2009; 17: 7743-7748.
66. Tera M, Iida K, Ikebukuro K, Seimiya H, Shin-ya K, Nagasawa K. Visualization of G-quadruplexes by using a BODIPY-labeled mac-rocyclic heptaoxazole. Org Biomol Chem 2010; 8: 2749-2755.
67. Maiti S, Chaudhury NK, Chowdhury S. Hoechst 33258 binds to G-quadruplex in the promoter region of human c-myc. Biochem Bio-phys Res Commun 2003; 310: 505-512.
68. Lu YJ, Yan SC, Chan FY, et al. Benzothiazole-substituted benzo-furoquinolinium dye: a selective switch-on fluorescent probe for G-quadruplex. Chem Commun 2011; 47: 4971-4973.
69. Rajput C, Rutkaite R, Swanson L, Haq I, Thomas JA. Dinuclear Monointercalating RuII Complexes That Display High Affinity Binding to Duplex and Quadruplex DNA. Chem - Eur J 2006; 12: 4611-4619.
70. Wilson T, Williamson MP, Thomas JA. Differentiating quadru-plexes: binding preferences of a luminescent dinuclear ruthe-nium(ii) complex with four-stranded DNA structures. Org Biomol Chem 2010; 8: 2617-2621.
71. Shi S, Liu J, Yao T, et al. Promoting the Formation and Stabilization of G-Quadruplex by Dinuclear RuII Complex Ru2(obip)L4. Inorg Chem 2008; 47: 2910-2912.
72. Xu L, Zhang D, Huang J, Deng M, Zhang M, Zhou X. High fluorescence selectivity and visual detection of G-quadruplex structures by a novel dinuclear ruthenium complex. Chem Commun 2010; 46: 743-5.
73. Shi S, Zhao J, Geng X, et al. Molecular light switch for G-quadruplexes and i-motif of human telomeric DNA: [Ru(phen)2 (dppz)]2+. Dalton Trans 2010; 39: 2490-2493.
74. 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: 370-7.
75. Sun J, An Y, Zhang L, et al. Studies on synthesis, characterization, and G-quadruplex binding of Ru(II) complexes containing two dppz ligands. J Inorg Biochem 2011; 105: 149-154.
76. Ma DL, Che CM, Yan SC. Platinum(II) Complexes with Dipyrido-phenazine Ligands as Human Telomerase Inhibitors and Luminescent Probes for G-Quadruplex DNA. J Am Chem Soc 2008; 131: 1835-1846.
77. Yu C, Chan KHY, Wong KMC, Yam VW-W. Nucleic acid-induced self-assembly of a platinum(ii) terpyridyl complex: detection of G-quadruplex formation and nuclease activity. Chem Com-mun 2009: 3756-3758.
78. 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. Chem Eur J 2010; 16: 6900-6911.
79. Wu P, Ma DL, Leung CH, et al. Stabilization of G-Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down-Regulation of c-myc Oncogene Expression. Chem Eur J 2009; 15: 13008-13021.
80. Alzeer J, Vummidi BR, Roth PJC, Luedtke NW. Guanidinium-Modified Phthalocyanines as High-Affinity G-Quadruplex Fluorescent Probes and Transcriptional Regulators. Angew Chem Int Ed 2009; 48: 9362-9365.
81. Qin H, Ren J, Wang J, Luedtke NW, Wang E. G-Quadruplex-Modulated Fluorescence Detection of Potassium in the Presence of a 3500-Fold Excess of Sodium Ions. Anal Chem 2010; 82: 8356-8360.
82. Ren J, Qin H, Wang J, Luedtke N, Wang E, Wang J. Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence. Anal Bioanal Chem 2011; 399: 2763-2770.
83. Gill MR, Garcia-Lara J, Foster SJ, Smythe C, Battaglia G, Thomas JA. A ruthenium(II) polypyridyl complex for direct imaging of DNA structure in living cells. Nat Chem 2009; 1: 662-667.
84. So PTC, Dong CY, Masters BR, Berland KM. Two-photon excitation fluorescence microscopy. Annu Rev Biomed Eng 2000; 2: 399-429.
85. Denk W, Strickler J, Webb W. Two-photon laser scanning fluorescence microscopy. Science 1990; 248: 73-76.