Skip to main content
SpringerLink
Log in

Human Telomeric G-Quadruplex Structures and G-Quadruplex-Interactive Compounds

  • Protocol
  • First Online:
Telomeres and Telomerase

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1587))

Abstract

G-quadruplexes are noncanonical secondary structures formed in DNA sequences containing consecutive runs of guanines. It has been shown that the 3′ G-rich single-stranded overhangs of human telomeres can form G-quadruplex structures, and the human telomeric DNA G-quadruplexes are considered attractive targets for anticancer drugs. G-quadruplex-interactive compounds have been shown to inhibit telomerase access as well as telomere capping. Nuclear magnetic resonance (NMR) spectroscopy is a powerful method in determining the G-quadruplex structures under physiologically relevant conditions. We present the NMR and biophysical methodology used in our research group for the study of G-quadruplex structures in physiologically relevant solution and their interactions with small-molecule compounds.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Yang D, Okamoto K (2010) Structural insights into G-quadruplexes: towards new anticancer drugs. Future Med Chem 2(4):619–646

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Sen D, Gilbert W (1990) A sodium-potassium switch in the formation of four-stranded G4-DNA. Nature 344(6265):410–414

    Article  CAS  PubMed  Google Scholar 

  3. Hud NV, Plavec J (2006) The role of cations in determining quadruplex structure and stability. In: Neidle S (ed) Quadruplex Nucleic Acids. Royal Society of Chemistry, RSCPublishing, Cambridge, pp 100–130

    Google Scholar 

  4. Neidle S, Parkinson G (2002) Telomere maintenance as a target for anticancer drug discovery. Nat Rev Drug Discov 1(5):383–393

    Article  CAS  PubMed  Google Scholar 

  5. Punchihewa C, Yang DZ (2009) Therapeutic targets and drugs-G-quadruplex inhibitors. In: Hiyama K (ed) Telomeres and telomerase in cancer. Humana Press, New York, pp 251–280

    Google Scholar 

  6. Qin Y, Hurley LH (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions. Biochimie 90(8):1149–1171

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Onel B, Lin C, Yang D (2014) DNA G-quadruplex and its potential as anticancer drug target. Sci China Chem 57(12):1605–1614

    Article  CAS  Google Scholar 

  8. Henderson E, Hardin CC, Walk SK, Tinoco I Jr, Blackburn EH (1987) Telomeric DNA oligonucleotides form novel intramolecular structures containing guanine-guanine base pairs. Cell 51(6):899–908

    Article  CAS  PubMed  Google Scholar 

  9. Moyazis RK, Buckingham JM, Cram LS, Dani M, Deaven LL, Jones MD, Meyne J, Ratliff RL, Wu JR (1988) A highly conserved repetitive DNA sequence (TTAGGG)n, present at the telomere of human chromosomes. Proc Natl Acad Sci U S A 85:6622–6626

    Article  Google Scholar 

  10. Wright WE, Tesmer VM, Huffman KE, Levene SD, Shay JW (1997) Normal human chromosomes have long G-rich telomeric overhangs at one end. Genes Dev 11(21):2801–2809

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Bodnar AG, Ouellette M, Frolkis M, Holt SE, Chiu CP, Morin GB, Harley CB, Shay JW, Lichtsteiner S, Wright WE (1998) Extension of life-span by introduction of telomerase into normal human cells. Science 279(5349):349–352

    Article  CAS  PubMed  Google Scholar 

  12. Sun D, Lopez C, Von Hoff DD, Hurley LH (1998) Modulation of the catalytic activity and processivity of human telomerase from HeLa cell. Proc Am Assoc Cancer Res 39:569

    Google Scholar 

  13. Paeschke K, Simonsson T, Postberg J, Rhodes D, Lipps HJ (2005) Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nat Struct Mol Biol 12(10):847–854

    Article  CAS  PubMed  Google Scholar 

  14. Oganesian L, Bryan TM (2007) Physiological relevance of telomeric G-quadruplex formation: a potential drug target. Bioessays 29(2):155–165

    Article  CAS  PubMed  Google Scholar 

  15. Granotier C, Pennarun G, Riou L, Hoffschir F, Gauthier LR, De Cian A, Gomez D, Mandine E, Riou JF, Mergny JL, Mailliet P, Dutrillaux B, Boussin FD (2005) Preferential binding of a G-quadruplex ligand to human chromosome ends. Nucleic Acids Res 33(13):4182–4190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Chang CC, Kuo IC, Lin JJ, Lu YC, Chen CT, Back HT, Lou PJ, Chang TC (2004) A novel carbazole derivative, BMVC: a potential antitumor agent and fluorescence marker of cancer cells. Chem Biodivers 1(9):1377–1384

    Article  CAS  PubMed  Google Scholar 

  17. Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem 5(3):182–186. doi:10.1038/nchem.1548

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Chambers VS, Marsico G, Boutell JM, Di Antonio M, Smith GP, Balasubramanian S (2015) High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat Biotechnol 33(8):877–881

    Article  PubMed  Google Scholar 

  19. Harley CB, Futcher AB, Greider CW (1990) Telomeres shorten during ageing of human fibroblasts. Nature 345(6274):458–460

    Article  CAS  PubMed  Google Scholar 

  20. Greider CW, Blackburn EH (1985) Identification of a specific telomere terminal transferase activity in tetrahymena extracts. Cell 43(2 Pt 1):405–413

    Article  CAS  PubMed  Google Scholar 

  21. Kim NW, Piatyszek MA, Prowse KR, Harley CB, West MD, Ho PLC, Coviello GM, Wright WE, Weinrich SL, Shay JW (1994) Specific association of human telomerase activity with immortal cells and cancer. Science 266(5193):2011–2015

    Article  CAS  PubMed  Google Scholar 

  22. Hanahan D, Weinberg RA (2000) The hallmarks of cancer. Cell 100(1):57–70

    Article  CAS  PubMed  Google Scholar 

  23. Zahler AM, Williamson JR, Cech TR, Prescott DM (1991) Inhibition of telomerase by G-quartet DNA structures. Nature 350(6320):718–720

    Article  CAS  PubMed  Google Scholar 

  24. Wang Y, Patel DJ (1993) Solution structure of the human telomeric repeat d[AG(3)(T(2)AG(3))3] G-tetraplex. Structure 1(4):263–282

    Article  CAS  PubMed  Google Scholar 

  25. Parkinson GN, Lee MPH, Neidle S (2002) Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417(6891):876–880

    Article  CAS  PubMed  Google Scholar 

  26. Ambrus A, Chen D, Dai JX, Bialis T, Jones RA, Yang DZ (2006) Human telomeric sequence forms a hybrid-type intramolecular G-quadruplex structure with mixed parallel/antiparallel strands in potassium solution. Nucleic Acids Res 34(9):2723–2735

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Dai JX, Punchihewa C, Ambrus A, Chen D, Jones RA, Yang DZ (2007) Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Nucleic Acids Res 35(7):2440–2450

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Dai JX, Carver M, Punchihewa C, Jones RA, Yang DZ (2007) Structure of the hybrid-2 type intramolecular human telomeric G-quadruplex in K+ solution: insights into structure polymorphism of the human telomeric sequence. Nucleic Acids Res 35(15):4927–4940

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Xu Y, Noguchi Y, Sugiyama H (2006) The new models of the human telomere d[AGGG(TTAGGG)(3)] in K+ solution. Bioorg Med Chem 14(16):5584–5591

    Article  CAS  PubMed  Google Scholar 

  30. Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ (2006) Structure of the human telomere in K+ solution: an intramolecular (3+1) G-quadruplex scaffold. J Am Chem Soc 128(30):9963–9970

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Phan AT, Kuryavyi V, Luu KN, Patel DJ (2007) Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res 35(19):6517–6525

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Phan AT, Luu KN, Patel DJ (2006) Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution. Nucleic Acids Res 34(19):5715–5719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Dai J, Carver M, Yang DZ (2008) Polymorphism of human telomeric quadruplex structures. Biochimie 90(8):1172–1183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Petraccone L, Spink C, Trent JO, Garbett NC, Mekmaysy CS, Giancola C, Chaires JB (2011) Structure and stability of higher-order human telomeric quadruplexes. J Am Chem Soc 133(51):20951–20961. doi:10.1021/ja209192a

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  35. Ambrus A, Chen D, Dai JX, Jones RA, Yang DZ (2005) Solution structure of the biologically relevant g-quadruplex element in the human c-MYC promoter. implications for g-quadruplex stabilization. Biochem 44(6):2048–2058

    Article  CAS  Google Scholar 

  36. Dai JX, Chen D, Jones RA, Hurley LH, Yang DZ (2006) NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res 34(18):5133–5144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Zhang Z, Dai J, Veliath E, Jones RA, Yang DZ (2010) Structure of a two-G-tetrad intramolecular G-quadruplex formed by a variant human telomeric sequence in K+ solution: insights into the interconversion of human telomeric G-quadruplex structures. Nucleic Acids Res 38(3):1009–1021

    Article  CAS  PubMed  Google Scholar 

  38. Chen Y, Yang DZ (2012) Sequence, stability, and structure of G-quadruplexes and their interactions with drugs. Curr Protoc Nucleic Acid Chem 50:17.15.11–17.15.17

    Google Scholar 

  39. Balasubramanian S, Hurley LH, Neidle S (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat Rev Drug Discov 10(4):261–275

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Neidle S (2016) Quadruplex nucleic acids as novel therapeutic targets. J Med Chem 59(13):5987–6011

    Article  CAS  PubMed  Google Scholar 

  41. Sun DY, Thompson B, Cathers BE, Salazar M, Kerwin SM, Trent JO, Jenkins TC, Neidle S, Hurley LH (1997) Inhibition of human telomerase by a G-quadruplex-interactive compound. J Med Chem 40(14):2113–2116

    Article  CAS  PubMed  Google Scholar 

  42. Brooks TA, Hurley LH (2009) The role of supercoiling in transcriptional control of MYC and its importance in molecular therapeutics. Nat Rev Cancer 9(12):849–861

    Article  CAS  PubMed  Google Scholar 

  43. Wheelhouse RT, Han FX, Sun D, Hurley LH (1998) The interaction of telomerase inhibitory porphyrines with G-quadruplex DNA. Proc Am Assoc Cancer Res 39:430

    Google Scholar 

  44. Shin-ya K, Wierzba K, Matsuo K, Ohtani T, Yamada Y, Furihata K, Hayakawa Y, Seto H (2001) Telomestatin, a novel telomerase inhibitor from streptomyces anulatus. J Am Chem Soc 123(6):1262–1263

    Article  CAS  PubMed  Google Scholar 

  45. Read M, Cuesta J, Basra I, Harrison J, Reszka A, Gowan S, Kelland LR, Neidle S (2001) Rational design approaches to increase the potency of G-quadruplex-mediated telomerase inhibitors. Clin Cancer Res 7(11):713

    Google Scholar 

  46. Zhou G, Liu X, Li Y, Xu S, Ma C, Wu X, Cheng Y, Yu Z, Zhao G, Chen Y (2016) Telomere targeting with a novel G-quadruplex-interactive ligand BRACO-19 induces T-loop disassembly and telomerase displacement in human glioblastoma cells. Oncotarget 7(12):14925–14939

    PubMed  PubMed Central  Google Scholar 

  47. Zhang W-J, Ou T-M, Lu Y-J, Huang Y-Y, Wu W-B, Huang Z-S, Zhou J-L, Wong K-Y, Gu L-Q (2007) 9-Substituted berberine derivatives as G-quadruplex stabilizing ligands in telomeric DNA. Bioorg Med Chem 15(16):5493–5501

    Article  CAS  PubMed  Google Scholar 

  48. Bessi I, Bazzicalupi C, Richter C, Jonker HR, Saxena K, Sissi C, Chioccioli M, Bianco S, Bilia AR, Schwalbe H (2012) Spectroscopic, molecular modeling, and NMR-spectroscopic investigation of the binding mode of the natural alkaloids berberine and sanguinarine to human telomeric G-quadruplex DNA. ACS Chem Biol 7(6):1109–1119

    Article  CAS  PubMed  Google Scholar 

  49. Collie GW, Promontorio R, Hampel SM, Micco M, Neidle S, Parkinson GN (2012) Structural basis for telomeric G-quadruplex targeting by naphthalene diimide ligands. J Am Chem Soc 134(5):2723–2731. doi:10.1021/ja2102423

    Article  CAS  PubMed  Google Scholar 

  50. Chung WJ, Heddi B, Hamon F, Teulade-Fichou MP, Phan AT (2014) Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC(3). Angew Chem Int Ed Engl 53(4):999–1002. doi:10.1002/anie.201308063

    Article  CAS  PubMed  Google Scholar 

  51. Dai JX, Carver M, Hurley LH, Yang DZ (2011) Solution structure of a 2:1 quindoline-c-MYC G-quadruplex: insights into G-quadruplex-interactive small molecule drug design. J Am Chem Soc 133(44):17673–17680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Zhang L, Liu H, Shao Y, Lin C, Jia H, Chen G, Yang D, Wang Y (2014) Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer. Anal Chem 87(1):730–737

    Article  PubMed  Google Scholar 

  53. Dai JX, Punchihewa C, Mistry P, Ooi AT, Yang DZ (2004) Novel DNA Bis-intercalation by MLN944, a potent clinical bisphenazine anticancer drug. J Biol Chem 279(50):46096

    Article  CAS  PubMed  Google Scholar 

  54. Goddard TD, Kneller DG (2004). SPARKY 3, University of California, San Francisco

    Google Scholar 

  55. Brünger AT (1993) Version 3.1: A system for X-ray crystallography and NMR. Yale University Press, New Haven, CT

    Google Scholar 

  56. Lazzeretti P (2000) Ring currents. Prog Nucl Magn Reson Spectrosc 36(1):1–88

    Article  CAS  Google Scholar 

  57. Vorlickova M, Kejnovska I, Sagi J, Renciuk D, Bednarova K, Motlova J, Kypr J (2012) Circular dichroism and guanine quadruplexes. Methods 57(1):64–75. doi:10.1016/j.ymeth.2012.03.011

    Article  CAS  PubMed  Google Scholar 

  58. Lakowicz JR (2010) Principles of fluorescence spectroscopy, 3rd ed. Springer, New York

    Google Scholar 

  59. Dai J, Dexheimer TS, Chen D, Carver M, Ambrus A, Jones RA, Yang DZ (2006) 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 128(4):1096–1098

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Hatzakis E, Okamoto K, Yang D (2010) Thermodynamic stability and folding kinetics of the major G-quadruplex and its loop isomers formed in the nuclease hypersensitive element in the human c-Myc promoter: effect of loops and flanking segments on the stability of parallel-stranded intramolecular G-quadruplexes. Biochem 49(43):9152–9160. doi:10.1021/bi100946g

    Article  CAS  Google Scholar 

  61. Dexheimer TS, Carey SS, Zuohe S, Gokhale VM, Hu X, Murata LB, Maes EM, Weichsel A, Sun D, Meuillet EJ, Montfort WR, Hurley LH (2009) NM23-H2 may play an indirect role in transcriptional activation of c-myc gene expression but does not cleave the nuclease hypersensitive element III1. Mol Cancer Ther 8(5):1363–1377

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Liu L, Shao Y, Peng J, Huang C, Liu H, Zhang L (2014) Molecular rotor-based fluorescent probe for selective recognition of hybrid G-quadruplex and as a K+ sensor. Anal Chem 86(3):1622–1631

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

This research was supported by the National Institutes of Health funding (1S10RR16659, CA122952, GM083117, and CA177585). We thank Dr. Megan Carver for proofreading the manuscript.

Author information

Authors and Affiliations

  1. Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, 575 Stadium Mall Dr., West Lafayette, IN, 47907, USA

    Clement Lin & Danzhou Yang

  2. Purdue Center for Cancer Research, Purdue University, 201 S. University St., West Lafayette, IN, 47907, USA

    Danzhou Yang

  3. Purdue Institute for Drug Discovery, Purdue University, 720 Clinic Dr., West Lafayette, IN, 47907, USA

    Danzhou Yang

Authors
  1. Clement Lin
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Danzhou Yang
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Danzhou Yang .

Editor information

Editors and Affiliations

  1. Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA

    Zhou Songyang

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer Science+Business Media LLC

About this protocol

Cite this protocol

Lin, C., Yang, D. (2017). Human Telomeric G-Quadruplex Structures and G-Quadruplex-Interactive Compounds. In: Songyang, Z. (eds) Telomeres and Telomerase. Methods in Molecular Biology, vol 1587. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6892-3_17

Download citation

  • DOI: https://doi.org/10.1007/978-1-4939-6892-3_17

  • Published:

  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6891-6

  • Online ISBN: 978-1-4939-6892-3

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation