Skip to main content
SpringerLink
Log in
Book cover

Quadruplex Nucleic Acids pp 67–86Cite as

Circular Dichroism of Quadruplex Structures

  • Chapter
  • First Online:

Part of the book series: Topics in Current Chemistry ((TOPCURRCHEM,volume 330))

Abstract

Circular dichroism (CD) is a widespread technique for studying the polymorphism of G-quadruplexes. In this chapter the CD spectral features characteristic of different folding topologies of G4-DNA are analyzed in terms of the sequence of the syn or anti glycosidic bond angle (GBA) within a quadruplex stem. Depending on the GBA sequence, the chiral disposition of two stacked guanines, adjacent along a strand, is different and this leads to a predictable contribution to the overall CD spectrum. The CD spectra of a series of G-quadruplexes, chosen as prototypal of the most common strand folding, are illustrated. The validity and the prediction power of the approach is corroborated by the analysis of CD spectra of structurally modified G4-DNA either with chemically modified guanines or polarity inversion site (5′-5′ or 3′-3′) along the strands or additional nucleobases contributing to the stacking.

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

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   259.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   329.99
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

Learn about institutional subscriptions

References

  1. Paramasivan S, Rujan I, Bolton PH (2007) Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding. Methods 43:324–331

    Article  CAS  Google Scholar 

  2. Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res 34:5402–5415

    Article  CAS  Google Scholar 

  3. Masiero S, Trotta R, Pieraccini S, De Tito S, Perone R, Randazzo A, Spada GP (2010) A non-empirical chromophoric interpretation of CD spectra of DNA G-quadruplex structures. Org Biomol Chem 8:2683–2692

    Article  CAS  Google Scholar 

  4. Kypr J, Kejnovská I, Renčiuk D, Vorlíčková M (2009) Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res 37:1713–1725

    Article  CAS  Google Scholar 

  5. Jaumot J, Eritja R, Navea S, Gargallo R (2009) Classification of nucleic acids structures by means of the chemometric analysis of circular dichroism spectra. Anal Chim Acta 642:117–126

    Article  CAS  Google Scholar 

  6. Berova N, Nakanishi K, Woody RW (2000) Circular dichroism: principles and applications, 2nd edn. Wiley-VCH, New York

    Google Scholar 

  7. Berova N, Di Bari L, Pescitelli G (2007) Application of electronic circular dichroism in configurational and conformational analysis of organic compounds. Chem Soc Rev 36:914–931

    Article  CAS  Google Scholar 

  8. Gottarelli G, Lena S, Masiero S, Pieraccini S, Spada GP (2008) The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: an overview. Chirality 20:471–485

    Article  CAS  Google Scholar 

  9. van Dijk L, Bobbert PA, Spano FC (2010) Extreme sensitivity of circular dichroism to long-range excitonic couplings in helical supramolecular assemblies. J Phys Chem B 114:817–825

    Article  Google Scholar 

  10. Fasman GD (1996) Circular dichroism and the conformational analysis of biomolecules. Plenum, New York

    Book  Google Scholar 

  11. Johnson JE, Smith JS, Kozak ML, Johnson FB (2008) In vivo veritas: using yeast to probe the biological functions of G-quadruplexes. Biochimie 90:1250–1263

    Article  CAS  Google Scholar 

  12. 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 51:899–908

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  14. Incles CM, Schultes CM, Neidle S (2003) Telomerase inhibitors in cancer therapy: current status and future directions. Curr Opin Investig Drugs 4:675–685

    CAS  Google Scholar 

  15. Neidle S, Balasubramanian S (2006) Quadruplex nucleic acids. RSC, Cambridge

    Book  Google Scholar 

  16. Parkinson GN (2006) Fundamentals of quadruplex structures. In: Neidle S, Balasubramanian S (eds) Quadruplex nucleic acids. RSC, Cambridge

    Google Scholar 

  17. Harada H, Nakanishi K (1983) Circular dichroic spectroscopy – exciton coupling in organic stereochemistry. University Science Book, Mill Valley

    Google Scholar 

  18. Berova N, Nakanishi K (2000) Principles and applications of exciton chirality method. In: Berova N, Nakanishi K, Woody RW (eds) Circular dichroism – principles and applications, 2nd edn. Wiley-VCH, New York

    Google Scholar 

  19. Superchi S, Giorgio E, Rosini C (2004) Structural determinations by circular dichroism spectra analysis using coupled oscillator methods: an update of the applications of the DeVoe polarizability model. Chirality 16:422–451

    Article  CAS  Google Scholar 

  20. Clark LB (1994) Electronic spectra of crystalline guanosine: transition moment directions of the guanine chromophore. J Am Chem Soc 116:5265–5270

    Article  CAS  Google Scholar 

  21. Füelsher MP, Serrano-Andrés L, Roos BO (1997) A theoretical study of the electronic spectra of adenine and guanine. J Am Chem Soc 119:6168–6176

    Article  Google Scholar 

  22. Gottarelli G, Palmieri P, Spada GP (1990) The exciton optical activity of the four-stranded helix of poly(G). Gazz Chim Ital 120:101–107

    CAS  Google Scholar 

  23. Gray DM, Wen JD, Gray CW, Repges R, Repges C, Raabe G, Fleischhauer J (2008) Measured and calculated CD spectra of G-quartets stacked with the same or opposite polarities. Chirality 20:431–440

    Article  CAS  Google Scholar 

  24. Webba da Silva M (2007) Geometric formalism for DNA quadruplex folding. Chemistry 13:9738–9745

    Article  CAS  Google Scholar 

  25. Webba da Silva M, Trajkovski M, Sannohe Y, Ma’ani Hessari N, Sugiyama H, Plavec J (2009) Design of a G-quadruplex topology through glycosidic bond angles. Angew Chem 121:9331–9334; Angew Chem Int Ed 48:9167–9170

    Google Scholar 

  26. Snatzke G (2000) Circular dichroism: an introduction. In: Berova N, Nakanishi K, Woody RW (eds) Circular dichroism – principles and applications, 2nd edn. Wiley-VCH, New York

    Google Scholar 

  27. Gottarelli G, Masiero S, Spada GP (1998) The use of CD spectroscopy for the study of the self-assembly of guanine derivatives. Enantiomer 3:429–438

    CAS  Google Scholar 

  28. Wen JD, Gray DN (2002) The Ff gene 5 single-stranded DNA-binding protein binds to the transiently folded form of an intramolecular G-quadruplex. Biochemistry 41:11438–11448

    Article  CAS  Google Scholar 

  29. Esposito V, Randazzo A, Piccialli G, Petraccone L, Giancola C, Mayol L (2004) Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)]4. Org Biomol Chem 2:313–318

    Article  CAS  Google Scholar 

  30. Uesugi S, Ikehara M (1977) Carbon-13 magnetic resonance spectra of 8-substituted purine nucleosides. Characteristic shifts for the syn conformation. J Am Chem Soc 99:3250–3253

    Article  CAS  Google Scholar 

  31. Jordan F, Niv H (1977) C8-amino purine nucleosides. A well-defined steric determinant of glycosyl conformational preferences. Biochim Biophys Acta 476:265–271

    Article  CAS  Google Scholar 

  32. Uesugi S, Ohkubo M, Urata H, Ikeara M, Kobayashi Y, Kyogoku Y (1984) Ribooligonucleotides, r(C-G-C-G) analogues containing 8-substituted guanosine residues, form left-handed duplexes with Z-form-like structure. J Am Chem Soc 106:3675–3676

    Article  CAS  Google Scholar 

  33. Virgilio A, Esposito V, Randazzo A, Mayol L, Galeone A (2005) 8-Methyl-2'-deoxyguanosine incorporation into parallel DNA quadruplex structures. Nucleic Acids Res 33:6188–6195

    Article  CAS  Google Scholar 

  34. Esposito V, Virgilio A, Pepe A, Oliviero G, Mayol L, Galeone A (2009) Effects of the introduction of inversion of polarity sites in the quadruplex forming oligonucleotide TGGGT. Bioorg Med Chem 17:1997–2001

    Article  CAS  Google Scholar 

  35. Petraccone L, Duro I, Randazzo A, Virno A, Mayol L, Giancola C (2007) Biophysical properties of quadruplexes containing two or three 8-bromodeoxyguanosine residues. Nucleosides Nucleotides Nucleic Acids 26:669–674

    Article  CAS  Google Scholar 

  36. Esposito V, Virgilio A, Randazzo A, Galeone A, Mayol L (2005) A new class of DNA quadruplexes formed by oligodeoxyribonucleotides containing a 3'-3' or 5'-5' inversion of polarity site. Chem Commun 31:3953–3955

    Article  Google Scholar 

  37. Virno A, Zaccaria F, Virgilio A, Esposito V, Galeone A, Mayol L, Randazzo A (2007) Molecular modelling studies of four stranded quadruplexes containing a 3'-3' or 5'-5' inversion of polarity site. Nucleosides Nucleotides Nucleic Acids 26(8–9):1139–1143

    Article  CAS  Google Scholar 

  38. Karsisiotis AI, Hessari NM, Novellino E, Spada GP, Randazzo A, Webba da Silva M (2011) Topological characterization of nucleic acid G-quadruplexes by UV absorption and circular dichroism. Angew Chem Int Ed Engl 50(45):10645–10648

    Article  CAS  Google Scholar 

  39. Hu LY, Lim KW, Bouaziz S, Phan AT (2009) Giardia telomeric sequence d(TAGGG)4 forms two intramolecular G-quadruplexes in K+ solution: effect of loop length and sequence on the folding topology. J Am Chem Soc 131:16824–16831

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Dipartimento di Chimica Farmaceutica e Tossicologica, Università degli Studi di Napoli “Federico II”, via D. Montesano 49, 80131, Napoli, Italy

    Antonio Randazzo

  2. Dipartimento di Chimica Organica “A. Mangini”, Alma Mater Studiorum-Università di Bologna, via San Giacomo 11, 40126, Bologna, Italy

    Gian Piero Spada

  3. School of Biomedical Sciences, University of Ulster, Cromore Road, Coleraine, BT52 1SA, UK

    Mateus Webba da Silva

Authors
  1. Antonio Randazzo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Gian Piero Spada
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Mateus Webba da Silva
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Antonio Randazzo .

Editor information

Editors and Affiliations

  1. James Graham Brown Cancer Center, University of Louisville, Louisville, 40202, New York, USA

    Jonathan B. Chaires

  2. , Department of Chemistry, University of Alamaba at Birmingham, 3rd Ave 1530, Birmingham, 35294-1240, Alaska, USA

    David Graves

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Randazzo, A., Spada, G.P., da Silva, M.W. (2012). Circular Dichroism of Quadruplex Structures. In: Chaires, J., Graves, D. (eds) Quadruplex Nucleic Acids. Topics in Current Chemistry, vol 330. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2012_331

Download citation

Publish with us

Policies and ethics

Search

Navigation