Analytical and Bioanalytical Chemistry

, Volume 409, Issue 9, pp 2285–2295 | Cite as

Assessment of human telomeric G-quadruplex structures using surface-enhanced Raman spectroscopy

  • Snežana MiljanićEmail author
  • Marina Ratkaj
  • Marija Matković
  • Ivo Piantanida
  • Paola Gratteri
  • Carla Bazzicalupi
Research Paper


G-Quadruplex (G4) structures of a human telomeric 24-mer (5′-TTAGGGTTAGGGTTAGGGTTAGGG-3′) sequence (Tel24) stabilized by sodium and potassium ions have been assessed using surface-enhanced Raman scattering (SERS) spectroscopy. The distinctive SERS spectra of Tel24 in the presence of 100 mM Na+ and 100 mM K+ were obtained and the SERS bands characteristic of the antiparallel basket-type and the mixed hybrid (3+1) structures, respectively, were identified and assigned. The influence of the SERS - active substrate on the scattering enhancement was studied using citrate- and chloride-covered silver nanoparticles, in the absence and presence of the aggregating agent (0.1 M Na2SO4 and 0.1 M K2SO4). The highly reproducible SERS spectra of Tel24 obtained in various SERS active media indicated the same adsorption mechanism of the cation - stabilized G-quadruplexes onto the metal surface, regardless of the silver colloid. The remarkable resemblance between the circular dichroism (CD) spectra of the Tel24 structures with and without the colloid confirmed that interaction with the enhancing silver surface did not affect the stability of the formed G4 structures. The presented study pointed to a great potential of the SERS spectroscopy for the sensitive structural analysis of various G4 topologies.

Graphical Abstract

SERS spectroscopy allowed identification of Na+ stabilized antiparallel basket-type and K+ stabilized hybrid (3+1) structures of the same 24-mer human telomeric sequence


Surface-enhanced Raman spectroscopy G-Quadruplex Human telomere Silver colloid DNA structure 



This work was supported by the Ministry of Science, Education and Sports of the Republic of Croatia and the Croatian Science Foundation (grant number 1477).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

216_2016_172_MOESM1_ESM.pdf (154 kb)
ESM 1 (PDF 153 kb)


  1. 1.
    Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34:5402–15.CrossRefGoogle Scholar
  2. 2.
    Ioannis Karsisiotis A, O’Kane C, Webba da Silva M. DNA quadruplex folding formalism—a tutorial on quadruplex topologies. Methods. 2013;64:28–35.CrossRefGoogle Scholar
  3. 3.
    Dai J, Carver M, Yang D. Polymorphism of human telomeric quadruplex structures. Biochimie. 2008;90:1172–83.CrossRefGoogle Scholar
  4. 4.
    Phan AT. Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J. 2010;277:1107–17.CrossRefGoogle Scholar
  5. 5.
    Bochman ML, Paeschke K, Zakian VA. DNA secondary structures: stability and function of G-quadruplex structures. Nat Rev Genet. 2012;3:770–80.CrossRefGoogle Scholar
  6. 6.
    König SLB, Evans AC, Huppert JL. Seven essential questions on G-quadruplexes. Biomol Concepts. 2010;1:197–213.CrossRefGoogle Scholar
  7. 7.
    Huppert JL. Four-stranded nucleic acids: structure, function and targeting of G-quadruplexes. Chem Soc Rev. 2008;27:1375–84.CrossRefGoogle Scholar
  8. 8.
    Huppert JL. Four-stranded DNA: cancer, gene regulation and drug development. Phil Trans R Soc A. 2007;365:2969–84.CrossRefGoogle Scholar
  9. 9.
    Luedtke NW. Targeting G-quadruplex DNA with small molecules. Chimia. 2009;63:134–9.CrossRefGoogle Scholar
  10. 10.
    Balagurumoorthy P, Brahmachari SK. Structure and stability of human telomeric sequence. J Biol Chem. 1994;269:21858–69.Google Scholar
  11. 11.
    Luu KN, Phan AT, Kuryavyi V, Lacroix L, Patel DJ. Structure of the human telomere in K+ solution: an intramolecular (3 + 1) G-quadruplex scaffold. J Am Chem Soc. 2006;128:9963–70.CrossRefGoogle Scholar
  12. 12.
    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 solution. Nucleic Acids Res. 2006;34:2723–35.CrossRefGoogle Scholar
  13. 13.
    Phan AT, Luu KN, Patel DJ. Different loop arrangements of intramolecular human telomeric (3+1) G-quadruplexes in K+ solution. Nucleic Acids Res. 2006;34:5715–9.CrossRefGoogle Scholar
  14. 14.
    Prislan I, Lah J, Milanic M, Vesnaver G. Kinetically governed polymorphism of d(G4T4G3) quadruplexes in K+ solutions. Nucleic Acids Res. 2011;39:1933–42.CrossRefGoogle Scholar
  15. 15.
    Boncina M, Lah J, Prislan I, Vesnaver G. Energetic basis of human telomeric DNA folding into G-quadruplex structures. J Am Chem Soc. 2012;134:9657–63.CrossRefGoogle Scholar
  16. 16.
    Aroca R. Surface-enhanced vibrational spectroscopy. Chichester: Wiley; 2006.CrossRefGoogle Scholar
  17. 17.
    Schlücker S. Surface-enhanced Raman spectroscopy: analytical, biophysical and life science applications. Weinheim: Wiley-VCH; 2011.Google Scholar
  18. 18.
    Miljanić S, Kenđel A, Novak M, Deliqeorqiev TG, Crnolatac I, Piantanida I, et al. Distinguishing binding modes of a new phosphonium dye with DNA by surface-enhanced Raman spectroscopy. RSC Adv. 2016;6:41927–36.CrossRefGoogle Scholar
  19. 19.
    Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. Nucleic Acids Res. 2013;41:1005–16.CrossRefGoogle Scholar
  20. 20.
    Benevides JM, Overman SA, Thomas GJ. Raman, polarized Raman and ultraviolet resonance Raman spectroscopy of nucleic acids and their complexes. J Raman Spectrosc. 2005;36:279–99.CrossRefGoogle Scholar
  21. 21.
    Pagba CV, Lane SM, Wachsmann-Hogiu S. Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy. Biomed Opt Express. 2011;2:207–17.CrossRefGoogle Scholar
  22. 22.
    Krafft C, Benevides JM, Thomas GJ. Secondary structure polymorphism in Oxytricha nova telomeric DNA. Nucleic Acids Res. 2002;30:3981–91.CrossRefGoogle Scholar
  23. 23.
    Friedman SJ, Terentis AC. Analysis of G-quadruplex conformations using Raman and polarized Raman spectroscopy. J Raman Spectrosc. 2016;47:259–68.CrossRefGoogle Scholar
  24. 24.
    Pagba CV, Lane SM, Wachsmann-Hogiu S. Raman and surface-enhanced Raman spectroscopic studies of the 15-mer DNA thrombin-binding aptamer. J Raman Spectrosc. 2010;41:241–7.Google Scholar
  25. 25.
    Rusciano G, De Luca AC, Pesce G, Sasso A, Oliviero G, Amato J, et al. Label-free probing of G-quadruplex formation by surface-enhanced Raman scattering. Anal Chem. 2011;83:6849–55.CrossRefGoogle Scholar
  26. 26.
    Gracie K, Dhamodharan V, Pradeepkumar PI, Faulds K, Graham D. Qualitative SERS analysis of G-quadruplex DNAs using selective stabilising ligands. Analyst. 2014;139:4458–65.CrossRefGoogle Scholar
  27. 27.
    Breuzard B, Millot J-M, Riou J-F, Manfait M. Selective interactions of ethidiums with G-quadruplex DNA revealed by surface-enhanced Raman scattering. Anal Chem. 2003;73:4305–11.CrossRefGoogle Scholar
  28. 28.
    Wei C, Jia G, Yuan J, Feng Z, Li C. A spectroscopic study on the interactions of porphyrin with G-quadruplex DNAs. Biochemistry. 2006;45:6681–91.CrossRefGoogle Scholar
  29. 29.
    Miljanić S, Ratkaj M, Avdejev I, Meglić K, Kenđel A. Surface-enhanced Raman scattering enhancement factors for RNA mononucleotides on silver nanoparticles. Croat Chem Acta. 2015;88:387–96.CrossRefGoogle Scholar
  30. 30.
    Munro CH, Smith WE, Garner M, Clarkson J, White PC. Characterization of the surface of a citrate-reduced colloid optimized for use as a substrate for surface-enhanced resonance Raman scattering. Langmuir. 1995;11:3712–20.CrossRefGoogle Scholar
  31. 31.
    Leoplod N, Lendl B. A new method for fast preparation of highly surface-enhanced Raman scattering (SERS) active silver colloids at room temperature by reduction of silver nitrate with hydroxylamine hydrochloride. J Phys Chem B. 2003;107:5723–7.CrossRefGoogle Scholar
  32. 32.
    Papadopulou E, Bell SEJ. Label-free detection of nanomolar unmodified single- and double-stranded DNA by using surface-enhanced Raman spectroscopy on Ag and Au colloids. Chem Eur J. 2012;18:5394–400.CrossRefGoogle Scholar
  33. 33.
    Papadopulou E, Bell SEJ. Label-free detection of single-base mismatches in DNA by surface-enhanced Raman spectroscopy. Angew Chem Int Ed. 2011;50:9058–61.CrossRefGoogle Scholar
  34. 34.
    Wu C-Y, Lo W-Y, Chiu C-R, Yang T-S. Surface enhanced Raman spectra of oligonucleotides induced by spermine. J Raman Spectrosc. 2006;27:799–807.CrossRefGoogle Scholar
  35. 35.
    Ke W, Zhou D, Wu J, Ji K. Surface-enhanced Raman spectra of calf thymus DNA adsorbed on concentrated silver colloid. Appl Spectrosc. 2005;59:418–23.CrossRefGoogle Scholar
  36. 36.
    Miljanić S, Dijanošić A, Matić I. Adsorption mechanisms of RNA mononucleotides on silver nanoparticles. Spectrochim Acta A. 2015;137:1357–62.CrossRefGoogle Scholar
  37. 37.
    Sharma VR, Sheardy RD. The human telomere sequence, (TTAGGG)4, in the absence and presence of cosolutes: a spectroscopic investigation. Molecules. 2014;19:595–608.CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Snežana Miljanić
    • 1
    Email author
  • Marina Ratkaj
    • 2
  • Marija Matković
    • 3
  • Ivo Piantanida
    • 3
  • Paola Gratteri
    • 4
  • Carla Bazzicalupi
    • 5
  1. 1.Division of Analytical Chemistry, Department of Chemistry, Faculty of ScienceUniversity of ZagrebZagrebCroatia
  2. 2.Teva Pharmaceutical Industries Ltd., Research and DevelopmentPLIVA CroatiaZagrebCroatia
  3. 3.Division of Organic Chemistry and BiochemistryRuđer Bošković InstituteZagrebCroatia
  4. 4.Department NEUROFARBA—Pharmaceutical and nutraceutical section, Laboratory of Molecular Modeling Cheminformatics & QSARUniversity of FirenzeSesto FiorentinoItaly
  5. 5.Department of Chemistry “Ugo Schiff”University of FirenzeSesto FiorentinoItaly

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