Abstract
Human telomeric G-quadruplexes are emerging targets in anticancer drug discovery since they are able to efficiently inhibit telomerase, an enzyme which is greatly involved in telomere instability and immortalization process in malignant cells. G-quadruplex (G4) DNA is highly polymorphic and can adopt different topologies upon addition of electrolytes, additives, and ligands. The study of G-quadruplex forms under various conditions, however, might be quite challenging. In this work, surface-enhanced Raman scattering (SERS) spectroscopy has been applied to study G-quadruplexes formed by human telomeric sequences, d[A3G3(TTAGGG)3A2] (Tel26) and d[(TTAGGG)4T2] (wtTel26), under dilute and crowding conditions. The SERS spectra distinctive of hybrid-1 and hybrid-2 G-quadruplexes of Tel26 and wtTel26, respectively, were observed for the sequences folded in the presence of K+ ions (110 mM) in a buffered solution, representing the diluted medium. Polyethylene glycol (5, 10, 15, 20, and 40% v/v PEG) was used to create a molecular-crowded environment, resulting in the formation of the parallel G-quadruplexes of both studied human telomeric sequences. Despite extensive overlap by the crowding agent bands, the SERS spectral features indicative of parallel G4 form of Tel26 were recognized. The obtained results implied that SERS of G-quadruplexes reflected not only the primary structure of the studied human telomeric sequence, including its nucleobase composition and sequence, but also its secondary structure in the sense of Hoogsteen hydrogen bonds responsible for the guanine tetrad formation, and finally its tertiary structure, defining a three-dimensional DNA shape, positioned close to the enhancing metallic surface.
Similar content being viewed by others
References
Murat P, Balasubramanian S. Existence and consequences of G-quadruplex structures in DNA. Curr Opin Genet Dev. 2014;25:22–9.
Maizels N, Gray LT. The G4 genome. PLoS Genet. 2013;9:e1003468.
Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S. Quadruplex DNA: sequence, topology and structure. Nucleic Acids Res. 2006;34:5402–15.
Zaccaria F, Paragi G, Guerra CF. The role of alkali metal cations in the stabilization of guanine quadruplexes: why K+ is the best. Phys Chem Chem Phys. 2016;18:20895–04.
Bhattacharyya D, Arachchilage GM, Basu S. Metal cations in G-quadruplex folding and stability. Front Chem. 2016;4:38.
Lam EYN, Beraldi D, Tannahill D, Balasubramanian S. G-quadruplex structures are stable and detectable in human genomic DNA. Nat Commun. 2013;4:1796.
Biffi G, Tannahill D, McCafferty J, Balasubramanian S. Quantitative visualization of DNA G-quadruplex structures in human cells. Nat Chem. 2013;5:182–6.
Biffi G, Tannahill D, Miller J, Howat WJ, Balasubramanian S. Elevated levels of G-quadruplex formation in human stomach and liver cancer tissues. PLoS One. 2014;9:e102711.
Chambers VS, Marsico G, Boutell JM, Di Antonio M, Smith GP, Balasubramanian S. High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat Biotechnol. 2015;33:877–81.
Hänsel-Hertsch R, Beraldi D, Lensing SV, Marsico G, Zyner K, Parry A, et al. G-quadruplex structures mark human regulatory chromatin. Nat Genet. 2016;48:1267–72.
Rhodes D, Lipps HJ. G-quadruplexes and their regulatory roles in biology. Nucleic Acids Res. 2015;43:8627–37.
Balasubramanian S, Neidle S. G-quadruplex nucleic acids as therapeutic targets. Curr Opin Chem Biol. 2009;13:345–53.
Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun. 2014;50:6422–38.
Ohnmacht SA, Neidle S. Small-molecule quadruplex-targeted drug discovery. Bioorganic Med Chem Lett. 2014;24:2602–12.
Neidle S. Quadruplex nucleic acids as novel therapeutic targets. J Med Chem. 2016;59:5987–11.
Li J, Correia JJ, Wang L, Trent JO, Chaires JB. Not so crystal clear: the structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res. 2005;33:4649–59.
Dai J, Carver M, Yang D. Polymorphism of human telomeric quadruplex structures. Biochimie. 2008;90:1172–83.
Phan AT. Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J. 2010;277:1107–17.
Parkinson GN, Lee MP, Neidle S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature. 2002;417:876–80.
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;34:2723–35.
Renčiuk D, Kejnovská I, Školáková P, Bednářová K, Motlová J, Vorlíčková M. Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions. Nucleic Acids Res. 2009;37:6625–34.
Hänsel-Hertsch R, Löhr F, Foldynová-Trantírková S, Bamberg E, Trantírek L, Dötsch V. The parallel G-quadruplex structure of vertebrate telomeric repeat sequences is not the preferred folding topology under physiological conditions. Nucleic Acids Res. 2011;39:5768–75.
Lane AN, Chaires JB, Gray RD, Trent JO. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 2008;36:5482–15.
Bugaut A, Balasubramanian S. A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes. Biochem. 2008;47:689–97.
Martino L, Pagano B, Fotticchia I, Neidle S, Giancola C. Shedding light on the interaction between TMPyP4 and human telomeric quadruplexes. J Phys Chem B. 2009;113:14779–86.
Petraccone L, Pagano B, Giancola C. Studying the effect of crowding and dehydration on DNA G-quadruplexes. Methods. 2012;57:76–83.
Tippana R, Xiao W, Myong S. G-quadruplex conformation and dynamics are determined by loop length and sequence. Nucleic Acids Res. 2014;42:8106–14.
Miyoshi D, Karimata H, Sugimoto N. Hydration regulates thermodynamics of G-quadruplex formation under molecular crowding conditions. J Am Chem Soc. 2006;128:7957–63.
Xu L, Feng S, Zhou X. Human telomeric G-quadruplexes undergo dynamic conversion in a molecular crowding environment. Chem Commun. 2011;47:3517–9.
Dai J, Punchihewa C, Ambrus A, Chen D, Jones RA, Yang D. Structure of the intramolecular human telomeric G-quadruplex in potassium solution: a novel adenine triple formation. Nucleic Acids Res. 2007;35:2440–50 (PDB ID: 2HY9).
Dai J, Carver M, Punchihewa C, Jones RA, Yang D. 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. 2007;35:4927–40 (PDB ID: 2JPZ).
Xue Y, Z-y K, Wang Q, Yao Y, Liu J, Hao Y-h, et al. Human telomeric DNA forms parallel-stranded intramolecular G-quadruplex in K+ solution under molecular crowding condition. J Am Chem Soc. 2007;129:11185–91.
Heddi B, Phan AT. Structure of human telomeric DNA in crowded solution. J Am Chem Soc. 2011;133:9824–33.
Lim KW, Amrane S, Bouaziz S, Xu W, Mu Y, Patel DJ, et al. Structure of the human telomere in K+ solution: a stable basket-type G-quadruplex with only two G-tetrad layers. J Am Chem Soc. 2009;131:4301–9.
Zhang Z, Dai J, Veliath E, Jones RA, Yang D. 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. 2009;38:1009–21.
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.
Phan AT, Kuryavyi V, Luu KN, Patel DJ. Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res. 2007;35:6517–25.
Hänsel-Hertsch R, Löhr F, Trantírek L, Dötsch V. High-resolution insight into G-overhang architecture. J Am Chem Soc. 2013;135:2816–24.
Buscaglia R, Miller MC, Dean WL, Gray RD, Lane AN, Trent JO, et al. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection. Nucleic Acids Res. 2013;41:7934–46.
Neidle S. The structures of quadruplex nucleic acids and their drug complexes. Curr Opin Struct Biol. 2009;19:239–50.
Alvarez-Puebla RA, Liz-Marzán LM. SERS-based diagnosis and biodetection. Small. 2010;6:604–10.
Bantz KC, Meyer AF, Wittenberg NJ, Im H, Kurtuluş Ö, Lee SH, et al. Recent progress in SERS biosensing. Phys Chem Chem Phys. 2011;13:11551–67.
Xie W, Schlücker S. Medical applications of surface-enhanced Raman scattering. Phys Chem Chem Phys. 2013;15:5329–44.
Cialla D, Pollok S, Steinbrücker C, Weber K, Popp J. SERS-based detection of biomolecules. Nanophotonics. 2014;3:383–11.
Joseph MM, Narayanan N, Nair JB, Karunakaran V, Ramya AN, Sujai PT, et al. Exploring the margins of SERS in practical domain: an emerging diagnostic modality for modern biomedical applications. Biomaterials. 2018;181:140–81.
Zheng X-S, Jahn IJ, Weber K, Cialla D, Popp J. Label-free SERS in biological and biomedical applications: recent progress, current challenges and opportunities. Spectrochim Acta A. 2018;197:56–77.
Miljanić S, Ratkaj M, Matković M, Piantanida I, Gratteri P, Bazzicalupi C. Assessment of human telomeric G-quadruplex structures using surface-enhanced Raman spectroscopy. Anal Bioanal Chem. 2017;409:2285–95.
Petraccone L, Malafronte A, Amato J, Giancola C. G-quadruplexes from human telomeric DNA: how many conformations in PEG containing solutions? J Phys Chem B. 2012;116:2294–305.
Munro C, Smith W, Garner M, Clarkson J, White P. 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.
Torres-Nunez A, Faulds K, Graham D, Alvarez-Puebla RA, Guerrini L. Silver colloids as plasmonic substrate for direct label-free surface-enhanced Raman scattering analysis of DNA. Analyst. 2016;141:5170–80.
Dick S, Bell SE. Quantitative surface-enhanced Raman spectroscopy of single bases in oligonucleotides. Faraday Discuss. 2017;205:517–36.
Guerrini L, Krpetić Ž, van Lierop D, Alvarez-Puebla RA, Graham D. Direct surface-enhanced Raman scattering analysis of DNA duplexes. Angew Chem Int Ed. 2015;54:1144–8.
Garcia-Rico E, Alavarez-Puebla RA, Guerrini L. Direct surface-enhanced Raman scattering (SERS) spectroscopy of nucleic acids: from fundamental to real-life applications. Chem Soc Rev. 2018;47:4909–23.
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.
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.
Li Y, Han X, Zhou S, Yan Y, Xiang X, Zhao B, et al. Structural features of DNA G-quadruplexes revealed by surface-enhanced Raman spectroscopy. J Phys Chem Lett. 2018;9:3245–52.
Nakamoto K, Tsuboi M, Strahan GD. Drug-DNA interactions: structures and spectra. Hoboken: Wiley; 2008.
Krafft C, Benevides JM, Thomas GJ. Secondary structure polymorphism in Oxytricha nova telomeric DNA. Nucleic Acids Res. 2002;30:3981–91.
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.
Pagba CV, Lane SM, Wachsmann-Hogiu S. Conformational changes in quadruplex oligonucleotide structures probed by Raman spectroscopy. Biomed Opt Express. 2011;2:207–17.
Palacký J, Vorlíčková M, Kejnovská I, Mojzeš P. Polymorphism of human telomeric quadruplex structure controlled by DNA concentration: a Raman study. Nucleic Acids Res. 2012;41:1005–16.
Friedman SJ, Terentis AC. Analysis of G-quadruplex conformations using Raman and polarized Raman spectroscopy. J Raman Spectrosc. 2016;47:259–68.
Aroca R. Surface-enhanced vibrational spectroscopy. Chichester: Wiley; 2006.
Schlücker S. Surface-enhanced Raman spectroscopy: analytical, biophysical and life science applications. Weinheim: Wiley-VCH; 2011.
Schlücker S. Surface-enhanced Raman spectroscopy: concepts and chemical applications. Angew Chem Int Ed. 2014;53:4756–95.
Papadopoulou E, Bell SE. Structure of adenine on metal nanoparticles: pH equilibria and formation of Ag+ complexes detected by surface-enhanced Raman spectroscopy. J Phys Chem C. 2010;114:22644–51.
Pagliai M, Caporali S, Muniz-Miranda M, Pratesi G, Schettino V. SERS, XPS, and DFT study of adenine adsorption on silver and gold surfaces. J Phys Chem Lett. 2012;3:242–5.
Miljanić S, Dijanošić A, Matić I. Adsorption mechanisms of RNA mononucleotides on silver nanoparticles. Spectrochim Acta A. 2015;137:1357–62.
Barhoumi A, Zhang D, Tam F, Halas NJ. Surface-enhanced Raman spectroscopy of DNA. J Am Chem Soc. 2008;130:5523–9.
Karakoti AS, Das S, Thevuthasan S, Seal S. PEGylated inorganic nanoparticles. Angew Chem Int Ed. 2011;50:1980–94.
Chang W-C, Tai J-T, Wang H-F, Ho R-M, Hsiao T-C, Tsai D-H. Surface PEGylation of silver nanoparticles: kinetics of simultaneous surface dissolution and molecular desorption. Langmuir. 2016;32:9807–15.
Paramasivan S, Rujan I, Bolton PH. Circular dichroism of quadruplex DNAs: applications to structure, cation effects and ligand binding. Methods. 2007;43:324–31.
Vorlíčková M, Kejnovská I, Sagi J, Renčiuk D, Bednářová K, Motlová J, et al. Circular dichroism and guanine quadruplexes. Methods. 2012;57:64–75.
Acknowledgments
We thank Ente Cassa Risparmio Firenze for a grant to FP (ECR2014.0309) and the University of Florence for funding FP’s stay in Zagreb (Contributo di Ateneo per la Promozione delle Attività Internazionali Anno 2015 and Piano di Internazionalizzazione di Ateneo 2013-2015).
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
The authors declare that they have no conflict of interest.
Additional information
Publisher’s note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Electronic supplementary material
ESM 1
(PDF 199 kb)
Rights and permissions
About this article
Cite this article
Papi, F., Kenđel, A., Ratkaj, M. et al. Effect of structure levels on surface-enhanced Raman scattering of human telomeric G-quadruplexes in diluted and crowded media. Anal Bioanal Chem 411, 5197–5207 (2019). https://doi.org/10.1007/s00216-019-01894-z
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00216-019-01894-z