Overview of RNA G-quadruplex structures

  • Magdalena Małgowska Institute of Bioorganic Chemistry Polish Academy of Sciences
Keywords: G-tetrad, U-tetrad, RNA G-quadruplex, NMR, crystallography, nucleic acids structure


G-quadruplexes are non-canonical secondary structures which may be formed by guanine rich sequences, both in vitro and in living cells. The number of biological functions assigned to these structural motifs has grown rapidly since the discovery of their involvement in the telomere maintenance. Knowledge of the three-dimensional structures of G-quadruplexes plays an important role in understanding their conformational diversity, physiological functions, and in the design of novel drugs targeting G-quadruplexes. For the last decades, structural studies have been mainly focused on the DNA G-quadruplexes. Their RNA counterparts gained an increased interest along with still-emerging recognition of the central role of RNA in multiple cellular processes. In this review we focus on structural properties of RNA G-quadruplexes, based on high-resolution structures, available in RCSB PDB data base and on structural models. In addition, we point out to the current challenges in this field of research.

Author Biography

Magdalena Małgowska, Institute of Bioorganic Chemistry Polish Academy of Sciences
Laboratory of Biomolecular NMR


Adrian M, Heddi B, Phan A. T, (2012) NMR Spectroscopy of G-Quadruplexes. Methods 57: 11–24. doi:10.1016/j.ymeth.2012.05.003

Agarwala P, Pandey S, Maiti S, (2015) The Tale of RNA G-Quadruplex. Org. Biomol. Chem. 13: 5570–5585. doi:10.1039/C4OB02681K

Ambrus A, Chen D, Dai J, Bialis T, Jones R, Yang D, (2006) Human Telomeric Sequence Forms a Hybrid-Type Intramolecular G-Quadruplex Structure with Mixed Parallel/antiparallel Strands in Potassium Solution. Nucleic Acids Research 34: 2723–2735. doi:10.1093/nar/gkl348

Awang G, Sen D, (1993) Mode of Dimerization of HIV-1 Genomic RNA. Biochemistry 32: 11453–11457. doi:10.1021/bi00093a024

Azzalin, Claus M, Reichenbach P, Khoriauli L, Giulotto E, Lingner J, (2007) Telomeric Repeat Containing RNA and RNA Surveillance Factors at

Mammalian Chromosome Ends. Science 318: 798–801. doi:10.1126/science.1147182

Balasubramanian S, Neidle S, (2009) G-Quadruplex Nucleic Acids as Therapeutic Targets. Current Opinion in Chemical Biology 13: 345–353. doi:10.1016/j.cbpa.2009.04.637

Biffi G, Tannahill D, McCafferty J, Balasubramanian S (2013) Quantitative Visualization of DNA G-Quadruplex Structures in Human Cells Nature Chemistry 5: 182–186. doi:10.1038/nchem.1548

Biffi G, Antonio M Di, Tannahill D, Balasubramanian S, (2014) Visualization and Selective Chemical Targeting of RNA G-Quadruplex Structures in the Cytoplasm of Human Cells Nature Chemistry 6: 75–80. doi:10.1038/nchem.1805

Bugaut A, Rodriguez R, Kumari S, Hsu STD, Balasubramanian S, (2010) Small Molecule-Mediated Inhibition of Translation by Targeting a Native RNA G-Quadruplex Organic & Biomolecular Chemistry 8: 2771-2776. doi:10.1039/c002418j

Burge S, Parkinson GN, Hazel P, Todd AK, Neidle S (2006) Quadruplex DNA: Sequence, Topology and Structure Nucleic Acids Research 34: 5402–5415. doi:10.1093/nar/gkl655

Cahoon, LA, Seifert HS, (2009) An Alternative DNA Structure Is Necessary for Pilin Antigenic Variation in Neisseria Gonorrhoeae. Science 325: 764–767. doi:10.1126/science.1175653

Campbell NH, Parkinson GN, (2007) Crystallographic Studies of Quadruplex Nucleic Acids Methods 43: 252–263. doi:10.1016/j.ymeth.2007.08.005

Campbell NH, Collie GW, Neidle S (2012) Crystallography of DNA and RNA G-Quadruplex Nucleic Acids and Their Ligand Complexes Current Protocols in Nucleic Acid Chemistry Chapter 17: Unit17.6. doi:10.1002/0471142700.nc1706s50

Cheong C, Moore PB, (1992) Solution Structure of an Unusually Stable RNA Tetraplex Containing G- and U-Quartet Structures Biochemistry 31: 8406–8414. doi:10.1021/bi00151a003

Collie GW, Parkinson GN (2011) The Application of DNA and RNA G-Quadruplexes to Therapeutic Medicines. Chemical Society Reviews 40: 5867–5892. doi:10.1039/c1cs15067g

Collie GW, Sparapani S, Parkinson GN, Neidle S, (2011) Structural Basis of Telomeric RNA Quadruplex–Acridine Ligand Recognition. Journal of the American Chemical Society 133: 2721–2728. doi:10.1021/ja109767y

Deng, J, Xiong Y, Sundaralingam M, (2001) X-Ray Analysis of an RNA Tetraplex (UGGGGU)4 with Divalent Sr2+ Ions at Subatomic Resolution (0.61 Å). Proceedings of the National Academy of Sciences of the United States of America 98: 13665–13670. doi:10.1073/pnas.241374798

Deng Z, Norseen J, Wiedmer A, Riethman H, Lieberman PM, (2009) TERRA RNA Binding to TRF2 Facilitates Heterochromatin Formation and ORC Recruitment at Telomeres. Molecular Cell 35: 403–413. doi:10.1016/j.molcel.2009.06.025

Di Antonio M, Biffi G, Mariani A, Raiber EA, Rodriguez R, Balasubramanian S (2012) Selective RNA Versus DNA G-Quadruplex Targeting by In Situ Click Chemistry. Angewandte Chemie International Edition 51: 11073–11078. doi:10.1002/anie.201206281

Eddy J, Maizels N, (2007) Conserved Elements with Potential to Form Polymorphic G-Quadruplex Structures in the First Intron of Human Genes. Nucleic Acids Research 36: 1321–1333. doi:10.1093/nar/gkm1138

Faudale M, Cogoi S, Xodo L. E, (2012) Photoactivated Cationic Alkyl-Substituted Porphyrin Binding to g4-RNA in the 5′-UTR of KRAS Oncogene Represses Translation. Chemical Communications. 48: 874–876. doi:10.1039/C1CC15850C

Fyfe AC, Dunten PW, Martick MM, Scott WG (2015) Structural Variations and Solvent Structure of r(UGGGGU) Quadruplexes Stabilized by Sr2+ Ions. Journal of Molecular Biology 427: 2205–2219. doi:10.1016/j.jmb.2015.03.022

Garant JM, Luce MJ, Scott MS, Perreault JP, (2015) G4RNA: An RNA G-Quadruplex Database. Database 2015: 1–5. doi:10.1093/database/bav059

Gavathiotis E, Searle MS, (2003) Structure of the Parallel-Stranded DNA Quadruplex d(TTAGGGT)4 Containing the Human Telomeric Repeat: Evidence for A-Tetrad Formation from NMR and Molecular Dynamics Simulations. Organic & Biomolecular Chemistry 1: 1650–1656. doi:10.1039/b300845m

Gomez D, Guedin A, Mergny J.-L, Salles B, Riou J.-F, Teulade-Fichou M.-P, Calsou P, (2010) A G-Quadruplex Structure within the 5′-UTR of TRF2 mRNA Represses Translation in Human Cells. Nucleic Acids Research 38: 7187–7198. doi:10.1093/nar/gkq563

Gudanis D, Popenda L, Szpotkowski K, Kierzek R, Gdaniec Z, (2016) Structural Characterization of a Dimer of RNA Duplexes Composed of 8-Bromoguanosine Modified CGG Trinucleotide Repeats: A Novel Architecture of RNA Quadruplexes. Nucleic Acids Research 44: 2409-2416. doi:10.1093/nar/gkv1534

Halder K, Largy E, Benzler M, Teulade-Fichou MP, Hartig JS, (2011) Efficient Suppression of Gene Expression by Targeting 5′-UTR-Based RNA Quadruplexes with Bisquinolinium Compounds. ChemBioChem 12: 1663–1668. doi:10.1002/cbic.201100228

Huang H, Suslov NB, Li NS, Shelke SA, Evans ME, Koldobskaya Y, Rice PA, Piccirilli JA, (2014) A G-Quadruplex–containing RNA Activates Fluorescence in a GFP-like Fluorophore. Nature Chemical Biology 10: 686–691. doi:10.1038/nchembio.1561

Huppert JL, Balasubramanian S, (2005) Prevalence of Quadruplexes in the Human Genome. Nucleic Acids Research 33: 2908–2916. doi:10.1093/nar/gki609

Huppert JL, Bugaut A, Kumari S, Balasubramanian S, (2008) G-Quadruplexes: The Beginning and End of UTRs Nucleic Acids Research 36: 6260–6268. doi:10.1093/nar/gkn511

Huppert J L, (2008) Hunting G-Quadruplexes. Biochimie 90: 1140–1148. doi:10.1016/j.biochi.2008.01.014

Ji, X, Sun H, Zhou H, Xiang J, Tang Y, Zhao C, (2011) Research Progress of RNA Quadruplex. Nucleic Acid Therapeutics 21: 185–200. doi:10.1089/nat.2010.0272

Kerwin, S. (2000) G-Quadruplex DNA as a Target for Drug Design. Current Pharmaceutical Design 6: 441–471. doi:10.2174/1381612003400849

Kimura T, Xu Y, Komiyama M, (2009) Human Telomeric RNA r(UAGGGU) Sequence Forms Parallel Tetraplex Structure with U-Quartet. Nucleic Acids Symposium Series 53: 239–240. doi:10.1093/nass/nrp120

Krishnan-Ghosh Y, Stephens E, Balasubramanian S, (2004) A PNA4 Quadruplex. Journal of the American Chemical Society 126: 5944–5945. doi:10.1021/ja031508f

Kumari S, Bugaut A, Huppert JL, Balasubramanian S (2007) An RNA G-Quadruplex in the 5′ UTR of the NRAS Proto-Oncogene Modulates Translation. Nature Chemical Biology 3: 218–221. doi:10.1038/nchembio864

Laguerre A, Hukezalie K, Winckler P, Katranji F, Chanteloup G, Pirrotta M, Perrier-Cornet JM, Wong JMY, Monchaud D, (2015) Visualization of RNA-Quadruplexes in Live Cells. Journal of the American Chemical Society 137: 8521–8525. doi:10.1021/jacs.5b03413

Le, TVT, Han S, Chae J, Park HJ, (2012) G-Quadruplex Binding Ligands: From Naturally Occurring to Rationally Designed Molecules. Current Pharmaceutical Design 18: 1948–1972. doi:10.2174/138161212799958431

Lipay JM, Mihailescu MR, (2009) NMR Spectroscopy and Kinetic Studies of the Quadruplex Forming RNA r(UGGAGGU). Molecular bioSystems 5: 1347–1355. doi:10.1039/b911555b

Liu H, Matsugami A, Katahira M, Uesugi S, (2002) A Dimeric RNA Quadruplex Architecture Comprised of Two G:G(:A):G:G(:A) Hexads, G:G:G:G Tetrads and UUUU Loops. Journal of Molecular Biology 322: 955–970. doi:10.1016/S0022-2836(02)00876-8

Malgowska M, Gudanis D, Kierzek R, Wyszko E, Gabelica V, Gdaniec Z, (2014) Distinctive Structural Motifs of RNA G-Quadruplexes Composed of AGG, CGG and UGG Trinucleotide Repeats. Nucleic Acids Research 42: 10196–10207. doi:10.1093/nar/gku710

Mariani P, Spinozzi F, Federiconi F, Amenitsch H, Spindler L, Drevensek-Olenik I, (2009) Small Angle X-Ray Scattering Analysis of Deoxyguanosine 5′-monophosphate Self-Assembing in Solution: Nucleation and Growth of G-Quadruplexes. The Journal of Physical Chemistry. B 113: 7934–44. doi:10.1021/jp809734p

Mariani, P, Spinozzi F, Federiconi F, Ortore MG, Amenitsch H, Spindler L, Drevensek-Olenik I, (2010) Guanosine Quadruplexes in Solution: A Small-Angle X-Ray Scattering Analysis of Temperature Effects on Self-Assembling of Deoxyguanosine Monophosphate Journal of Nucleic Acids 2010: 1-10. doi:10.4061/2010/472478

Marquet R, Paillart JC, Skripkin E, Ehresmann C, Ehresmann B, (1994) Dimerization of Human Immunodeficiency Virus Type 1 RNA Involves Sequences Located Upstream of the Splice Donor Site Nucleic Acids Research 22: 145–151. doi:10.1093/nar/22.2.145

Martadinata H, Phan AT, (2009) Structure of Propeller-Type Parallel-Stranded RNA G-Quadruplexes, Formed by Human Telomeric RNA Sequences in K+ Solution. Journal of the American Chemical Society 131: 2570–2578. doi:10.1021/ja806592z

Martadinata H, Heddi B, Lim KW, Phan AT, (2011) Structure of Long Human Telomeric RNA (TERRA): G-Quadruplexes Formed by Four and Eight UUAGGG Repeats Are Stable Building Blocks. Biochemistry 50 (29): 6455–6461. doi:10.1021/bi200569f

Martadinata H, Phan AT, (2013) Structure of Human Telomeric RNA (TERRA): Stacking of Two G-Quadruplex Blocks in K+ Solution. Biochemistry 52: 2176–21783. doi:10.1021/bi301606u

Mashima T, Matsugami A, Nishikawa F, Nishikawa S, Katahira M, (2009) Unique Quadruplex Structure and Interaction of an RNA Aptamer against Bovine Prion Protein. Nucleic Acids Research 37: 6249–6258. doi:10.1093/nar/gkp647

Medic Š, Podbevšek P, Plavec J, (2014) Solution Structure of a Prion Protein Aptamer Analogue. Croatica Chemica Acta 87: 321–325. doi:10.5562/cca2430

Metifiot M., Amrane S, Litvak S, Andreola ML, (2014) G-Quadruplexes in Viruses: Function and Potential Therapeutic Applications. Nucleic Acids Research 42: 12352–12366. doi:10.1093/nar/gku999

Millevoi, Stefania, Hervé Moine, and Stéphan Vagner. (2012) G-Quadruplexes in RNA Biology. Wiley Interdisciplinary Reviews. RNA 3: 495–507. doi:10.1002/wrna.1113

Morris MJ, Wingate KL, Silwal J, Leeper TC, Basu S, (2012) The Porphyrin TmPyP4 Unfolds the Extremely Stable G-Quadruplex in MT3-MMP mRNA and Alleviates Its Repressive Effect to Enhance Translation in Eukaryotic Cells. Nucleic Acids Research 40: 4137–4145. doi:10.1093/nar/gkr1308

Murat P, Zhong J, Lekieffre L, Cowieson NP, Clancy JL, Preiss T, Balasubramanian S, Khanna R, Tellam J, (2014) G-Quadruplexes Regulate Epstein-Barr Virus-Encoded Nuclear Antigen 1 mRNA Translation. Nature Chemical Biology 10: 358–364. doi:10.1038/nchembio.1479

Nandakumar J, Podell ER, Cech TR, (2010) How Telomeric Protein POT1 Avoids RNA to Achieve Specificity for Single-Stranded DNA. Proceedings of the National Academy of Sciences of the United States of America 107: 651–656. doi:10.1073/pnas.0911099107

Pan B , Xiong Y, Shi K, Deng J, Sundaralingam M, (2003) Crystal Structure of an RNA Purine-Rich Tetraplex Containing Adenine Tetrads. Structure 11: 815–823. doi:10.1016/S0969-2126(03)00107-2

Pan B, Xiong Y, Shi K, Sundaralingam M, (2003a) An Eight-Stranded Helical Fragment in RNA Crystal Structure. Structure 11: 825–831. doi:10.1016/S0969-2126(03)00108-4

Pan B, Xiong Y, Shi K, Sundaralingam M, (2003b) Crystal Structure of a Bulged RNA Tetraplex at 1.1 Å Resolution. Structure 11: 1423–1430. doi:10.1016/j.str.2003.09.017

Pan B, Shi K, Sundaralingam M, (2006a) Base-Tetrad Swapping Results in Dimerization of RNA Quadruplexes: Implications for Formation of the I-Motif RNA Octaplex. Proceedings of the National Academy of Sciences of the United States of America 103: 3130–3134. doi:10.1073/pnas.0507730103

Pan B, Shi K, Sundaralingam M, (2006b) Crystal Structure of an RNA Quadruplex Containing Inosine Tetrad: Implications for the Roles of NH2 Group in Purine Tetrads. Journal of Molecular Biology 363: 451–459. doi:10.1016/j.jmb.2006.08.022

Parkinson GN, Lee MP, Neidle S, (2002) Crystal Structure of Parallel Quadruplexes from Human Telomeric DNA. Nature 417: 876–880. doi:10.1038/nature755

Randazzo A, Esposito V, Ohlenschläger O, Ramachandran R, Mayola L, (2004) NMR Solution Structure of a Parallel LNA Quadruplex. Nucleic Acids Research 32: 3083–3092. doi:10.1093/nar/gkh629

Redon S, Reichenbach P, Lingner J, (2010) The Non-Coding RNA TERRA Is a Natural Ligand and Direct Inhibitor of Human Telomerase. Nucleic Acids Research 38: 5797–5806. doi:10.1093/nar/gkq296

Russo Krauss I, Parkinson GR, Merlino A, Mattia CA, Randazzo A, Novellino E, Mazzarella L, Sica F, (2014) A Regular Thymine Tetrad and a Peculiar Supramolecular Assembly in the First Crystal Structure of an All-LNA G-Quadruplex. Acta Crystallographica. Section D, Biological Crystallography 70: 362–370. doi:10.1107/S1399004713028095

Satyanarayana M, Kim YA, Rzuczek SG, Pilch DS, Liu AA, Liu LF, Rice JE, LaVoie EJ, (2010) Macrocyclic Hexaoxazoles: Influence of Aminoalkyl Substituents on RNA and DNA G-Quadruplex Stabilization and Cytotoxicity. Bioorganic & Medicinal Chemistry Letters 20: 3150–3154. doi:10.1016/j.bmcl.2010.03.086

Schaffitzel C, Berger I, Postberg J, Hanes J, Lipps HJ, Plückthun A, (2001) In Vitro Generated Antibodies Specific for Telomeric Guanine-Quadruplex DNA React with Stylonychia Lemnae Macronuclei. Proceedings of the National Academy of Sciences of the United States of America 98: 8572–8577. doi:10.1073/pnas.141229498

Shen W, Gorelick RJ, Bambara RA, (2011) HIV-1 Nucleocapsid Protein Increases Strand Transfer Recombination by Promoting Dimeric G-Quartet Formation. Journal of Biological Chemistry 286: 29838–29847. doi:10.1074/jbc.M111.262352

Shrestha P, Shan X, Dhakal S, Tan Z, Mao H, (2014) Nascent RNA Transcripts Facilitate the Formation of G-Quadruplexes Nucleic Acids Research 42: 7236–7246. doi:10.1093/nar/gku416

Sket P, Plavec J, (2015) Diversity of DNA and RNA G-Quadruplex Structures. Future Science Chapter 2: 22–36. doi:10.4155/fseb12013.13.28.

Spindler L, Drevensek-Olenik I, Copic M, Cerar J, Skerjanc J, Mariani P, (2004) Dynamic Light Scattering and 31P NMR Study of the Self-Assembly of Deoxyguanosine 5′-monophosphate: The Effect of Added Salt. The European Physical Journal. E, Soft Matter 13: 27–33. doi:10.1140/epje/e2004-00037-0

Sundquist WI, Heaphy S, (1993) Evidence for Interstrand Quadruplex Formation in the Dimerization of Human Immunodeficiency Virus 1 Genomic RNA. Proceedings of the National Academy of Sciences 90: 3393–3397. doi:10.1073/pnas.90.8.3393

Vummidi BR, Alzeer J, Luedtke NW, (2013) Fluorescent Probes for G-Quadruplex Structures. ChemBioChem 14: 540–558. doi:10.1002/cbic.201200612

Wang Y, Patel DJ (1993) Solution Structure of the Human Telomeric Repeat d[AG3(T2AG3)3] G-Tetraplex. Structure 1: 263–282. doi:10.1016/0969-2126(93)90015-9

Warner KD, Chen MC, Song W, Strack RL, Thorn A, Jaffrey SR, Ferré-D’Amaré AR, (2014) Structural Basis for Activity of Highly Efficient RNA Mimics of Green Fluorescent Protein. Nature Structural & Molecular Biology 21: 658–663. doi:10.1038/nsmb.2865

Webba da Silva M, (2007) NMR Methods for Studying Quadruplex Nucleic Acids. Methods 43: 264–277. doi:10.1016/j.ymeth.2007.05.007

Xiong YX, Huang ZS, Tan JH, (2015) Targeting G-Quadruplex Nucleic Acids with Heterocyclic Alkaloids and Their Derivatives. European Journal of Medicinal Chemistry 97: 538–551. doi:10.1016/j.ejmech.2014.11.021

Xu S, Li Q, Xiang J, Yang Q, Sun H, Guan A, Wang L, (2015) Directly Lighting up RNA G-Quadruplexes from Test Tubes to Living Human Cells. Nucleic Acids Research 43: 9575–9586. doi:10.1093/nar/gkv1040

Xu Y, Kaminaga K, Komiyama M, (2008a) Human Telomeric RNA in G-Quadruplex Structure. Nucleic Acids Symposium Series 52: 175–176. doi:10.1093/nass/nrn089

Xu Y, Kaminaga K, Komiyama M, (2008b) G-Quadruplex Formation by Human Telomeric Repeats-Containing RNA in Na+ Solution. Journal of the American Chemical Society 130: 11179–11184. doi:10.1021/ja8031532

Xu Y, Suzuki Y, Komiyama M, (2009) Click Chemistry for the Identification of G-Quadruplex Structures: Discovery of a DNA-RNA G-Quadruplex. Angewandte Chemie 48: 3281–3284. doi:10.1002/anie.200806306

Xu Y, Ishizuka T, Kimura T, Komiyama M, (2010) A U-Tetrad Stabilizes Human Telomeric RNA G-Quadruplex Structure. Journal of the American Chemical Society 132: 7231–7233. doi:10.1021/ja909708a

Xu Y, Komiyama M, (2012) Structure, Function and Targeting of Human Telomere RNA Methods 57: 100–105. doi:10.1016/j.ymeth.2012.02.015

Zhang N, Phan AT, Patel DJ, (2005) (3 + 1) Assembly of Three Human Telomeric Repeats into an Asymmetric Dimeric G-Quadruplex. Journal of the American Chemical Society 127: 17277–17285. doi:10.1021/ja0543090

Zhang S, Wu Y, Zhang W, (2014) G-Quadruplex Structures and Their Interaction Diversity with Ligands. ChemMedChem 9: 899–911. doi:10.1002/cmdc.201300566