Crystallography of DNA and RNA G‐Quadruplex Nucleic Acids and Their Ligand Complexes

Nancy Campbell1, Gavin W. Collie1, Stephen Neidle1

1 Cancer Research UK Biomolecular Structure Group, The UCL School of Pharmacy, London, United Kingdom
Publication Name:  Current Protocols in Nucleic Acid Chemistry
Unit Number:  Unit 17.6
DOI:  10.1002/0471142700.nc1706s50
Online Posting Date:  September, 2012
GO TO THE FULL TEXT: PDF or HTML at Wiley Online Library

Abstract

Quadruplexes are higher‐order structures formed by natural guanine‐rich nucleic acid sequences. They may play a role in gene regulation and in telomere function. This article focuses on the crystallization of quadruplexes and their complexes with small‐molecule ligands. Protocols for successful crystallization, as used in the author's laboratory, are described in detail. Curr. Protoc. Nucleic Acid Chem. 50:17.6.1‐17.6.22. © 2012 by John Wiley & Sons, Inc.

Keywords: crystallography; crystallization; quadruplex; nucleic acids; small molecules; complex

     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Table of Contents

  • Introduction
  • Using X‐Ray Crystallography to Study G‐Quadruplex‐Ligand Interactions
  • Sequence Selection
  • Sequence Selection: Case Study—Unimolecular G‐Quadruplexes
  • Crystallization of RNA G‐Quadruplexes
  • Crystallization Protocols for Quadruplexes: General Guidelines
  • Example Protocol: Crystallization of Human Telomeric G‐Quadruplexes
  • Data Collection
  • Conclusions
  • Acknowledgments
  • Literature Cited
  • Figures
  • Tables
     
 
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Materials

GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library

Figures

Videos

Literature Cited

Literature Cited
   Aboul‐ela, F., Murchie, A.I., Norman, D.G. and Lilley, D.M. 1994. Solution structure of a parallel‐stranded tetraplex formed by d(TG4T) in the presence of sodium ions by nuclear magnetic resonance spectroscopy. J. Mol. Biol. 243:458‐471.
   Bang, I. 1910. Untersuchungen über die Guanylsäure. Biochem. Zeitschrift 26:293‐311.
   Cáceres, C., Wright, G., Gouyette, C., Parkinson, G., and Subirana, J.A. 2004. A thymine tetrad in d(TGGGGT) quadruplexes stabilized with Tl+/Na+ ions. Nucleic Acids Res. 32:1097‐1102.
   Campbell, N.H., Parkinson, G.N., Reszka, A.P., and Neidle, S. 2008. Structural basis of DNA quadruplex recognition by an acridine drug. J. Amer. Chem. Soc. 130:6722‐6724.
   Campbell, N.H., Patel, M., Tofa, A.B., Ghosh, R., Parkinson, G.N., and Neidle, S. 2009. Selectivity in ligand recognition of G‐quadruplex loops. Biochemistry 48:1675‐1680.
   Campbell, N.H., Smith, D.L., Reszka, A.P., Neidle, S., and O'Hagan, D. 2011. Fluorine in medicinal chemistry: β‐fluorination of peripheral pyrrolidines attached to acridine ligands affects their interactions with G‐quadruplex DNA. Org. Biomol. Chem. 9:1328‐1331.
   Campbell, N.H., Karim, N.H.A., Parkinson, G.N., Gunaratnam, M., Petrucci, V., Todd, A.K., Vilar, R., and Neidle, S. 2012. Molecular basis of structure‐activity relationships between salphen metal complexes and human telomeric DNA quadruplexes. J. Med. Chem. 55:209‐222.
   Clark, G.R., Pytel, P.D., Squire, C.J., and Neidle, S. 2003. Structure of the first parallel DNA quadruplex‐drug complex. J. Amer. Chem. Soc. 125:4066‐4067.
   Clark, G.R., Pytel, P.D., and Squire, C.J. 2012. The high‐resolution crystal structure of a parallel intermolecular DNA G‐4 quadruplex/drug complex employing syn glycosyl linkages. Nucleic Acids Res. 40:5731‐5738.
   Collie, G.W., Haider, S.M., Neidle, S., and Parkinson, G.N. 2010a. A crystallographic and modelling study of a human telomeric RNA (TERRA) quadruplex. Nucleic Acids Res. 38:5569‐5580.
   Collie, G.W., Parkinson, G.N., Neidle, S., Rosu, F., De Pauw, E., and Gabelica, V. 2010b. Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric complex structures. J. Amer. Chem. Soc. 132:9328‐9334.
   Collie, G.W., Sparapani, S., Parkinson, G.N., and Neidle, S. 2011. Structural basis of telomeric RNA quadruplex‐acridine ligand recognition. J. Amer. Chem. Soc. 133:2721‐2728.
   Collie, G.W., Promontorio, R., Hampel, S.M., Micco, M., Neidle, S., and Parkinson, G.N. 2012. Structural basis for telomeric G‐quadruplex targeting by naphthalene diimide ligands. J. Amer. Chem. Soc. 134:2723‐2731.
   Deng, J., Xiong, Y., and Sundaralingam, M. 2001. X‐ray analysis of an RNA tetraplex (UGGGGU)(4) with divalent Sr(2+) ions at subatomic resolution (0.61 Å). Proc. Natl. Acad. Sci. U.S.A. 98:13665‐13670.
   Eddy, J. and Maizels, N. 2006. Gene function correlates with potential for G4 DNA formation in the human genome. Nucleic Acids Res. 34:3887‐3896.
   Eddy, J. and Maizels, N. 2008. Conserved elements with potential to form polymorphic G‐quadruplex structures in the first intron of human genes. Nucleic Acids Res. 36:1321‐1330.
   Gellert, M., Lipsett, M.N., and Davies, D.R. 1962. Helix formation by guanylic acid. Proc. Natl. Acad. Sci. U.S.A. 48:2013‐2018.
   Gill, M.L., Strobel, S.A., and Loria, J.P. 2006. Crystallization and characterization of the thallium form of the Oxytricha nova G‐quadruplex. Nucleic Acids Res. 34:4506‐4514.
   Haider, S.M., Parkinson, G.N., and Neidle, S. 2002. Crystal structure of the potassium form of an Oxytricha nova G‐quadruplex. J. Mol. Biol. 320:189‐200.
   Haider, S.M., Parkinson, G.N., and Neidle, S. 2003. Structure of a G‐quadruplex‐ligand complex. J. Mol. Biol. 326:117‐125.
   Hazel, P., Parkinson, G.N., and Neidle, S. 2006. Topology variation and loop structural homology in crystal and simulated structures of a bimolecular DNA quadruplex. J. Amer. Chem. Soc. 128:5480‐5487.
   Horvath, M.P. and Schultz, S.C. 2001. DNA G‐quartets in a 1.86 Å resolution structure of an Oxytricha nova telomeric protein‐DNA complex. J. Mol. Biol. 310:367‐377.
   Huppert, J.L. and Balasubramanian, S. 2005. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33:2908‐2916.
   Huppert, J.L. and Balasubramanian, S. 2007. G‐quadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35:406‐413.
   Huppert, J.L., Bugaut, A., Kumari, S., and Balasubramanian, S. 2008. G‐quadruplexes: The beginning and end of UTRs. Nucleic Acids Res. 36:6260‐6268.
   Kang, C., Zhang, X., Ratliff, R., Moyzis, R., and Rich, A. 1992. Crystal structure of four‐stranded Oxytricha telomeric DNA. Nature 356:126‐131.
   Laughlan, G., Murchie, A.I., Norman, D.G., Moore, M.H., Moody, P.C., Lilley, D.M., and Luisi, B. 1994. The high‐resolution crystal structure of a parallel‐stranded guanine tetraplex. Science 265:520‐524.
   López de Silanes, I., d'Alcontres, M.S., and Blasco, M.A. 2010. TERRA transcripts are bound by a complex array of RNA‐binding proteins. Nature Commun. 1:1‐9.
   Luke, B. and Lingner, J. 2009. TERRA: Telomeric repeat‐containing RNA. EMBO J. 28:2503‐2510.
   Neidle, S. 2009. The structures of quadruplex nucleic acids and their drug complexes. Curr. Opin. Struct. Biol. 19:239‐250.
   Neidle, S. 2011. Therapeutic Applications of Quadruplex Nucleic Acids. Academic Press, San Diego.
   Pan, B., Xiong, Y., Shi, K., Deng, J., and Sundaralingam, M. 2003a. Crystal structure of an RNA purine‐rich tetraplex containing adenine tetrads: implications for specific binding in RNA tetraplexes. Structure 11:815‐823.
   Pan, B., Xiong, Y., Shi, K., and Sundaralingam, M. 2003b. An eight‐stranded helical fragment in RNA crystal structure: implications for tetraplex interaction. Structure 11:825‐831.
   Pan, B., Xiong, Y., Shi, K., and Sundaralingam, M. 2003c. Crystal structure of a bulged RNA tetraplex at 1.1 Å resolution: Implications for a novel binding site in RNA tetraplex. Structure 11:1423‐1430.
   Pan, B., Shi, K., and Sundaralingam, M. 2006a. Base‐tetrad swapping results in dimerization of RNA quadruplexes: Implications for formation of the i‐motif RNA octaplex. Proc. Natl. Acad. Sci. U.S.A. 103:3130‐3134.
   Pan, B., Shi, K., and Sundaralingam, M. 2006b. Crystal structure of an RNA quadruplex containing inosine tetrad: Implications for the roles of NH2 group in purine tetrads. J. Mol. Biol. 363:451‐459.
   Parkinson, G.N., Lee, M.P.H., and Neidle, S. 2002. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417:876‐880.
   Parkinson, G.N., Ghosh, R., and Neidle, S. 2007. Structural basis for binding of porphyrin to human telomeres. Biochemistry 46:2390‐2397.
   Parkinson, G.N., Cuenca, F., and Neidle, S. 2008. Topology conservation and loop flexibility in quadruplex‐drug recognition: Crystal structures of inter‐ and intramolecular telomeric DNA quadruplex‐drug complexes. J. Mol. Biol. 381:1145‐1156.
   Phan, A.T. 2010. Human telomeric G‐quadruplex: Structures of DNA and RNA sequences. FEBS J. 277:1107‐1117.
   Phan, A.T., Kuryavyi, V., and Patel, D.J. 2006. DNA architecture: From G to Z. Curr. Opin. Struct. Biol. 16:1‐11.
   Phillips, K., Dauter, Z., Murchie, A.I., Lilley, D.M., and Luisi, B. 1997. The crystal structure of a parallel‐stranded guanine tetraplex at 0.95 Å resolution. J. Mol. Biol. 273:171‐182.
   Smith, F.W. and Feigon, J. 1992. Quadruplex structure of Oxytricha telomeric DNA oligonucleotides. Nature 356:164‐168.
   Todd, A.K. and Neidle, S. 2011. Mapping the sequences of potential guanine quadruplex motifs. Nucleic Acids Res. 39:4917‐4927.
   Todd, A.K., Johnston, M., and Neidle, S. 2005. Highly prevalent putative quadruplex sequence motifs in human DNA. Nucleic Acids Res. 33:2901‐2907.
   Wei, D., Parkinson, G.N., Reszka, A.P., and Neidle, S. 2012. Crystal structure of a c‐kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation. Nucleic Acids Res. 40:4691‐4700.
GO TO THE FULL PROTOCOL:
PDF or HTML at Wiley Online Library