Stability and structure of long intramolecular G-quadruplexes

Biochemistry

Volumn 51, Issue 15, 2012, Pages 3154-3161

  Payet, Linda ^a,b   Huppert, Julian L ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b Centre National de la Recherche Scientifique   (France)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL FUNCTIONS; CELLULAR PROCESS; CIRCULAR DICHROISM DATA; FOLDED STATE; G-QUADRUPLEXES; GEL ELECTROPHORESIS; IN-VITRO; IN-VIVO; SINGLE STRUCTURE; UV MELTING;

ELECTROPHORESIS; HIGH ENERGY PHYSICS; POSITIVE IONS; RNA;

DNA SEQUENCES;

DNA; GUANINE QUADRUPLEX; OLIGONUCLEOTIDE; RNA;

ARTICLE; CIRCULAR DICHROISM; DNA SEQUENCE; GEL ELECTROPHORESIS; PRIORITY JOURNAL; STRUCTURE ANALYSIS; THERMODYNAMICS; ULTRAVIOLET RADIATION;

BASE SEQUENCE; CIRCULAR DICHROISM; ELECTROPHORESIS, POLYACRYLAMIDE GEL; G-QUADRUPLEXES; NUCLEIC ACID CONFORMATION; OLIGONUCLEOTIDES; STRUCTURE-ACTIVITY RELATIONSHIP; THERMODYNAMICS;

EID: 84859910289     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/bi201750g     Document Type: Article

References (48)

1. Neidle, S. and Balasubramanian, S., Eds. (2006) Quadruplex Nucleic Acids; Royal Society of Chemistry, Cambridge.
2. Burge, S., Parkinson, G. N., Hazel, P., Todd, A. K., and Neidle, S. (2006) Quadruplex DNA: sequence, topology and structure Nucleic Acids Res. 34, 5402-5415 (Pubitemid 44742430)
3. Huppert, J. L. and Balasubramanian, S. (2005) Prevalence of quadruplexes in the human genome Nucleic Acids Res. 33, 2908-2916 (Pubitemid 41511230)
4. Todd, A. K., Johnston, M., and Neidle, S. (2005) Highly prevalent putative quadruplex sequence motifs in human DNA Nucleic Acids Res. 33, 2901-2907 (Pubitemid 41511229)
5. Huppert, J. L. and Balasubramanian, S. (2007) G-quadruplexes in promoters throughout the human genome Nucleic Acids Res. 35, 406-413 (Pubitemid 46232058)
6. Hazel, P., Huppert, J., Balasubramanian, S., and Neidle, S. (2004) Loop-length-dependent folding of G-quadruplexes J. Am. Chem. Soc. 126, 16405-16415 (Pubitemid 40081938)
7. Bugaut, A. and Balasubramanian, S. (2008) A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes Biochemistry 47, 689-697 (Pubitemid 351195440)
8. Guédin, A., Gros, J., Alberti, P., and Mergny, J.-L. (2010) How long is too long? Effects of loop size on G-quadruplex stability Nucleic Acids Res. 38, 7858-7868
9. Shirude, P., Okumus, B., Ying, L., Ha, T., and Balasubramanian, S. (2007) Single-molecule conformational analysis of G-quadruplex formation in the promoter DNA duplex of the proto-oncogene C-kit J. Am. Chem. Soc. 129, 7484-7485 (Pubitemid 46981898)
10. Schaffitzel, C., Berger, I., Postberg, J., Hanes, J., Lipps, H. J., and Plückthun, A. (2001) In vitro generated antibodies specific for telomeric guanine-quadruplex DNA react with Stylonychia lemnae macronuclei Proc. Natl. Acad. Sci. U.S.A. 98, 8572-8577 (Pubitemid 32678069)
11. Fry, M. and Loeb, L. A. (1999) Human Werner syndrome DNA helicase unwinds tetrahelical structures of the fragile X syndrome repeat sequence d(CGG)n J. Biol. Chem. 274, 12797-12802
12. Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D., and Lipps, H. J. (2005) Telomere end-binding proteins control the formation of G-quadruplex DNA structures in vivo Nat. Struct. Mol. Biol. 12, 847-854 (Pubitemid 41486707)
13. Oganesian, L. and Bryan, T. M. (2007) Physiological relevance of telomeric G-quadruplex formation: a potential drug target Bioessays 29, 155-165 (Pubitemid 46340250)
14. Lipps, H. J. and Rhodes, D. (2009) G-quadruplex structures: in vivo evidence and function Trends Cell Biol. 19, 414-422
15. Kim, N., Piatyszek, M., Prowse, K., Harley, C., West, M., Ho, P., Coviello, G., Wright, W., Weinrich, S., and Shay, J. (1994) Specific association of human telomerase activity with immortal cells and cancer Science 266, 2011-2015
16. Neidle, S. and Parkinson, G. (2002) Telomere maintenance as a target for anticancer drug discovery Nat. Rev. Drug Discovery 1, 383-393 (Pubitemid 37361468)
17. Qin, Y. and Hurley, L. H. (2008) Structures, folding patterns, and functions of intramolecular DNA G-quadruplexes found in eukaryotic promoter regions Biochimie 90, 1149-1171
18. Balasubramanian, S., Hurley, L. H., and Neidle, S. (2011) Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nat. Rev. Drug. Discovery 10, 261-275
19. Wong, H. M., Payet, L., and Huppert, J. L. (2009) Function and targeting of G-quadruplexes Curr. Opin. Mol. Ther. 11, 146-155
20. Murat, P., Singh, Y., and Defrancq, E. (2011) Methods for investigating G-quadruplex DNA/ligand interactions Chem. Soc. Rev. 40, 5293-5307
21. Teng, Y., Girvan, A. C., Casson, L. K., Pierce, W. M., Qian, M., Thomas, S. D., and Bates, P. J. (2007) AS1411 alters the localization of a complex containing protein arginine methyltransferase 5 and nucleolin Cancer Res. 67, 10491-10500 (Pubitemid 350070825)
22. Soundararajan, S., Chen, W., Spicer, E. K., Courtenay-Luck, N., and Fernandes, D. J. (2008) The nucleolin targeting aptamer AS1411 destabilizes Bcl-2 messenger RNA in human breast cancer cells Cancer Res. 68, 2358-2365 (Pubitemid 351521810)
23. Alberti, P., Bourdoncle, A., Sacca, B., Lacroix, L., and Mergny, J.-L. (2006) DNA nanomachines and nanostructures involving quadruplexes Org. Biomol. Chem. 4, 3383-3391 (Pubitemid 44319622)
24. Sen, D. and Fahlman, R. P. DNA conformational switches as sensitive electronic sensors of analytes. U.S. Patent 7,943,301 B2, 2011.
25. Stegle, O., Payet, L., Mergny, J.-L., MacKay, D. J. C., and Huppert, J. L. (2009) Predicting and understanding the stability of G-quadruplexes Bioinformatics 25, i374-i382
26. Parkinson, G. N., Lee, M. P. H, and Neidle, S. (2002) Crystal structure of parallel quadruplexes from human telomeric DNA Nature 417, 876-880 (Pubitemid 34670337)
27. Vorlíčková, M., Chládková, J., Kejnovská, I., Fialová, M., and Kypr, J. (2005) Guanine tetraplex topology of human telomere DNA is governed by the number of (TTAGGG) repeats Nucleic Acids Res. 33, 5851-5860 (Pubitemid 41742604)
28. Yu, H.-Q., Miyoshi, D., and Sugimoto, N. (2006) Characterization of structure and stability of long telomeric DNA G-quadruplexes J. Am. Chem. Soc. 128, 15461-15468 (Pubitemid 44876022)
29. Pedroso, I. M., Duarte, L. F., Yanez, G., Burkewitz, K., and Fletcher, T. M. (2007) Sequence specificity of inter- and intramolecular G-quadruplex formation by human telomeric DNA Biopolymers 87, 74-84 (Pubitemid 47401783)
30. Petraccone, L., Trent, J. O., and Chaires, J. B. (2008) The tail of the telomere J. Am. Chem. Soc. 130, 16530-16532
31. Haider, S., Parkinson, G. N., and Neidle, S. (2008) Molecular dynamics and principal components analysis of human telomeric quadruplex multimers Biophys. J. 95, 296-311
32. Martadinata, H. and Phan, A. T. (2009) Structure of propeller-type parallel-stranded RNA G-quadruplexes, formed by human telomeric RNA sequences in K+ solution J. Am. Chem. Soc. 131, 2570-2578
33. Collie, G. W., Parkinson, G. N., Neidle, S., Rosu, F., De Pauw, E., and Gabelica, V. (2010) Electrospray mass spectrometry of telomeric RNA (TERRA) reveals the formation of stable multimeric G-quadruplex structures J. Am. Chem. Soc. 132, 9328-9334
34. Martadinata, H., Heddi, B., Lim, K. W., and Phan, A. T. (2011) Structure of long human telomeric RNA (TERRA): G-quadruplexes formed by four and eight UUAGGG repeats are stable building blocks Biochemistry 50, 6455-6461
35. Bauer, L., Tlučková, K., Tóthová, P., and Viglaský, V. (2011) G-quadruplex motifs arranged in tandem occurring in telomeric repeats and the insulin-linked polymorphic region Biochemistry 50, 7484-7492
36. Phan, A. T., Kuryavyi, V., Gaw, H. Y., and Patel, D. J. (2005) Small-molecule interaction with a five-guanine-tract G-quadruplex structure from the human MYC promoter Nat. Chem. Biol. 1, 167-173
37. Kumar, N. and Maiti, S. (2008) A thermodynamic overview of naturally occurring intramolecular DNA quadruplexes Nucleic Acids Res. 36, 5610-5622
38. Todd, A. K. and Neidle, S. (2011) Mapping the sequences of potential guanine quadruplex motifs Nucleic Acids Res. 39, 4917-4927
39. Kejnovská, I., Kypr, J., and Vorlíčková, M. (2007) Oligo(dT) is not a correct native PAGE marker for single-stranded DNA Biochem. Biophys. Res. Commun. 353, 776-779 (Pubitemid 46048738)
40. Mergny, J. and Lacroix, L. (2003) Analysis of thermal melting curves Oligonucleotides 13, 515-537 (Pubitemid 38296149)
41. Risitano, A. and Fox, K. R. (2003) Stability of intramolecular DNA quadruplexes: comparison with DNA duplexes Biochemistry 42, 6507-6513 (Pubitemid 36665826)
42. Brown, N. M., Rachwal, P. A., Brown, T., and Fox, K. R. (2005) Exceptionally slow kinetics of the intramolecular quadruplex formed by the Oxytricha telomeric repeat Org. Biomol. Chem. 3, 4153-4157 (Pubitemid 41729676)
43. Merkina, E. E. and Fox, K. R. (2005) Kinetic stability of intermolecular DNA quadruplexes Biophys. J. 89, 365-373 (Pubitemid 41098291)
44. Rachwal, P., Brown, T., and Fox, K. (2007) Sequence effects of single base loops in intramolecular quadruplex DNA FEBS Lett. 581, 1657-1660 (Pubitemid 46528934)
45. Tang, J., Kan, Z.-y., Yao, Y., Wang, Q., Hao, Y.-h., and Tan, Z. (2008) G-quadruplex preferentially forms at the very 3′ end of vertebrate telomeric DNA Nucleic Acids Res. 36, 1200-1208 (Pubitemid 351330937)
46. Dai, J., Dexheimer, T. S., Chen, D., Carver, M., Ambrus, A., Jones, R. A., and Yang, D. (2006) An intramolecular G-quadruplex structure with mixed parallel/antiparallel G-strands formed in the human BCL-2 promoter region in solution J. Am. Chem. Soc. 128, 1096-1098 (Pubitemid 43190620)
47. Henson, J. D., Neumann, A. A., Yeager, T. R., and Reddel, R. R. (2002) Alternative lengthening of telomeres in mammalian cells Nature 21, 598-610 (Pubitemid 34146260)
48. Rivera, M. A. and Blackburn, E. H. (2004) Processive utilization of the human telomerase template J. Biol. Chem. 279, 53770-53781