Resolution of quadruplex polymorphism unit 17.3 by size-exclusion chromatography

Current Protocols in Nucleic Acid Chemistry

Volumn , Issue SUPPL. 45, 2011, Pages

  Miller, M Clarke ^a   Trent, John O ^a  

^a UNIVERSITY OF LOUISVILLE   (United States)

Author keywords

Quadruplex; SEC; Size exclusion chromatography; Telomere

Indexed keywords

GUANINE QUADRUPLEX;

ANION EXCHANGE CHROMATOGRAPHY; ARTICLE; DNA POLYMORPHISM; DNA SEQUENCE; FILTRATION; GEL PERMEATION CHROMATOGRAPHY; PRIORITY JOURNAL; REVERSED PHASE HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; TELOMERE;

EID: 84857652094     PISSN: 19349270     EISSN: 19349289     Source Type: Journal    
DOI: 10.1002/0471142700.nc1703s45     Document Type: Article

References (74)

1. Ambrus, A., Chen, D., Dai, J., Jones, R.A., and Yang, D. 2005. Solution structure of the biologically relevant G-quadruplex element in the human c-MYC promoter. Implications for Gquadruplex stabilization. Biochemistry 44:2048-2058.
2. Balagurumoorthy, P., Brahmachari, S.K.,Mohanty, D., Bansal, M., and Sasisekharan, V. 1992. Hairpin and parallel quartet structures for telomeric sequences. Nucleic Acids Res. 20:4061-4067.
3. Bishop, J.S., Guy-Caffey, J.K., Ojwang, J.O., Smith, S.R., Hogan, M.E.,Cossum, P.A.,Rando, R.F., and Chaudhary, N. 1996. Intramolecular G-quartet motifs confer nuclease resistance to a potent anti-HIV oligonucleotide. J. Biol. Chem. 271:5698-5703.
4. Blume, S.W., Guarcello, V., Zacharias, W., and Miller, D.M. 1997. Divalent transition metal cations counteract potassium-induced quadruplex assembly of oligo(dG) sequences. Nucleic Acids Res. 25:617-625.
5. Bonifacio, L., Church, F.C., and Jarstfer, M.B. 2008. Effect of locked-nucleic acid on a biologically active G-quadruplex. A structure-activity relationship of the thrombin aptamer. Int. J. Mol. Sci. 9:422-433.
6. Cogoi, S., Quadrifoglio, F., andXodo, L.E. 2004. Grich oligonucleotide inhibits the binding of a nuclear protein to the Ki-ras promoter and strongly reduces cell growth in human carcinoma pancreatic cells. Biochemistry 43:2512-2523.
7. Counter, C.M., Avilion, A.A., LeFeuvre, C.E., Stewart, N.G., Greider, C.W., Harley, C.B., and Bacchetti, S. 1992. Telomere shortening associated with chromosome instability is arrested in immortal cells which express telomerase activity. EMBO J. 11:1921-1929.
8. Dai, J., Chen, D., Jones, R.A., Hurley, L.H., and Yang, D. 2006a. NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region. Nucleic Acids Res. 34:5133-5144.
9. Dai, J., Dexheimer, T.S., Chen, D., Carver, M., Ambrus, A., Jones, R.A., and Yang, D. 2006b. 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.
10. Dai, J., Punchihewa, C., Ambrus, A., Chen, D., Jones, R.A., and Yang, D. 2007. Structure of the intramolecular human telomeric G-quadruplex in potassium solution: A novel adenine triple formation. Nucleic Acids Res. 35:2440-2450.
11. Dai, J., Carver, M., and Yang, D. 2008. Polymorphism of human telomeric quadruplex structures. Biochimie 90:1172-1183.
12. Dailey, M., Miller, M.C., Bates, P.J., Lane, A.N., andTrent, J.O. 2010. Resolution and characterization of the structural polymorphism of a single quadruplex-forming sequence. Nucleic Acids Res. 38:4877-4888
13. Dapic, V., Bates, P.J., Trent, J.O., Rodger, A., Thomas, S.D., and Miller, D.M. 2002. Antiproliferative activity of G-quartet-forming oligonucleotides with backbone and sugar modifications. Biochemistry 41:3676-3685.
14. Dapic, V., Abdomerović, V., Marrington, R., Peberdy, J., Rodger, A., Trent, J.O., and Bates,P.J. 2003. Biophysical and biological properties of quadruplex oligodeoxyribonucleotides. Nucleic Acids Res. 31:2097-2107.
15. De Armond, R., Wood, S., Sun, D., Hurley, L.H., and Ebbinghaus, S.W. 2005. Evidence for the presence of a guanine quadruplex forming region within a polypurine tract of the hypoxia inducible factor 1 alpha promoter. Biochemistry 44:16341-16350.
16. Drygin, D., Siddiqui-Jain, A., O'Brien, S., Schwaebe, M., Lin, A., Bliesath, J., Ho, C.B., Proffitt, C., Trent, K., Whitten, J.P., Lim, J.K., Von Hoff, D., Anderes, K., and Rice, W.G. 2009. Anticancer activity of CX-3543: A direct inhibitor of rRNA biogenesis. Cancer Res. 69:7653-7661.
17. Esposito, V., Randazzo, A., Piccialli, G., Petraccone, L., Giancola, C., and Mayol, L. 2004. Effects of an 8-bromodeoxyguanosine incorporation on the parallel quadruplex structure [d(TGGGT)](4). Org. Biomol. Chem. 2:313-318.
18. Esposito, V., Virgilio, A., Randazzo, A., Galeone, A., and Mayol, L. 2005. A new class of DNA quadruplexes formed by oligodeoxyribonucleotides containing a 3′3′or 5′5′inversion of polarity site. Chem. Commun. (Camb) 31:3953-3955.
19. Fernando, H.,Reszka, A.P.,Huppert, J., Ladame, S., Rankin, S., Venkitaraman, A.R., Neidle, S., and Balasubramanian, S. 2006.Aconserved quadruplex motif located in a transcription activation site of the human c-kit oncogene. Biochemistry 45:7854-7860.
20. Frigon, R.P., Leypoldt, J.K., Uyeji, S., and Henderson, L.W. 1983. Disparity between Stokes radii of dextrans and proteins as determined by retention volume in gel permeation chromatography. Anal. Chem. 55:1349-1354.
21. Garbett, N.C., Mekmaysy, C.S., and Chaires, J.B. 2009. Sedimentation velocity ultracentrifugation analysis for hydrodynamic characterization of G-quadruplex structures. In G-Quadruplex DNA (P. Bauman andJ.M. Walker, eds) pp. 97-120. Springer, New York.
22. Giraldo, R., Suzuki, M., Chapman, L., and Rhodes, D. 1994. Promotion of parallel DNA quadruplexes by a yeast telomere binding protein: A circular dichroism study. Proc. Natl. Acad. Sci. U.S.A. 91:7658-7662.
23. Gray, R.D., Li, J., and Chaires, J.B. 2009. Energetics and kinetics of a conformational switch in G-quadruplexDNA. J. Phys.Chem.B113:2676-2683.
24. Gray, R.D., Petraccone, L., Trent, J.O., and Chaires, J.B. 2010. Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence. Biochemistry 49:179-194.
25. Gros, J., Aviñó, A., Lopez de la Osa, J., González, C., Lacroix, L., Pérez, A., Orozco,M., Eritja, R., andMergny, J.L. 2008. 8-Amino guanine accelerates tetramolecular G-quadruplex formation. Chem. Commun. 25:2926-2928.
26. Hahn, W.C., Stewart, S.A., Brooks, M.W., York, S.G., Eaton, E., Kurachi, A., Beijersbergen, R.L., Knoll, J.H., Meyerson, M., and Weinberg, R.A. 1999. Inhibition of telomerase limits the growth of human cancer cells. Nat. Med. 5:1164-1170.
27. Hazel, P., Huppert, J., Balasubramanian, S., and Neidle, S. 2004. Loop-length-dependent folding of G-quadruplexes. J. Am. Chem. Soc. 126:16405-16415.
28. Hopkins, A.L. 2009. Drug discovery: Predicting promiscuity. Nature 462:167-168.
29. Hsu, S.T.D., Varnai, P., Bugaut, A., Reszka, A.P., Neidle, S., and Balasubramanian, S. 2009. A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics. J. Am. Chem. Soc. 131:13399-13409.
30. Huppert, J.L. 2007. Four-stranded DNA: Cancer, gene regulation and drug development. Philos. Transact. A Math Phys. Eng. Sci. 365:2969-2984.
31. Huppert, J.L. and Balasubramanian, S. 2005. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33:2908-2916.
32. Huppert, J.L. and Balasubramanian, S. 2007. Gquadruplexes in promoters throughout the human genome. Nucleic Acids Res. 35:406-413.
33. Ireson, C.R. and Kelland, L.R. 2006. Discovery and development of anticancer aptamers. Mol. Cancer Therapeut. 5:2957-2962.
34. Ireson, C., Djeha, H., Cook, J., Ritchie, C., Jones, D., Green, C., Trent, J., Bates, P., Miller, D., and Kelland, L. 2005. Preclinical anticancer properties of a G-rich oligonucleotide-based aptamer, AS1411. Clin. Cancer Res. 11:9114s-9114s.
35. Jing, N.J. and Tweardy, D.J. 2005. Targeting Stat3 in cancer therapy. Anticancer Drugs 16:601-607.
36. Jing, N.J., Rando, R.F., Pommier, Y., and Hogan, M.E. 1997. Ion selective folding of loop domains in a potent anti-HIV oligonucleotide. Biochemistry 36:12498-12505.
37. Jing, N.J., Li, Y., Xu, X., Sha, W., Li, P., Feng, L., and Tweardy, D.J. 2003. Targeting Stat3 with Gquartet oligodeoxynucleotides in human cancer cells. DNA Cell Biol. 22:685-696.
38. Jing, N.J., Sha,W., Li, Y., Xiong,W., and Tweardy, D.J. 2005. Rational drug design of G-quartet DNA as anti-cancer agents. Curr. Pharm. Des. 11:2841-2854.
39. Keiser, M.J., Setola, V., Irwin, J.J., Laggner, C., Abbas, A.I., Hufeisen, S.J., Jensen, N.H., Kuijer, M.B., Matos, R.C., Tran, T.B., Whaley, R., Glennon, R.A., Hert, J., Thomas, K.L., Edwards, D.D., Shoichet, B.K., and Roth, B.L. 2009. Predicting new molecular targets for known drugs. Nature 462:175-181.
40. Kim, N.W., Piatyszek,M.A., Prowse, K.R., Harley, C.B., West, M.D., Ho, P.L., Coviello, G.M., Wright, W.E., Weinrich, S.L., and Shay, J.W. 1994. Specific association of human telomerase activity with immortal cells and cancer. Science 266:2011-2015.
41. Kumar, N. and Maiti, S. 2007. Role of locked nucleic acid modified complementary strand in quadruplex/Watson-Crick duplex equilibrium. J. Phys. Chem. B 111:12328-12337.
42. Kypr, J., Kejnovská, I., Renciuk, D., and Vorlícková, M. 2009. Circular dichroism and conformational polymorphism of DNA. Nucleic Acids Res. 37:1713-1725.
43. Lane, A.N., Chaires, J.B., Gray, R.D., and Trent, J.O. 2008. Stability and kinetics of G-quadruplex structures. Nucleic Acids Res. 36:5482-5515.
44. Le Maire, M., Aggerbeck, L.P., Monteilhet, C., Andersen, J.P., and Møller, J.V. 1986. The use of high-performance liquid chromatography for the determination of size and molecular weight of proteins: A caution and a list of membrane proteins suitable as standards. Anal. Biochem. 154:525-535.
45. Le Maire, M., Ghazi, A., Møller, J.V., and Aggerbeck, L.P. 1987. The use of gel chromatography for the determination of sizes and relative molecular masses of proteins. Interpretation of calibration curves in terms of gelpore-size distribution. Biochem. J. 243:399-404.
46. Li, J., Correia, J.J., Wang, L., Trent, J.O., and Chaires, J.B. 2005. Not so crystal clear: The structure of the human telomere G-quadruplex in solution differs from that present in a crystal. Nucleic Acids Res. 33:4649-4659.
47. Marathias, V.M., Sawicki, M.J., and Bolton, P.H. 1999. 6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation. Nucleic Acids Res. 27:2860-2867.
48. Mekmaysy, C.S., Petraccone, L., Garbett, N.C., Ragazzon, P.A., Gray, R., Trent, J.O., and Chaires, J.B. 2008. Effect of O6-methylguanine on the stability of G-quadruplex DNA. J. Am. Chem. Soc. 130:6710-6711.
49. Miller, M.C., Buscaglia, R., Chaires, J.B., Lane, A.N., andTrent, J.O. 2010. Hydration is a major determinant of the G-quadruplex stability and conformation of the human telomere 3'sequence of d(AG(3)(TTAG(3))(3)). J. Am. Chem. Soc. 132:1705-1707.
50. Miyoshi, D., Nakao, A., and Sugimoto, N. 2001. Structural transition of d(G4T4G4) from antiparallel to parallel G-quartet induced by divalent cations. Nucleic Acids Res. 1:259-260.
51. Neidle, S. 2010. Human telomeric G-quadruplex: The current status of telomeric G-quadruplexes as therapeutic targets in human cancer. FEBS J. 277:1118-1125.
52. Neidle, S. and Parkinson, G. 2002. Telomere maintenance as a target for anticancer drug discovery. Nat. Rev. Drug Discov. 1:383-393.
53. Patel, D.J., Phan, A.T., and Kuryavyi, V. 2007. Human telomere, oncogenic promoter and 5′-UTR G-quadruplexes: Diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res. 35:7429-7455.
54. Petrovic, A.G. and Polavarapu, P.L. 2008. Quadruplex structure of polyriboinosinic acid: Dependence on alkali metal ion concentration, pH and temperature. J. Phys. Chem. B 112:2255-2260.
55. Phan, A.T., Kuryavyi, V., Burge, S., Neidle, S., and Patel, D.J. 2007a. Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter. J. Am. Chem. Soc. 129:4386-4392.
56. + solution. Nucleic Acids Res. 35:6517-6525.
57. Qi, J. and Shafer, R.H. 2007. Human telomere quadruplex: Refolding and selection of individual conformers via RNA/DNA chimeric editing. Biochemistry 46:7599-7606.
58. Qi, H., Lin, C.P., Fu, X., Wood, L.M., Liu, A.A., Tsai, Y.C., Chen, Y., Barbieri, C.M., Pilch, D.S., and Liu, L.F. 2006. G-quadruplexes induce apoptosis in tumor cells. Cancer Res. 66:11808-11816.
59. Rawal, P., Kummarasetti, V.B.R., Ravindran, J., Kumar, N., Halder, K., Sharma, R.,Mukerji, M., Das, S.K., and Chowdhury, S. 2006. Genomewide prediction of G4 DNA as regulatory motifs: Role in Escherichia coli global regulation. Genome Res. 16:644-655.
60. Shay, J.W. and Bacchetti, S. 1997. A survey of telomerase activity in human cancer. Eur. J. Cancer 33:787-791.
61. Siddiqui-Jain, A., Grand, C.L., Bearss, D.J., and Hurley, L.H. 2002. Direct evidence for a Gquadruplex in a promoter region and its targeting with a small molecule to repress c-MYCtranscription. Proc.Natl. Acad. Sci.U.S.A. 99:11593-11598.
62. Simonsson, T., Pecinka, P., and Kubista, M. 1998. DNA tetraplex formation in the control region of c-myc. Nucleic Acids Res. 26:1167-1172.
63. Spackova, N., Cubero, E., Sponer, J., and Orozco, M. 2004. Theoretical study of the guanine→6-thioguanine substitution in duplexes, triplexes, and tetraplexes. J. Am. Chem. Soc. 126:14642-14650.
64. Sun, D., Thompson, B., Cathers, B.E., Salazar, M., Kerwin, S.M., Trent, J.O., Jenkins, T.C., Neidle, S., and Hurley, L.H. 1997. Inhibition of human telomerase by a G-quadruplex-interactive compound. J. Med. Chem. 40:2113-2116.
65. Sun, D.Y., Guo, K.X., Rusche, J.J., and Hurley, L.H. 2005. Facilitation of a structural transition in the polypurine/polypyrimidine tract within the proximal promoter region of the human VEGF gene by the presence of potassium and G-quadruplex-interactive agents. Nucleic Acids Res. 33:6070-6080.
66. Suzuki, J., Miyano-Kurosaki, N., Kuwasaki, T., Takeuchi, H., Kawai, G., and Takaku, H. 2002. Inhibition of human immunodeficiency virus type 1 activity in vitro by a new self-stabilized oligonucleotide with guanosinethymidine quadruplex motifs. J. Virol. 76:3015-3022.
67. Szalai, V.A., Singer, M.J., and Thorp, H.H. 2002. Site-specific probing of oxidative reactivity and telomerase function using 7, 8-dihydro-8-oxoguanine in telomeric DNA. J. Am. Chem. Soc. 124:1625-1631.
68. Tang, C.F. and Shafer, R.H. 2006. Engineering the quadruplex fold: Nucleoside conformation determines both folding topology and molecularity in guanine quadruplexes. J. Am. Chem. Soc. 128:5966-5973.
69. Virgilio, A., Esposito, V., Randazzo, A., Mayol, L., and Galeone, A. 2005a. 8-Methyl-2′-deoxyguanosine incorporation into parallel DNA quadruplex structures. Nucleic Acids Res. 33:6188-6195.
70. Virgilio, A., Esposito, V., Randazzo, A., Mayol, L., and Galeone, A. 2005b. Effects of 8-methyl-2′-deoxyadenosine incorporation into quadruplex forming oligodeoxyribonucleotides. Bioorg. Med. Chem. 13:1037-1044.
71. Webba da Silva, M. 2007. Geometric formalism for DNA quadruplex folding. Chemistry 13:9738-9745.
72. Wright, W.E., Tesmer, V.M., Huffman, K.E., Levene, S.D., and Shay, J.W. 1997. Normal human chromosomes have long G-rich telomeric overhangs at one end. Genes Dev. 11:2801-2809.
73. + solution under molecular crowding condition. J. Am. Chem. Soc. 129:11185-11191.
74. Yang, D. and Okamoto, K. 2010. Structural insights into G-quadruplexes: Towards new anticancer drugs. Future Med. Chem. 2:619-646.