Engineering of interlocked DNA G-quadruplexes as a robust scaffold

Nucleic Acids Research

Volumn 41, Issue 4, 2013, Pages 2683-2688

  Phan, Anh Tuân ^a   Do, Ngoc Quang ^a,b  

^a NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

^b NANYANG TECHNOLOGICAL UNIVERSITY   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

GUANINE QUADRUPLEX; MOLECULAR SCAFFOLD;

ARTICLE; BIOENGINEERING; CONTROLLED STUDY; DNA DETERMINATION; DNA SEQUENCE; ENZYME ACTIVITY; ENZYME INHIBITION; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN FOLDING; PROTEIN LOCALIZATION; SEQUENCE ANALYSIS;

DNA; G-QUADRUPLEXES; HIV INTEGRASE; HIV INTEGRASE INHIBITORS; MODELS, MOLECULAR; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR;

EID: 84876380983     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gks1304     Document Type: Article

References (34)

1. Davis, J.T. (2004) G-quartets 40 years later: from 50-GMP to molecular biology and supramolecular chemistry. Angew. Chem. Int. Ed. Engl., 43, 668-698.
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.
3. Phan, A.T., Kuryavyi, V. and Patel, D.J. (2006) DNA architecture: from G to Z. Curr. Opin. Struct. Biol., 16, 288-298.
4. Patel, D.J., Phan, A.T. and Kuryavyi, V. (2007) Human telomere, oncogenic promoter and 50-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics. Nucleic Acids Res., 35, 7429-7455.
5. Neidle, S. (2009) The structures of quadruplex nucleic acids and their drug complexes. Curr. Opin. Struct. Biol., 19, 239-250.
6. Phan, A.T. (2010) Human telomeric G-quadruplex: structures of DNA and RNA sequences. FEBS J., 277, 1107-1117.
7. 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.
8. Balasubramanian, S. and Neidle, S. (2009) G-quadruplex nucleic acids as therapeutic targets. Curr. Opin. Chem. Biol., 13, 345-353.
9. Bock, L.C., Griffin, L.C., Latham, J.A., Vermaas, E.H. and Toole, J.J. (1992) Selection of single-stranded-DNA molecules that bind and inhibit human thrombin. Nature, 355, 564-566.
10. de Soultrait, V.R., Lozach, P.Y., Altmeyer, R., Tarrago-Litvak, L., Litvak, S. and Andréola, M.L. (2002) DNA aptamers derived from HIV-1 RNase H inhibitors are strong anti-integrase agents. J. Mol. Biol., 324, 195-203.
11. Jing, N., Li, Y., Xiong, W., Sha, W., Jing, L. and Tweardy, D.J. (2004) G-quartet oligonucleotides: a new class of signal transducer and activator of transcription 3 inhibitors that suppresses growth of prostate and breast tumors through induction of apoptosis. Cancer Res., 64, 6603-6609.
12. 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.
13. Bates, P.J., Laber, D.A., Miller, D.M., Thomas, S.D. and Trent, J.O. (2009) Discovery and development of the G-rich oligonucleotide AS1411 as a novel treatment for cancer. Exp. Mol. Pathol., 86, 151-164.
14. Schultze, P., Macaya, R.F. and Feigon, J. (1994) Three-dimensional solution structure of the thrombin-binding DNA aptamer d(GGT TGGTGTGGTTGG). J. Mol. Biol., 235, 1532-1547.
15. Martino, L., Virno, A., Randazzo, A., Virgilio, A., Esposito, V., Giancola, C., Bucci, M., Cirino, G. and Mayol, L. (2006) A new modified thrombin binding aptamer containing a 5′-5′ inversion of polarity site. Nucleic Acids Res., 34, 6653-6662.
16. Phan, A.T., Kuryavyi, V., Ma, J.-B., Faure, A., Andréola, M.-L. and Patel, D.J. (2005) An interlocked dimeric parallel-stranded DNA quadruplex: a potent inhibitor of HIV-1 integrase. Proc. Natl Acad. Sci. USA, 102, 634-639.
17. Huang, Y.C. and Sen, D. (2010) A contractile electronic switch made of DNA. J. Am. Chem. Soc., 132, 2663-2671.
18. Chinnapen, D.J.F. and Sen, D. (2004) A deoxyribozyme that harnesses light to repair thymine dimers in DNA. Proc. Natl Acad. Sci. USA, 101, 65-69.
19. Wieland, M. and Hartig, J.S. (2006) Turning inhibitors into activators: A hammerhead ribozyme controlled by a guanine quadruplex. Angew. Chem. Int. Ed. Engl., 45, 5875-5878.
20. Tang, Z., Goncalves, D.P.N., Wieland, M., Marx, A. and Hartig, J.S. (2008) Novel DNA catalysts based on G-quadruplex recognition. Chembiochem, 9, 1061-1064.
21. Cai, J., Shapiro, E.M. and Hamilton, A.D. (2009) Self-assembling DNA quadruplex conjugated to MRI contrast agents. Bioconjug. Chem., 20, 205-208.
22. Li, T., Wang, E.K. and Dong, S.J. (2009) Potassium-lead-switched G-quadruplexes: A new class of DNA logic gates. J. Am. Chem. Soc., 131, 15082-15083.
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.
24. Majumdar, A., Kettani, A., Skripkin, E. and Patel, D.J. (2001) Pulse sequences for detection of NH2. . . N hydrogen bonds in sheared G. A mismatches via remote, non-exchangeable protons. J. Biomol. NMR, 19, 103-113.
25. Krishnan-Ghosh, Y., Liu, D.S. and Balasubramanian, S. (2004) Formation of an interlocked quadruplex dimer by d(GGGT). J. Am. Chem. Soc., 126, 11009-11016.
26. Miyoshi, D., Karimata, H., Wang, Z.-M., Koumoto, K. and Sugimoto, N. (2007) Artificial G-wire switch with 2, 20-bipyridine units responsive to divalent metal ions. J. Am. Chem. Soc., 129, 5919-5925.
27. Phan, A.T. and Patel, D.J. (2002) A site-specific low-enrichment 15N, 13C isotope-labeling approach to unambiguous NMR spectral assignments in nucleic acids. J. Am. Chem. Soc., 124, 1160-1161.
28. Phan, A.T. (2000) Long-range imino proton-13C J-couplings and the through-bond correlation of imino and non-exchangeable protons in unlabeled DNA. J. Biomol. NMR, 16, 175-178.
29. Huang, X.N., Yu, P.L., LeProust, E. and Gao, X.L. (1997) An efficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences. Nucleic Acids Res., 25, 4758-4763.
30. Lim, K.W., Alberti, P., Guédin, A., Lacroix, L., Riou, J.-F., Royle, N.J., Mergny, J.-L. and Phan, A.T. (2009) Sequence variant (CTAGGG)n in the human telomere favors a G-quadruplex structure containing a G.C.G.C tetrad. Nucleic Acids Res., 37, 6239-6248.
31. Xu, Y., Noguchi, Y. and Sugiyama, H. (2006) The new models of the human telomere d[AGGG(TTAGGG)3] in K+ solution. Bioorgan. Med. Chem., 14, 5584-5591.
32. Phan, A.T., Kuryavyi, V., Luu, K.N. and Patel, D.J. (2007) Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution. Nucleic Acids Res., 35, 6517-6525.
33. Chow, S.A., Vincent, K.A., Ellison, V. and Brown, P.O. (1992) Reversal of integration and DNA splicing mediated by integrase of human immunodeficiency virus. Science, 255, 723-726.
34. Do, N.Q., Lim, K.W., Teo, M.H., Heddi, B. and Phan, A.T. (2011) Stacking of G-quadruplexes: NMR structure of a G-rich oligonucleotide with potential anti-HIV and anticancer activity. Nucleic Acids Res., 39, 9448-9457.