Small-molecule-mediated G-quadruplex isolation from human cells (original) (raw)

References

  1. Taunton, J., Hassig, C. A. & Schreiber, S. L. A mammalian histone deacetylase related to the yeast transcriptional regulator Rpd3p. Science 272, 408–411 (1996).
    Article CAS Google Scholar
  2. Kielkopf, C. L. et al. A structural basis for recognition of A·T and T·A base pairs in the minor groove of B-DNA. Science 282, 111–115 (1998).
    Article CAS Google Scholar
  3. Schaeffer, C. et al. The fragile X mental retardation protein binds specifically to its mRNA via a purine quartet motif. EMBO J. 20, 4803–4813 (2001).
    Article CAS Google Scholar
  4. Siddiqui-Jain, A., Grand, C. L., Bearss, D. J. & Hurley, L. H. Direct evidence for a G-quadruplex in a promoter region and its targeting with a small molecule to repress c-MYC transcription. Proc. Natl Acad. Sci. USA 99, 11593–11598 (2002).
    Article CAS Google Scholar
  5. Zahler, A. M., Williamson, J. R., Cech, T. R. & Prescott, D. M. Inhibition of telomerase by G-quartet DNA structures. Nature 350, 718–720 (1991).
    Article CAS Google Scholar
  6. Rizzo, A. et al. Stabilization of quadruplex DNA perturbs telomere replication leading to the activation of an ATR-dependent ATM signalling pathway. Nucleic Acids Res. 37, 5353–5364 (2009).
    Article CAS Google Scholar
  7. Huppert, J. L. & Balasubramanian, S. Prevalence of quadruplexes in the human genome. Nucleic Acids Res. 33, 2908–2916 (2005).
    Article CAS Google Scholar
  8. Barski, A. et al. High-resolution profiling of histone methylation in the human genome. Cell 129, 823–837 (2007).
    Article CAS Google Scholar
  9. Johnson, D. S., Mortazavi, A., Myers, R. M. & Wold, B. Genome-wide mapping of in vivo protein–DNA interactions. Science 316, 1497–1502 (2007).
    Article CAS Google Scholar
  10. Bentley, D. R. et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456, 53–59 (2008).
    Article CAS Google Scholar
  11. Rodriguez, R. et al. A novel small molecule that alters shelterin integrity and triggers a DNA-damage response at telomeres. J. Am. Chem. Soc. 130, 15758–15759 (2008).
    Article CAS Google Scholar
  12. Buguat, A., Rodriguez, R., Kumari, S., Hsu, S.-T. D. & Balasubramanian, S. Small molecule-mediated inhibition of translation by targeting a native RNA G-quadruplex. Org. Biomol. Chem. 8, 2771–2776 (2010).
    Article Google Scholar
  13. d'Adda di Fagagna, F. et al. A DNA damage checkpoint response in telomere-initiated senescence. Nature 426, 194–198 (2003).
    Article CAS Google Scholar
  14. Hunter, C. A. & Sanders, J. K. M. The nature of π–π interactions. J. Am. Chem. Soc. 112, 5525–5534 (1990).
    Article CAS Google Scholar
  15. Müller, S., Pantoş, G. D., Rodriguez, R. & Balasubramanian, S. Controlled-folding of a small molecule modulates DNA G-quadruplex recognition. Chem. Commun. 80–82 (2009).
  16. Berl, B., Huc, I., Khoury, R. G., Krische, M. J. & Lehn, J.-M. Interconversion of single and double helices formed from synthetic molecular strands. Nature 402, 720–723 (2000).
    Article Google Scholar
  17. Jain, S. L. et al. New pyridine carboxamide ligands and their complexation to copper(II). X-ray crystal structure of mono-, di, tri- and tetranuclear copper complexes. Dalton Trans. 862–871 (2004).
  18. Parkinson, G. N., Lee, M. P. H. & Neidle, S. Crystal structure of parallel quadruplexes from human telomeric DNA. Nature 417, 876–880 (2002).
    Article CAS Google Scholar
  19. Phan, A. T., Kuryavyi, V., Burge, S., Neidle, S. & Patel, D. J. Structure of an unprecedented G-quadruplex scaffold in the human c-kit promoter. J. Am. Chem. Soc. 129, 4386–4392 (2007).
    Article CAS Google Scholar
  20. Hsu, S.-T. D. et al. 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 (2009).
    Article CAS Google Scholar
  21. Kumari, S., Bugaut, A., Huppert, J. L. & Balasubramanian, S. An RNA G-quadruplex in the 5′ UTR of the NRAS proto-oncogene modulates translation. Nature Chem. Biol. 3, 218–221 (2007).
    Article CAS Google Scholar
  22. Rodriguez, R., Pantoş, G. D., Gonçalves, D. P. N., Sanders, J. K. M. & Balasubramanian, S. Ligand-driven G-quadruplex conformational switching by using an unusual mode of interaction. Angew. Chem. Int. Ed. 46, 5405–5407 (2007).
    Article CAS Google Scholar
  23. Temime-Smaali, N. et al. The G-quadruplex ligand telomestatin impairs binding of topoisomerase IIIα to G-quadruplex-forming oligonucleotides and uncaps telomeres in ALT cells. PloS One 4, e6919 (2009).
    Article Google Scholar
  24. d'Adda di Fagagna, F. Living on a break: cellular senescence as a DNA-damage response. Nature Rev. Cancer 8, 512–522 (2008).
    Article CAS Google Scholar
  25. Frye, S. V. The art of the chemical probe. Nature Chem. Biol. 6, 159–161 (2010).
    Article CAS Google Scholar
  26. Cawthon, C. Telomere measurement by quantitative PCR. Nucleic Acids Res. 30, e47 (2002).
    Article Google Scholar
  27. Paeschke, K., Simonsson, T., Postberg, J., Rhodes, D. & Lipps, H. J. Telomeres end-binding proteins control the formation of G-quadruplex DNA structures in vivo. Nature Struct. Mol. Biol. 12, 847–854 (2005).
    Article CAS Google Scholar

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