Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Small-molecule-mediated G-quadruplex isolation from human cells

Abstract

Nucleic acids containing stretches of tandem guanines can fold into four-stranded structures called G-quadruplexes. The existence of such sequences in genomic DNA suggests the occurrence of these motifs in cells, with potential implications in a number of biological processes relevant to cancer. Small molecules have proven to be valuable tools to dissect cell circuitry. Here, we describe a synthetic small molecule derived from an N,N′-bis(2-quinolinyl)pyridine-2,6-dicarboxamide, which is designed to mediate the selective isolation of G-quadruplex nucleic acids. The methodology was successfully applied to a range of DNA and RNA G-quadruplexes in vitro. We demonstrate the general applicability of the method by isolating telomeric DNA-containing G-quadruplex motifs from cells. We show that telomeres are targets for the probe, providing further evidence of the formation of G-quadruplexes in human cells.

This is a preview of subscription content, access via your institution

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Molecular structures of 1 and 2.
Figure 2: Molecular probe 2 mediates selective G-quadruplex isolation from solution.
Figure 3: Molecular probe 2 induces in cellulo G-overhang shortening and mediates G-quadruplex-containing telomeric fragment isolation from human cells.

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 

Download references

Acknowledgements

The authors thank D.A. Sanders, R. Kranaster, J.–F. Riou, D. Gomez, A.R. Venkitaraman, A.J. Bannister and K. Holmes for fruitful discussions and advice. The authors also acknowledge Cancer Research UK for a studentship (S.M.) and programme funding, and the Biotechnology and Biological Sciences Research Council for project funding. R.R. is a Herchel Smith Research Fellow.

Author information

Authors and Affiliations

Authors

Contributions

R.R. and S.B. conceptualized the study. R.R. is the inventor of pyridostatin and related analogues. All the authors designed the experiments and analysed the data. S.M. and S.K. performed the experiments. R.R. and S.B wrote the manuscript with contributions from S.M. and S.K.

Corresponding authors

Correspondence to Raphaël Rodriguez or Shankar Balasubramanian.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 1914 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Müller, S., Kumari, S., Rodriguez, R. et al. Small-molecule-mediated G-quadruplex isolation from human cells. Nature Chem 2, 1095–1098 (2010). https://doi.org/10.1038/nchem.842

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nchem.842

This article is cited by

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing