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

Nature Chemistry volume 2, pages 1095–1098 (2010)Cite this article

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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.

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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.

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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.

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  1. Sebastian Müller and Sunita Kumari: These authors contributed equally to this work

Authors and Affiliations

  1. Department of Chemistry, The University of Cambridge, Cambridge, CB2 1EW, UK

    Sebastian Müller, Sunita Kumari, Raphaël Rodriguez & Shankar Balasubramanian

  2. Cancer Research UK, Cambridge Research Institute, Li Ka Shing Center, Cambridge, CB2 0RE, UK

    Shankar Balasubramanian

  3. School of Clinical Medicine, The University of Cambridge, Cambridge, CB2 0SP, UK

    Shankar Balasubramanian

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  1. Sebastian Müller
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  2. Sunita Kumari
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  3. Raphaël Rodriguez
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  4. Shankar Balasubramanian
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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.

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Correspondence to Raphaël Rodriguez or Shankar Balasubramanian.

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The authors declare no competing financial interests.

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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

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