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A clamp-like biohybrid catalyst for DNA oxidation

Nature Chemistry volume 5, pages 945–951 (2013)Cite this article

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Abstract

In processive catalysis, a catalyst binds to a substrate and remains bound as it performs several consecutive reactions, as exemplified by DNA polymerases. Processivity is essential in nature and is often mediated by a clamp-like structure that physically tethers the catalyst to its (polymeric) template. In the case of the bacteriophage T4 replisome, a dedicated clamp protein acts as a processivity mediator by encircling DNA and subsequently recruiting its polymerase. Here we use this DNA-binding protein to construct a biohybrid catalyst. Conjugation of the clamp protein to a chemical catalyst with sequence-specific oxidation behaviour formed a catalytic clamp that can be loaded onto a DNA plasmid. The catalytic activity of the biohybrid catalyst was visualized using a procedure based on an atomic force microscopy method that detects and spatially locates oxidized sites in DNA. Varying the experimental conditions enabled switching between processive and distributive catalysis and influencing the sliding direction of this rotaxane-like catalyst.

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Figure 1: Molecular structures and schematic representation of the concept for a catalytic clamp.
Figure 2: AFM-based method for detecting DNA oxidation.
Figure 3: Octapeptide 3 dictates whether processive or distributive catalysis can take place.
Figure 4: Guiding the direction of the catalytic clamp.
Figure 5: AFM analysis of plasmids oxidized by a guided catalytic clamp.

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Change history

  • 26 September 2013

    In the version of this Article originally published online, the co-author Tom G. Bloemberg should have been included in affiliation 1 as well as 2. This has now been corrected in all versions of the Article.

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Acknowledgements

We thank M. M. Spiering and Z. Zhuang for their assistance and for useful discussions. We thank M. B. Castells and D. van de Mosselaar for synthetic assistance. This work was supported by the Royal Netherlands Academy of Arts and Sciences (R.J.M.N.), NWO Vici (A.E.R.), a research grant from the European Research Council (ERC-2011-AdG 290886 ALPROS to S.F.M.v.D. and R.J.M.N.) and finance from the Dutch Ministry of Education, Culture and Science (Gravity program 024.001.035).

Author information

Author notes

  1. Stijn F. M. van Dongen and Joost Clerx: These authors contributed equally to this report

Authors and Affiliations

  1. Institute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 AJ, The Netherlands

    Stijn F. M. van Dongen, Joost Clerx, Kasper Nørgaard, Tom G. Bloemberg, Jeroen J. L. M. Cornelissen, Alan E. Rowan & Roeland J. M. Nolte

  2. Education Institute for Molecular Sciences, Radboud University Nijmegen, Heyendaalseweg 135, Nijmegen, 6525 ED, The Netherlands

    Tom G. Bloemberg

  3. Department of Chemistry, 801 Chevron Science Center, 219 Parkman Avenue, Pittsburgh, 15260, Pennsylvania, USA

    Michael A. Trakselis

  4. Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, 50011, Indiana, USA

    Scott W. Nelson

  5. Department of Chemistry, Wartik Laboratory

    Stephen J. Benkovic

  6. The Pennsylvania State University, University Park, 16802, Pennsylvania, USA

    Stephen J. Benkovic

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  1. Stijn F. M. van Dongen
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Contributions

S.J.B. and R.J.M.N. conceived the experiments and A.E.R., R.J.M.N., S.F.M.v.D. and J.C. designed the experiments. J.C. performed the experimental work and was supervised by J.J.L.M.C. K.N. developed the AFM-analysis. M.A.T. and S.W.N. provided expertise on protein design and expression. T.G.B. performed statistical analysis. S.F.M.v.D. performed additional experimental work. J.C., S.F.M.v.D., K.N., T.G.B., A.E.R. and R.J.M.N. analysed and interpreted the results. S.F.M.v.D. and J.C. co-wrote the manuscript and S.J.B., A.E.R., R.J.M.N., K.N., M.A.T., S.W.N. and T.G.B. commented on it.

Corresponding authors

Correspondence to Alan E. Rowan or Roeland J. M. Nolte.

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The authors declare no competing financial interests.

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van Dongen, S., Clerx, J., Nørgaard, K. et al. A clamp-like biohybrid catalyst for DNA oxidation. Nature Chem 5, 945–951 (2013). https://doi.org/10.1038/nchem.1752

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