Department of Biochemistry University of Oxford Department of Biochemistry
University of Oxford
South Parks Road
Oxford OX1 3QU

Tel: +44 (0)1865 613200
Fax: +44 (0)1865 613201
Image showing the global movement of lipids in a model planar membrane
Matthieu Chavent, Sansom lab
Anaphase bridges in fission yeast cells
Whitby lab
Lactose permease represented using bending cylinders in Bendix software
Caroline Dahl, Sansom lab
Epithelial cells in C. elegans showing a seam cell that failed to undergo cytokinesis
Serena Ding, Woollard lab
Collage of Drosophila third instar larva optic lobe
Lu Yang, Davis lab
First year Biochemistry students at a practical class
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Stephan Uphoff
Bacterial DNA repair and mutagenesis

Co-workers: Valentine Lagage, Nehir Banaz, Emma Jones

DNA repair and mutagenesis are essential for the maintenance and plasticity of genomes in all organisms. Our research group studies these fundamental processes in bacteria, where mutagenesis underlies the evolution of antibiotic resistance. When bacterial cells are exposed to DNA damage or antibiotic treatment they launch stress responses that increase their survival. Intriguingly, these responses also upregulate mutation rates, accelerating genetic adaptation. Our recent findings show that stochasticity, or "noise", plays key roles in these responses, modulating mutation rates and diversifying cell phenotypes to evade drug treatment. Our goal is to understand the molecular processes that regulate DNA damage responses, repair, and mutagenesis and how they determine cell fates.

To this end, we take a quantitative multi-disciplinary approach. We are developing fluorescence microscopy and microfluidics methods to measure protein function at the level of single molecules in individual cells. By combining super-resolution microscopy and single-molecule tracking, we can directly watch the movement of individual proteins inside living cells.

The single-molecule analysis resolves transient protein-DNA and protein-protein interactions. With this approach, we obtain unprecedented insight into the mechanisms of DNA repair pathways in the natural cellular context.

In particular, we explore the consequences of gene expression noise and stochastic processes on the fidelity of genome maintenance. We design custom microfluidic devices to observe and manipulate single cells. Using these tools, we discovered that the activation of a bacterial DNA damage response is highly stochastic, causing cell-to-cell variation in mutation rates. Random phenotypic variation can therefore lead to heritable genetic changes. We are currently exploring how bacterial cell heterogeneity influences the efficacy of antibiotic treatment.

We also collaborate with groups at Oxford and internationally on a range of projects related to genome maintenance in bacteria and eukaryotes. Visit the lab website for more information.


  1. Uphoff, S. (2018). Real-time dynamics of mutagenesis reveal the chronology of DNA repair and damage tolerance responses in single cells. PNAS 201801101
  2. Scc2/Nipbl Hops Between Chromosomal Cohesin Rings After Loading
    Rhodes J, Mazza D, Nasmyth K, Uphoff S
    eLife e30000 (2017)
  3. Single-molecule analysis of bacterial DNA repair and mutagenesis
    Uphoff S, Sherratt DJ
    Annual Reviews of Biophysics, 46, 411-432 (2017)
  4. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
    Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P
    Nature Communications, 7, 12568 (2016)
  5. Stochastic activation of a DNA damage response causes cell-to-cell mutation rate variation
    Uphoff S, Lord ND, Potvin-Trottier L, Okumus B, Sherratt DJ, Paulsson J
    Science, 27290, 1094-1097 (2016)
  6. Studying the organization of DNA repair by single-cell and single-molecule imaging
    Uphoff S, Kapanidis AN
    DNA Repair, 20, 32-40 (2014)
  7. Single-molecule DNA repair in live bacteria
    Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN
    Proc Natl Acad Sci U S A , 110(20), 8063-8068 (2013)
  8. In vivo architecture and action of bacterial structural maintenance of chromosome proteins
    Badrinarayanan A, Reyes-Lamothe R, Uphoff S, Leake MC, Sherratt DJ
    Science, 338(6106), 528-531 (2012)
  9. DAOSTORM: an algorithm for high- density super-resolution microscopy
    Holden SJ, Uphoff S, Kapanidis AN
    Nature Methods, 8(4), 279-280 (2011)
More Publications...

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Graduate Student and Postdoctoral Positions: Enquiries with CV welcome

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