- See a full list of publications
- Browse activities and projects
- Explore connections, collaborators, related work and more
|2003 -||Lecturer in Molecular Biophysics||Department of Biology, University of York|
|1998 - 2003||Postdoctoral Research Fellow||Department of Biology, University of York|
|1998||PhD in Biochemistry, Molecular Biology and Biophysics||University of Minnesota, St Paul, MN|
|1992||BS in Biochemistry||University of Minnesota, Minneapolis, MN|
A variety of cellular processes, including transcription, replication and recombination, involve simultaneous melting and unwinding of the two DNA strands, and translocation of the strands within a DNA-bound protein complex. In vivo DNA behaves as a closed structure lacking free ends (not unlike a covalently closed circular DNA), thus helix rotation about a free end or fixed ends is not possible. As a consequence, DNA strand separation and translocation results in local regions of over wound and under wound DNA, i.e. positive and negative supercoiling, respectively. I am interested in understanding how these topological changes in DNA are driven by the action of motor proteins, and how the resulting topological changes can directly modulate the function of a motor protein. The enzymes involved in these cellular processes do mechanical work on DNA by harnessing the energy within deoxy- or ribonucleotide triphosphates. They are referred to as molecular machines or molecular motors. I am interested in understanding the molecular mechanism whereby these motor proteins couple biochemical turnover to mechanical work. Using optical tweezers and single-fluorophore detection (total internal reflection fluorescence microscopy), respectively, the mechanical forces generated by these enzymes can be measured at the single-molecule level, while following the biochemical turnover of fluorescently labelled substrates.
|PhD student||Rosalyn Leaman||Probing the role of outer membrane transport processes in host-pathogen interactions|
|MSc by Research||Daniel Jones||Tracking the real-time translocation of a protein across the Escherichia coli cell envelope|
|PhD student||Herman Fung||Biophysical and structural characterisation of an in vitro-assembled viral DNA packaging system|
Design and characterisation of novel fluorescent nucleotide substrates for RNA polymerases (2015-16)
The ability to follow the polymerisation of ribonucleotide triphosphates (NTP) by a DNA-dependent RNA polymerase using fluorescence techniques requires NTP analogues with a fluorophore attached to either the gamma phosphate or the nucleobase. Attachment of a fluorophore at these positions allows both base pairing with the template DNA and phosphodiester bond formation. NTP analogues with the fluorescent group attached to the nucleobase have the added benefit that the newly synthesised polynucleotide chain is rendered fluorescent. In collaboration with the Department of Chemistry at York, we are developing novel classes of fluorescent NTP analogues. This project will involve studying the photo-physical properties of these analogues using ensemble-averaged and single-molecule fluorescence spectroscopy techniques, and following their incorporation into nascent RNA chains by single- and multi-subunit RNAPs using equilibrium and kinetic methods.
Co directors - Ian Fairlamb