Title of project: Flavivirus Replication: Drug development using high throughput enzymatic
analysis.
Director of Studies: Dr T Sabir
Second Supervisor: Professor N Gamper
Overview of project
There has been unprecedented change in the geographic distribution of mosquito borne flaviviruses
due to spread of invasive mosquito species, with half the world's population at risk of infection with
Dengue (DEN). Transmission of DEN was reported in France and Croatia in 2010 and in Portugal in
2012. DEN infection causes flu-like illness, but can develop into severe DEN, which can be lethal.
There is a complete lack of effective drug treatments. Replication enzymes (RNA polymerase) are
highly conserved among flaviviruses so this proposal will use the non-pathogenic Langat virus as a
model for enzymatic analysis of replication. New drug treatments will be identified as well as carrying
out informed drug development for virus replication inhibitors.
The virus genome contains short 5' and 3’ untranslated regions (UTR) required for replication.
Conserved RNA stem loops in this UTR region are essential for binding of the RNA polymerase.
Examination of the interaction of the RNA polymerase with these stem loops using single molecule
total internal reflection fluorescence spectroscopy (smTIRF) and fluorescence resonance energy
transfer (FRET) will allow investigation of the behaviour of these interactions at a new level; revealing
previously unknown information and opening new avenues for drug design.
RNA stem loops (15-30 nucleotides long) will be synthesised with fluorophore dyes attached, kinetic
and enzymatic studies using smTIRF and FRET will be carried out to identify the important nucleotide
residues for replication. Hybridization and thermal characterization of RNA stem loops will be carried
out. Ensemble determination of global structure of the RNA stems loops and changes with and
without the presence of replication enzyme will determined. The PhD student will learn about new
instrumentation and key techniques in biochemistry and molecular biology, including data analysis,
allowing employment in industry and or academia post qualification. This proposal will generate novel
data using smTIRF and FRET to examine virus replication for publication in JACS (impact factor
11.44) and/or Journal of Virology (impact factor of 4.6) submission to the MRC for program grant
funding.
Link to Faculty Research Themes
School of Rehabilitation and Health Sciences.
Further information
To apply you must be eligible for NHS Continuing Professional Development (CPD) funding and have
the support of your line manager in writing. General enquiries should be directed by email to the
Faculty Research Director r.hogston@leedsbeckett.ac.uk to discuss the project further please contact
the Director of Studies T.Sabir@leedsbeckett.ac.uk
Applications should be made on line here
http://www.leedsbeckett.ac.uk/research/research-degrees/research-studentships-andfees-only-bursaries/