... understanding life in molecular detail

Dr Andrew Tuplin

Virus, virology, RNA structure, replication

Research in my group is focused on investigating the molecular mechanisms by which RNA secondary structures, encoded by viral genomes, act as dynamic RNA-switches controlling critical aspects of virus replication through switching conformation and interactions. Specifically, we are interested in how such functions are mediated by alternative conformations of RNA-switches influencing critical dynamic interactions with host/viral proteins and small molecules such as microRNA.  As well as advancing our understanding of fundamental mechanisms by which RNA viruses control different aspects of their replication cycle we are interested in the potential of RNA-switches as therapeutic targets.

Current major projects include:
  • Structure and function of dynamic RNA pseudoknots in RNA viruses
  • Dynamics of viral RNA structure/host cellular factor interactions
  • In vivo mapping of dynamic RNA structures in real time virus infection
  • Functional RNA structures as therapeutic drug targets

Many RNA viruses encode functional RNA structures that act as dynamic switches, changing their conformation and protein interactions to control virus replication. Such ‘RNA-switches’ can regulate critical stages of virus infection such as translation, replication and packaging. For example, in flaviviruses evidence suggests that switches in RNA-structure conformation modulate and initiate genome translation and replication. Our limited understanding of such critical RNA-switches is predominantly based on in silico modelling, in vitro chemical mapping and reverse genetics. We have little understanding of their in vivo interactions or dynamics, either during different stages of real-time virus infection or within different cellular compartments.

One of the key focuses of our research is mapping viral RNA-structures and their dynamic RNA/protein interactions within different cellular compartments during real time virus infection. We use an intracellular chemical probing method – 2’hydroxyl acylation analysed by primer extension (SHAPE) – to quantitatively map viral RNA structures at the single nucleotide resolution within different cellular compartments during live virus replication. We are also developing fluorescently labelled tags, specific to alternative RNA conformations, to track changes through different stages of a viruses replication cycle.

Currently research in my group is focused on positive sense RNA viruses including HCV, Dengue virus and Chikungunya virus. These viruses are extremely important human pathogens to which there are no vaccines and either no or only limited antiviral therapies. The ultimate goal of our work is that a better understanding of essential virus RNA structures and their dynamic interactions will further their exploitation as a therapeutic target. With collaborators this work has led to patents showing how small molecule inhibitors can be used to block RNA conformational switching in the HCV genome, inhibiting virus translation and replication.

As with most research our work depends on vital collaborations with a number of other laboratories.

External collaborators:

  • Prof. David Evans at the University of Warwick is a long-standing collaborator on our HCV research.
  • Dr. Andrew Davidson at the University of Bristol - Dengue virus research.
  • Dr. Alain Kohl at the MRC, University of Glasgow Centre for Virus Research and Prof. Andres Merits at the University of Tartu, Estonia - Chikungunya virus research.


Detailed research programme                  Close ▲

PhD (University of Edinburgh) 1999 - 2003

Research fellow, (CEH Oxford) 2004 - 2007
Research fellow, (University of Warwick) 2007 - 2011
Senior research fellow, (University of Warwick) 2011 - 2012

Garstang 8.58
School of Molecular and Cellular Biology
0113 3435582


Selected Publications

  1. Tuplin A, Struthers M, Cook J, Bentley K, Evans DJ Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail Nucleic Acids Research 43 2914-2926, 2015

  2. Tuplin AK Diverse roles and interactions of RNA structures during the replication of positive-stranded RNA viruses of humans and animals Journal of General Virology 96 1497-1503, 2015

  3. Andrew Tuplin, Madeleine Struthers, Peter Simmonds and David J. Evans.  (2012)  RNA structural rearrangements that influence the replication phenotype of hepatitis C virus. Nucleic Acids Research40 (14), 6908

  4. Tuplin, A., Evans, D. J., E.A.Gould and T S Gritsun. (2011)  Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus. Nucleic Acids Research 39 (16), 7034