Dr Joe Vyle

Image Dr Joe Vyle

Dr J.S. Vyle
BSc (University of Birmingham), 1986
PhD (University of Liverpool), 1989

Lecturer in Organic Chemistry

Tel:     + 44 (0) 28 9097 5485
Fax:    + 44 (0) 28 9097 6524
E-mail: j.vyle@qub.ac.uk

Research Keywords

Catalytic nucleic acids
Nucleic acid analogues
Solid phase synthesis
RNA processing
Prebiotic chemistry
Molecular computing		 Publications
Research Group

Research

Ribozyme photoregulation

fig 2
Figure 2. RNA conformation
under photocontrol.

The fact that the information content within nucleic acids can be readily read, manipulated and understood has led to considerable interest in their potential in molecular computing. Since Adleman first demonstrated the ability of DNA to perform parallel calculations, there has been considerable interest in molecular computing with nucleic acids. Following Wellcome Trust funding (Sir Henry Wellcome Commemorative Award for Innovative research) of a project based upon extending the use of nucleic acids in molecular devices, current work continues this research. Controlled ribozyme activity is of potential relevance to photodynamic gene therapy, photocontrollable “riboswitches” and also in molecular computing. We have prepared azobenene-deoxyribonucleotide phosphoramidites and used these to incorporate this photoswitch into RNA sequences at sites known to be (Figure 2). Preliminary photoswitching experiments have shown significant differences in physical properties and the effect on RNA activity is currently under investigation.

 

Nucleoside cyclic phosphate preparation and applications

Currently, there is considerable interest in uncovering the prebiotic origins of current life processes. Sequences of RNA which show high levels of conserved structure between different kingdoms but adopt a variety of roles, e.g., the tRNA cloverleaf motif, have lead to the proposal that such sequences are molecular fossils; remnants of an “RNA world” in which RNA coded for both information and activity. This is in comparison with the current division of these prerequisites for life between DNA and proteins. As a fundamental part of the mechanism for translating information from DNA into functional proteins, RNA editing is a target of considerable interest both with a view to understanding the prebiotic origins of current cell phenotypes and as a potential target for therapeutic intervention. Current research interests are loosely based upon studying and harnessing processes involving DNA and RNA. Recent reports linking Alzheimer’s disease with the unfolded protein response (UPR) have stimulated interest in the mechanism involved in the regulation of the UPR. This mechanism involves splicing of mRNA by an unprecedented route that closely resembles pre-tRNA splicing and uses the same enzymes. The co-existence of two parallel pre-tRNA splicing pathways in vertebrates has also led to speculation that the non-tRNA products of splicing may also have important functions in cell signalling. Cyclic phosphates are involved in pre-tRNA splicing both as an initial product of the splicing reaction (to give a 2',3'-cyclic phosphate – Figure 2) and also following transfer of the 2'-phosphate from the spliced RNA to NAD (to give ADP-ribose 1"-2'' cyclic phosphate).

Fig 1
Figure 1. Cyclic phosphates involved in tRNA ligase-mediated tRNA splicing

 

These 5-membered cyclic phosphates are very susceptible to chemical and enzymatic degradation and should thus be constructed only at the end of the synthesis of the target molecule. 

We are currently developing methodology for the preparation of such cyclic phosphates and their analogues in order to facilitate study of the enzymes involved in pre-tRNA splicing and also to understand under what pre-biotic conditions RNA polymerisation might have occurred. Organophosphorus compounds isolated from the Murchison meteorite have led to the proposal that the chemistry in prebiotic “RNA” may have been based around phosphorus in oxidation states lower than that ubiquitous in current biological molecules. Ribozyme-mediated phosphonate cleavage has already been reported and a further research interest lies in studying the effect of phosphonate RNA substrates on ligating activity of ribozymes and thus how an “RNA” mediated transition from phosphonate to phosphate based chemistry may have occurred.