Position: Professor of Molecular Biology and Director of the Cancer Research UK Nucleic Acid Structure Research Group
Division: Nucleic Acid Structure Research Group
Address: College of Life Sciences,
University of Dundee,
Dundee
Telephone: +44 1382 384243, int ext. 84243
Fax: +44 1382 322558
Email: d.m.j.lilley@dundee.ac.uk
Website: Lilley / Norman Lab
This laboratory has a general interest in the structures of helical branchpoints in nucleic acids, and their recognition by proteins. These are important intermediates in the repair and recombination of DNA, and architectural elements in functional RNA molecules.
The four-way DNA (Holliday) junction is the central intermediate of genetic recombination. The general structure of this junction was deduced some years ago in Dundee, using some relatively novel approaches including fluorescence resonance energy transfer (FRET). The structure has recently been confirmed in every respect by crystallography. Significant work in the group is going into the study of junction-resolving enzymes - nucleases that are selective for DNA junctions, that resolve them into their component duplex species. They exhibit exquisite structural selectivity, and a general understanding of the recognition of global DNA structure by proteins is a major goal for the laboratory. We have recently solved the structure of T7 endonuclease I.
FRET is constantly being developed as a unique means of obtaining long-range distance information. FRET is very powerful in the analysis of larger nucleic acid structure in solution, and time-resolved fluorescence is providing important dynamic information. These methods have recently been extended to single molecules, providing a powerful new perspective on the dynamic properties of DNA and RNA molecules. For example, we have recently demonstrated the exchange of four-way DNA junctions between stacking conformers, which was previously inaccessible by ensemble measurements. We are increasingly applying these approaches to the study of catalytic RNA molecules.
A major part of our structural work on nucleic acids is being directed towards RNA, especially ribozymes. In most RNA species the functional structure is determined by the tertiary folding, and branchpoints act as important scaffold elements in the assembly of these structures. A major goal is to understand the origin of catalysis in RNA, and its relationship to the structure of the ribozyme. We have made particular studies of three ribozymes:
a. The hammerhead ribozyme. We have shown that this ribozyme folds in two distinct stages, each of which is induced by the non-cooperative binding of divalent metal ions.
b. The hairpin ribozyme. We have analysed the folding of the natural form of the ribozyme, based around a four-way RNA junction. This is critical to the folding, reducing the magnesium ion concentration requirement by 1000-fold, and accelerating the folding by 500-fold due to a juxtaposition of the loops that must interact to crate the local environmental required for catalysis.
c. The Varkud satellite ribozyme. We have deduced the global structure for the VS ribozyme, and identified the active site together with a candidate catalytic nucleobase.
The crystal structure of the junction-resolving enzyme T7 endonuclease I (Hadden et al 2001).
