Structure and Dynamics of the Four-way DNA Junction

Sunday, September 16, 2007 - 10:45am - 11:45am
EE/CS 3-180
David Lilley (University of Dundee)
Genetic recombination is important in the repair of double strand DNA breaks, the processing of stalled replication forks and in the generation of genetic diversity in evolution. During this process, two homologous DNA molecules undergo strand exchange to form a four-way DNA (Holliday) junction. The junction adopts a folded structure in the presence of divalent metal ions, generated by pairwise coaxial stacking of helical arms.

DNA junctions display rich dynamic properties including stacking conformer exchange transitions and branch migration. These processes cannot be synchronized, and so are difficult to study in bulk. Single-molecule fluorescence methods have allowed us to detect the transitions directly and to gain new insights into the energy landscape of conformer transitions and branch migration.

Electrostatic interactions are very important in the DNA junction. Folding and dynamics are strongly affected by the presence of metal ions. Conversion of a centrally-located phosphate group to an electrically-neutral methyl phosphonate group in a four-way DNA junction can exert a major influence on its conformation, allowing folding to occur in the absence of metal ions. However, the effect can be strongly dependent on stereochemistry. It is likely that the stereochemical environment of the methyl group affects the interaction with metal ions in the centre of the junction.

Four-way junctions are selectively bound by resolving enzymes; these serve as paradigms for the molecular recognition of DNA structure on a larger scale. We have recently solved the crystal structure of T7 endonuclease I bound to a DNA junction. This reveals how the geometry of the branched DNA can be recognized, while at the same time being distorted by the enzyme. The recognition process exploits the dynamic character of the junction to mould it onto the large binding surface of the protein.

D.M.J. Lilley Structures of helical junctions in nucleic acids Quart. Rev. Biophys. 33, 109-159 (2000).

S.A. McKinney, A.-C. Déclais, D.M.J. Lilley and T. Ha Structural dynamics of individual Holliday junctions Nature Struct. Biol. 10, 93-97 (2003).

J. Liu, A.-C. Déclais and D.M.J. Lilley Electrostatic interactions and the folding of the four-way DNA junction: analysis by selective methyl phosphonate substitution J. Molec. Biol. 343, 851–864 (2004).

S. A. McKinney, A. D. Freeman, D. M. J. Lilley and T. Ha Observing spontaneous branch migration of Holliday junctions one step at a time Proc. Natl. Acad. Sci. USA 102, 5715-5720 (2005).

J. Liu, A.-C. Déclais, S. McKinney, T. Ha, D.G. Norman and D.M.J. Lilley Stereospecific effects determine the structure of a four-way DNA junction Chem. & Biol. 12, 217-228 (2005).

J.M. Hadden, A.-C. Déclais, S.B. Carr, D.M.J. Lilley and S.E.V. Phillips The structural basis of Holliday junction resolution. Submitted for publication (2007).
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