The Holliday Junction (HJ), first proposed by Robin Holliday in 1964, is a four stranded DNA junction and is a key intermediate in homologous recombination (HR).1 HR is a type of genetic recombination or rearrangement that occurs between two strands of DNA and requires two homologous chromosomes (or nearly homologous) to come together and exchange DNA. This is an equal and reciprocal process and in order to do so the HJ must be formed. This mixing or crossing over of DNA is important and underlies many biological pathways including meiosis. A second and more relevant example is the role it plays in DNA repair mechanisms where HR becomes a DNA maintenance pathway, specifically repairing double strand breaks (DSB) in DNA and ensuring genetic integrity.

The HJ consists of four double helical strands of DNA linked together. Electrostatic interactions influence the folding processes and the structure is therefore dependent on the type and concentration of the divalent cation. In the absence of cations the junction adopts the open square like structure where the four arms are directed to each corner of the square and the central region is open.2 On addition of divalent ions such as Mg2+, the junction folds involving pairwise coaxial stacking of helical arms and a right-handed rotation of the axes resulting in the stacked X-structure.3 There are two kinds of strands present; two continuous strands run the length of the stacked helices and two exchanging strands which cross over from one helix to the other resulting in the strand crossover point. In the stacked X-structure the continuous strands are antiparallel to each other and the HJ is able to migrate through the breaking and reforming of hydrogen bonds. In addition to the open and closed forms of the junction isomers are also possible for the folded form of the junction (some resulting in immobile junctions).

In our previous work utilising immobile HJ's we identified, through crystallography, the first small molecule4 to bind to a HJ and more recently have shown that an analogue of this compound can promote the formation of an X-stacked HJ structure at room temperature without the need of divalent metal cations or a thermal annealing step.5 We will now investigate the effect this molecule and others have on strand migration of mobile HJ's and what the therapeutic outcome of this could be. The project will combine synthetic medicinal chemistry and single molecule studies using AFM with biological assays in tumour cell lines.

1. Holliday, R., Genetics Research, 1964, 5, 282-304
2. Clegg, R. M., Murchie, A. I. H., Zechrel, A., Lilley, D. M. J., Biophysical Journal, 1994, 66 99-109
3.  Duckett, D. R., Murchie, A. I., Diekmann, S., von Kitzing, E., Kemper, B., Lilley, D. M. J., Cell, 1988, 55, 79-89
4. Brogden, A. L., Hopcroft, N. H., Searcey, M., Cardin, C. J., Angewandte Chemie 2007, 119, 3924-3928; Angewandte Chemie International Edition, 2007, 46, 3850-3854

5. Howell, L. A., Waller, Z. A. E., Bowater, R., O'Connell. M. A., Searcey, M., Chem. Comm., 2011, 47, 8262-8264