The Zechiedrich laboratory has proposed that type II topoisomerases recognize angle and curvature between two DNA helices characteristic of knotted and catenated DNA to account for the enzyme's preference to unlink instead of link DNA. Specifically, it is proposed that these enzymes act on so-called "hooked" juxtapositions (where the helices curve towards each other) and ignore "free" juxtapositions (where the helices curve away from each other). The electrostatics of DNA-DNA interactions are poorly understood and represent one possible driver of hooked versus free juxtaposition formation. Previous data showed that a hooked juxtaposition of charged strings in vacuum tended to persist because of electrostatic interactions, thus a type II topoisomerase would be more likely to encounter the juxtaposition and act. I have been considering the effect of electrolytes on the persistence of hooked versus free juxtapositions to better understand the physics behind DNA-DNA interactions and to determine the possibility of juxtapositions occurring through Brownian diffusion.

Molecular modeling of topoisomerase is complicated by the fact that despite years of study and several attempts by many laboratory researchers, no complete crystal structure of a type II topoisomerase exists. This may be due to the size of the molecule (~350 kDa), its conformational malleability required to carry out its function, or its extreme hydrophobicity. I am also attempting to supplement my molecular models with structural data produced by three-dimensional reconstructions of human topoisomerase II-alpha using images acquired by electron cryo-microscopy.

This work is supported by a training fellowship from the Keck Center for Computational and Structural Biology of the Gulf Coast Consortia (NLM Grant No. 5T15LM07093).