... simulations. 1 To whom correspondence should be addressed (email tony.maxwell@jic.ac.uk ). 2 11 2012 © The Authors Journal compilation © 2013 Biochemical Society 2013 atomistic simulation DNA circle minicircle supercoiling topoisomerase Although the role of DNA...

...David Swigon; Sookkyung Lim; Yongsam Kim In the present article, we summarize our recent studies of DNA dynamics using the generalized immersed boundary method. Our analysis of the effects of electrostatic repulsion on the dynamics of DNA supercoiling revealed that, after perturbation, a pre...

... ( andrzej.stasiak@unil.ch ). 24 1 2013 © The Authors Journal compilation © 2013 Biochemical Society 2013 catenane chromatin chromosome DNA knot protein folding recombinase supercoiling topoisomerase The structure and function of DNA and proteins are affected by the topology...

...Jorge B. Schvartzman; María-Luisa Martínez-Robles; Pablo Hernández; Dora B. Krimer DNA topology changes dynamically during DNA replication. Supercoiling, precatenation, catenation and knotting interplay throughout the process that is finely regulated by DNA topoisomerases. In the present article...

...Andrew D. Bates; Anthony Maxwell Type II DNA topoisomerases catalyse changes in DNA topology in reactions coupled to the hydrolysis of ATP. In the case of DNA gyrase, which can introduce supercoils into DNA, the requirement for free energy is clear. However, the non-supercoiling type II enzymes...

... couples the free energy of ATP hydrolysis to the introduction of negative supercoiling, and the structural details of this process are now becoming clearer. The homologous type IIA enzymes such as topo IV and eukaryotic topo II also require ATP and it has more recently been shown that the energy...