Significance of Knotted Structures for Function of Proteins and Nucleic Acids - September 17-21, 2014

Significance of Knotted Structures for Function of Proteins and Nucleic Acids

Saturday Abstracts

DNA Topology, DNA Topoisomerases and Small DNA Circles Anthony Maxwell . John Innes Centre, Norwich, United Kingdom.

DNA topology is vitally important to many biological processes and is controlled by DNA topoisomerases. There are two types, I and II, depending on whether their reactions proceed via single- or double-strand breaks. Type IIs cleave DNA in both strands and transport another segment of DNA through the break. This leads to DNA relaxation, decatenation and unknotting, and, in the case of DNA gyrase, supercoiling, in reactions coupled to ATP hydrolysis. It is clear why supercoiling by gyrase requires ATP, but not obvious with other type IIs. One potential role for ATP in the non-supercoiling topoisomerases is in topology simplification: generating steady- state distributions of topoisomers that are simpler than at equilibrium. However, the energetic requirements for topology simplification are very small. Therefore we propose that the ATP free energy is used to disrupt protein-protein interfaces, which are very stable in order to prevent unwanted DNA breaks. Although the biological significance of topology simplification is questionable, its mechanism is the subject of debate. It is accepted that DNA bending by is likely to contribute to this process, but we have shown that this cannot be the sole determinant. Recent work points to a protein interface, known as the ‘exit gate’, to be an important feature of the ability of these enzymes to carry out topology simplification. We have used small DNA circles as probes in this work. This has led to research towards understanding how topology controls gene expression: investigating how DNA recognition is influenced by supercoiling, using a combined molecular dynamics and biochemical/biophysical approach. Using small circles of varying linking differences, we are analysing the binding of two probes: a triplex-forming oligonucleotide and a repressor. Coupled with atomistic simulations, this work is giving insight into topology-dependent DNA recognition.

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