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

Sunday Abstracts

DNA Unlinking in Bacteria Koya Shimokawa 1 , Kai Ishihara 2 , Ian Grainge 3 , David Sherratt 4 , Mariel Vazquez 5 . 5 University of California, Davis, USA. 1 Saitama University, Saitama, Japan, 2 Yamaguchi University, Yamaguchi, Japan, 3 University of Newcastle, Callaghan, Australia, 4 University of Oxford, Oxford, United Kingdom, Chromosomes are long, rod-shaped,DNA molecules encoding the genetic code of an organism. The genome of bacterium Escherichia coli (E. Coli) is encoded in one single circular chromosome. Multiple cellular processes such as DNA replication and recombination change the topology of circular DNA. In particular, newly replicated circular chromosomes are topologically linked. Controlling these topological changes, and returning the chromosomes to an unlinked monomeric state is essential to cell survival. The cell uses enzymes to simplify the topology of DNA. We use mathematical techniques from knot theory, aided by computational tools, to study the action of these enzymes. DNA Knots Reveal Enzyme Mechanism and Viral Capsid Packing Geometry De Witt Sumners . Florida State University, Tallahassee, USA. Cellular DNA is a long, thread-like molecule with remarkably complex topology. Enzymes that manipulate the geometry and topology of cellular DNA perform many vital cellular processes (including segregation of daughter chromosomes, gene regulation, DNA repair, and generation of antibody diversity). Some enzymes pass DNA through itself via enzyme-bridged transient breaks in the DNA; other enzymes break the DNA apart and reconnect it to different ends. In the topological approach to enzymology, circular DNA is incubated with an enzyme, producing an enzyme signature in the form of DNA knots and links. By observing the changes in DNA geometry (supercoiling) and topology (knotting and linking) due to enzyme action, the enzyme binding and mechanism can often be characterized. This talk will discuss topological models for DNA strand passage and exchange, including the analysis of site-specific recombination experiments on circular DNA and the analysis of packing geometry of DNA in viral capsids.

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