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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