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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