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SUMMARY:DNA-DNA electrostatic helix specific interactions and their possib
 le role in supercoiling - Dr Dominic Lee\, Imperial College London
DTSTART:20111130T141500Z
DTEND:20111130T151500Z
UID:TALK32455@talks.cam.ac.uk
CONTACT:Robert Best
DESCRIPTION:In the first part of my talk\, I discuss general features of h
 elix specific interactions\, particularly those of DNA. I review the form 
 of the potential for a mean field theory of the electrostatics of helical 
 molecules in electrolyte solution- the Kornyshev-Leikin theory. However\, 
 real DNA is not an ideal helix\, nor straight\, due to structural and ther
 mal distortions. I consider how one can quantify helix disorder due to a r
 andom base pair text and thermal fluctuations\, and how these affect the f
 orm of the interaction energy.\n\nIn the second part\, I start by consider
 ing a free ended braid formed from two molecules. It is possible to show t
 hat where there is attraction\, for long molecules\, a left handed\, braid
 ed state may have lower energy than two parallel molecules. This effect is
  most pronounced when the two molecules have the same base pair text\, as 
 opposed to uncorrelated texts. Next\, I review the topological law/constra
 int for closed loop DNA. Lastly\, I present a simple model for a closed lo
 op plasmid\, based around the free braided state\, but with the topologica
 l constraint as well as end-loops. The simple model suggests that when hel
 ix specific interactions are large\, positive supercoiling is actually mor
 e energetically favourable than negative supercoiling\, and that the state
  of lowest energy could be one of positive writhe (a braided configuration
 ) instead of zero writhe (open circle or a flat loop). This might be reali
 zed under certain experimental conditions\, discussed here. Finally\, I po
 int to future work.
LOCATION:Department of Chemistry\, Cambridge\, Pfizer lecture theatre
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