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SUMMARY:Base flipping in DNA using potential energy landscapes - Nicy\, Un
 iversity of Cambridge
DTSTART:20211117T143000Z
DTEND:20211117T150000Z
UID:TALK162424@talks.cam.ac.uk
CONTACT:Lisa Masters
DESCRIPTION:Energy landscape theory is a fundamental framework that is use
 d to explore the structure\,  thermodynamics  and  kinetics  associated  w
 ith  a  chemical  process. Here\, we have explored  the  process  of  base
   flipping  in  a  deoxyribonucleic  acid (DNA) duplex with the sequence 5
 ’-GAGAGAGAGAGA-3’ from the energy landscape perspective.  Experimental
 ly\, NMR imino-proton exchange and fluorescence correlation studies have b
 een used  to  obtain  lifetimes  of  bases  in  paired  and  extra helical
   states.   However\,  the difference of almost four orders of magnitude i
 n lifetimes obtained by the two methods implies that they are exploring di
 fferent pathways\, and possibly different open states. In our work\, flipp
 ing pathways for four central bases: adenine\, guanine\, cytosine\, and th
 ymine were investigated in a DNA duplex modelled using the AMBER force fie
 ld with an implicit solvent model.  The pathway between closed and open st
 ates is visualised using disconnectivity graphs. Our results support the p
 revious suggestion that minor groove opening may be favoured by bending\, 
 and reveal links between sequence effects and the direction of opening\, i
 .e.\, whether the base flips towards the major or the  minor groove side. 
 The calculated rate constants are compared with previous experimental and 
 computational studies\,  and a rationale for differences is provided in te
 rms of mechanism\, sequence effects\, and the experimental or computationa
 l framework in question.\n
LOCATION:Zoom and Dept of Chemistry\, Wolfson Lecture Theatre
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