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SUMMARY:All-atom simulations of DNA in complex 3D arrangements - Dr Agnes 
 Noy\, University of York
DTSTART:20240124T143000Z
DTEND:20240124T153000Z
UID:TALK202312@talks.cam.ac.uk
CONTACT:Lisa Masters
DESCRIPTION:In my lab\, we are interested in studying DNA at atomic level\
 , not only in the form of short relaxed fragments (up to 50 bp)\, but cons
 idering longer sequences (300-400 bp) under mechanical stress. This is a m
 ore physiological representation as DNA constitutes a very long polymer an
 d rarely exists in a relaxed state inside living beings. Rather\, it is su
 bjected to variety of mechanical stress generated in cellular processes su
 ch as gene expression\, replication\, and more generally protein recogniti
 on. These tensions cause severe distortions on the double helix\, which\, 
 in turn\, influences its dynamic and recognition properties. I will show a
 ll-atom MD simulations in combination with experiments of how DNA structur
 e is affected by DNA supercoiling [1\,2]\, DNA-bending proteins [3] and wh
 ich is the interplay between the two [4].\n1. ALB Pyne\, A Noy\, K Main\, 
 V Velasco-Berrelleza\, MM Piperakis\, LA Mitchenall\, FM Cugliandolo\, JG 
 Beton\, CEM Stevenson\, BW Hoogenboom\, AD Bates\, A Maxwell\, SA Harris (
 2021). “Base-pair resolution analysis of the effect of supercoiling on D
 NA flexibility and major groove recognition by triplex-forming oligonucleo
 tides” Nat Commun\, 12\, 1053\n2. M Burman and A Noy (2023) “Atomic de
 scription of the reciprocal action between supercoils and melting bubbles 
 on linear DNA” Submitted. bioRxiv: https://doi.org/10.1101/2023.06.21.54
 5919\n3. S Yoshua\, G Watson\, J Howard\, V Velasco-Berrelleza\, MC Leake\
 , A Noy (2021). “A nucleoid- associated protein bends and bridges DNA in
  a multiplicity of topological states with varying specificity” Nuc Acid
 s Res\, 49\,8684-8698\n4. GD Watson\, EW Chan\, MC Leake\, A Noy (2022) 
 “Structural interplay between DNA-shape protein recognition and supercoi
 ling: the case of IHF” Comput Struct Biotech J\, 20\, 5264-5274
LOCATION:Unilever Lecture Theatre\, Yusuf Hamied Department of Chemistry
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