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 considering longer sequences (300-400 bp) under mechanical stress. This is a more physiological representation as DNA constitutes a very long polymer and rarely exists in a relaxed state inside living beings. Rather, it is subjected to variety of mechanical stress generated in cellular processes such as gene expression, replication, and more generally protein recognition. These tensions cause severe distortions on the double helix, which, in turn, influences its dynamic and recognition properties. I will show all-atom MD simulations in combination with experiments of how DNA structure is affected by DNA supercoiling [1,2], DNA-bending proteins [3] and which is the interplay between the two [4].
1. 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 DNA flexibility and major groove recognition by triplex-forming oligonucleotides” Nat Commun, 12, 1053
2. M Burman and A Noy (2023) “Atomic description of the reciprocal action between supercoils and melting bubbles on linear DNA” Submitted. bioRxiv: https://doi.org/10.1101/2023.06.21.545919
3. 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 Acids Res, 49,8684-8698
4. GD Watson, EW Chan, MC Leake, A Noy (2022) “Structural interplay between DNA-shape protein recognition and supercoiling: the case of IHF” Comput Struct Biotech J, 20, 5264-5274
