Speaker
Description
After almost seventy years from the discovery of DNA double helix structure, we know very much about nucleic acid organization and functions. However, there are still many structural and dynamical features - at different spatial and time scales - that have to be understood better. Molecular simulations are essential to understand many properties at the molecular level. With a fast increase in the computer power together with method and software development, systems over increasing sizes and longer and longer timescales can be simulated. However, studies of DNA at the atomistic level have a practical maximum size allowing a few nucleosome core particles, on the microsecond time scale to be studied. To reach larger spatial and longer temporal time scales, necessary when studying many of the biological problems involving DNA (e.g. those connected to DNA flexibility, or to chromatin folding etc.) all-atom simulations are far too expensive. It is necessary to coarsen the description of the system of interest, by removing many details non-relevant to the phenomenon under investigation [1-4]. In this talk I will present selected coarse-grain (CG) models, some of which can be applied to the double helix conformation as well as to other nucleic acid structural motifs found in the cells, like DNA quadruplexes [5-6]. Special attention will be given to the methods that can be used to study the counter-ions interactions with this highly charged poly-ion.
References:
[1] Mocci F, Laaksonen A (2012). Insight into nucleic acid counterion interactions from inside molecular dynamics simulations is “worth its salt”. Soft Matter, 8, 9268-9284
[2] Potoyan DA, Savelyev A, Papoian G A (2013) Recent successes in coarse-grained modeling of DNA. WIREs Computational Molecular Science, 3, 69-8
[3] Dans PD, Walther J, Gómez H, Orozco M (2016) Multiscale simulation of DNA, Current Opinion in Structural Biology, 37, 29-45
[4] Sun T, Mirzoev A, Minhas V, Korolev N, Lyubartsev AP, Nordenskiöld L (2019) , A multiscale analysis of DNA phase separation: from atomistic to mesoscale level, Nucleic Acids Research, 47:11, 5550–5562,
[5] Rebič M, Mocci F, Lyubartsev AP, Uličný J, Laaksonen A (2017) Coarse-Grained Simulation of Rodlike Higher-Order Quadruplex Structures at Different Salt Concentrations ACS Omega 2 (2), 386-396
[6] Rebič M, Mocci F, Laaksonen A, Uličný J (2015) Multiscale simulations of human telomeric G-quadruplex DNA. The Journal of Physical Chemistry B 119 (1), 105-113
