Double-stranded coarse grained model for DNA: applications to supercoiling and denaturation

DNA supercoiling is the name given to the under or overwinding of the two strands of a DNA double helix. It is of great interest because it is relevant in several crucial biological processes. However, the principles governing its dynamics and its precise role under different circumstances remain elusive. Despite advances in single molecule experimental techniques, measuring supercoiling dynamics persist a challenge; this is where computer simulations are useful. In this thesis, I first introduce a single-nucleotide resolution coarse-grained computational model of DNA, that faithfully reproduces the geometry of the double-stranded helix and also part of its elastic behaviour. The dynamic of the system is implemented using a molecular dynamics scheme, and the results obtained are interpreted through methods of equilibrium and non-equilibrium statistical mechanics. I then employ this model to specifically study DNA supercoiling. This phenomenon, although topological in nature, is extremely important for the survival of cells because it has a deep impact on the regulation of gene expression, the compaction of DNA inside the cell and DNA replication. In particular, this work finds its motivations in: (i) an experimentally unresolved problem about the effect of supercoiling on DNA melting; (ii) the dynamics of supercoiling under physiological conditions during transcription; and (iii) the relation between supercoiling and DNA-binding proteins. Given that these phenomena may be relevant in vivo, they have recently received a a great deal of attention. However, until now, no computational model existed to study these kind of process. The techniques used here have been successful in providing insight into the key elements in the system. This would have been impossible before by using, for example, 1D models. The major achievement of this work is the quantitative characterisation of the role played by DNA supercoiling in a range of situations that are commonly found in vivo

Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling

We study the effect of transcription on the kinetics of DNA supercoiling in three dimensions by means of Brownian dynamics simulations of a single-nucleotide–resolution coarse-grained model for double-stranded DNA. By explicitly accounting for the action of a transcribing RNA polymerase (RNAP), we characterize the geometry and nonequilibrium dynamics of the ensuing twin supercoiling domains. Contrary to the typical textbook picture, we find that the generation of twist by RNAP results in the formation of plectonemes (writhed DNA) some distance away. We further demonstrate that this translates into an “action at a distance” on DNA-binding proteins; for instance, positive supercoils downstream of an elongating RNAP destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. We also analyze the relaxation dynamics of supercoiled double-stranded DNA, and characterize the widely different timescales of twist diffusion, which is a simple and fast process, and writhe relaxation, which is much slower and entails multiple steps

Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation

How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models neglect the dynamics of TopoII which is characteristics for proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo

Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation

: How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expected of proteins searching their targets via facilitated diffusion. Here, we show that dynamic binding of TopoII speeds up the topological relaxation of knotted substrates by enhancing the search of the knotted arc. Intriguingly, this in turn implies that the timescale of topological relaxation is virtually independent of the substrate length. We then discover that considering binding biases due to facilitated diffusion on looped substrates steers the sampling of the topological space closer to the boundaries between different topoisomers yielding an optimally fast topological relaxation. We discuss our findings in the context of topological simplification in vitro and in vivo

Coarse-graining DNA: Symmetry, non-local elasticity and persistence length

While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein interactions and the nucleosome diffusion mechanism. Here, by employing the rigid base pair model, we connect its microscopic parameters to the persistence length. Combined with all-atom molecular dynamic simulations, our scheme identifies relevant couplings between different degrees of freedom at each coarse-graining step. This allows us to clarify how the scale dependence of the elastic moduli is determined in a systematic way encompassing the role of previously unnoticed off site couplings between deformations with different parity