The RNA polymerase II (Pol II) is the central enzyme transcribing protein coding genes in all eukaryotes. Modifications of DNA might interfere with normal action of Pol II: some disrupting correct gene expression, others serving a regulatory role. Since transcription lies in the foundation of all life, studying its mechanisms is of paramount importance. We employ molecular dynamics simulations with Markov state models (MSMs) to reveal the atomic level dynamics of Pol II in the elongation phase of transcription. First, we describe a complete protocol to build MSMs which is tailored to functional conformational changes of large complexes, such as Pol II. Next, we investigate incorrect transcription caused by the 8-oxo-guanine (8OG) base - the most frequent DNA lesion. We find that 8OG eva...[ Read more ]

The RNA polymerase II (Pol II) is the central enzyme transcribing protein coding genes in all eukaryotes. Modifications of DNA might interfere with normal action of Pol II: some disrupting correct gene expression, others serving a regulatory role. Since transcription lies in the foundation of all life, studying its mechanisms is of paramount importance. We employ molecular dynamics simulations with Markov state models (MSMs) to reveal the atomic level dynamics of Pol II in the elongation phase of transcription. First, we describe a complete protocol to build MSMs which is tailored to functional conformational changes of large complexes, such as Pol II. Next, we investigate incorrect transcription caused by the 8-oxo-guanine (8OG) base - the most frequent DNA lesion. We find that 8OG evades Pol II proofreading at two distinct checkpoints of the transcription cycle: before and after incorporation into the nascent RNA. Further, we explore how 5-carboxy-cytosine (5caC) diminishes transcription. 5caC is an important epigenetic marker of DNA, often found in promoter regions of genes and its mis regulation is responsible for multiple diseases. We disentangle the web of interactions that 5caC forms with Pol II to slow transcription, revealing both direct and indirect effects induced by this modification. Finally, we present an overview and preliminary results in a study of nucleosome unwrapping – a process required for gene accessibility to the Pol II.