Loading...
Search for:
nucleosomes
0.01 seconds
Rigid-body molecular dynamics of DNA inside a nucleosome
, Article European Physical Journal E ; Volume 36, Issue 3 , March , 2013 ; 12928941 (ISSN) ; Berdy Besya, A ; Ejtehadi, M. R ; Schiessel, H ; Sharif University of Technology
2013
Abstract
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use...
Coarse Grained Molecular Dynamics Simulation of DNA Nanomechanics
, Ph.D. Dissertation Sharif University of Technology ; Ejtehadi, Mohammad Reza (Supervisor) ; Khoei, Amir Reza (Co-Advisor)
Abstract
DNA is the most important biological molecule which contains all the genetic information of living organisms. The mechanical behavior of this molecule has a significant role on its functions. In this study, we introduce a model to for DNA nanomechanics. This model is called rigid base-pair chain in which every base pair is considered as a rigid object. The base-pairs only interact with their nearest neighbors via a harmonic potential. We have used this model to study the nanomechanical behavior of the DNA such as its bending, twisting, and stretching elasticity. Also the model was successful to predict the structure of DNA minicircles with extra amount of twist. After that we used the model...
Dna-Rna hybrid (R-loop): From a unified picture of the mammalian telomere to the genome-wide profile
, Article Cells ; Volume 10, Issue 6 , 2021 ; 20734409 (ISSN) ; Sharifi Zarchi, A ; Kianmehr, L ; Sharif University of Technology
MDPI
2021
Abstract
Local three-stranded DNA/RNA hybrid regions of genomes (R-loops) have been detected either by binding of a monoclonal antibody (DRIP assay) or by enzymatic recognition by RNaseH. Such a structure has been postulated for mouse and human telomeres, clearly suggested by the identification of the complementary RNA Telomeric repeat-containing RNA “TERRA”. However, the tremendous disparity in the information obtained with antibody-based technology drove us to investigate a new strategy. Based on the observation that DNA/RNA hybrids in a triplex complex genome co-purify with the double-stranded chromosomal DNA fraction, we developed a direct preparative approach from total protein-free cellular...