Nucleosome dynamics: sequence matters

B Eslami-Mossallam, H Schiessel… - Advances in colloid and …, 2016 - Elsevier
About three quarter of all eukaryotic DNA is wrapped around protein cylinders, forming
nucleosomes. Even though the histone proteins that make up the core of nucleosomes are highly …

[PDF][PDF] Hybridization kinetics explains CRISPR-Cas off-targeting rules

M Klein, B Eslami-Mossallam, DG Arroyo, M Depken - Cell reports, 2018 - cell.com
Due to their specificity, efficiency, and ease of programming, CRISPR-associated nucleases
are popular tools for genome editing. On the genomic scale, these nucleases still show …

[PDF][PDF] Global DNA compaction in stationary-phase bacteria does not affect transcription

…, Z Rivai, ND Sunday, B Eslami-Mossallam… - Cell, 2018 - cell.com
In stationary-phase Escherichia coli, Dps (DNA-binding protein from starved cells) is the
most abundant protein component of the nucleoid. Dps compacts DNA into a dense complex …

[HTML][HTML] Multiplexing genetic and nucleosome positioning codes: a computational approach

B Eslami-Mossallam, RD Schram, M Tompitak… - PLoS …, 2016 - journals.plos.org
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is
known that their positions are strongly influenced by the mechanical properties of the …

[HTML][HTML] A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity

B Eslami-Mossallam, M Klein, CVD Smagt… - Nature …, 2022 - nature.com
The S. pyogenes (Sp) Cas9 endonuclease is an important gene-editing tool. SpCas9 is
directed to target sites based on complementarity to a complexed single-guide RNA (sgRNA). …

Why do nucleosomes unwrap asymmetrically?

…, M Tompitak, B Eslami-Mossallam… - The Journal of …, 2016 - ACS Publications
Nucleosomes, DNA spools with a protein core, engage about three-quarters of eukaryotic
DNA and play a critical role in chromosomal processes, ranging from gene regulation, …

[PDF][PDF] High-throughput single-molecule experiments reveal heterogeneity, state switching, and three interconnected pause states in transcription

R Janissen, B Eslami-Mossallam, I Artsimovitch… - Cell Reports, 2022 - cell.com
Pausing by bacterial RNA polymerase (RNAp) is vital in the recruitment of regulatory factors,
RNA folding, and coupled translation. While backtracking and intra-structural isomerization …

Confinement dynamics of a semiflexible chain inside nano-spheres

A Fathizadeh, M Heidari, B Eslami-Mossallam… - The Journal of …, 2013 - pubs.aip.org
We study the conformations of a semiflexible chain, confined in nano-scaled spherical
cavities, under two distinct processes of confinement. Radial contraction and packaging are …

Space heating demand profiles of districts considering temporal dispersion of thermostat settings in individual buildings

FGHF Koene, BB Eslami-Mossallam - Building and Environment, 2023 - Elsevier
Future energy infrastructures are expected to be smart, with the application of energy storage
and demand-side management strategies. To size the energy storage and assess the …

[PDF][PDF] A unifying mechanistic model of bacterial transcription with three interconnected pause states and non-diffusive backtrack recovery

R Janissen, B Eslami-Mossallam, I Artsimovitch… - Biophysical …, 2020 - cell.com
Pausing by RNA polymerase (RNAp) facilitates the recruitment of regulatory factors, RNA
folding, and other related processes. While backtracking and intra-structural isomerization …