Chiral systems made from DNA
The very chemical structure of DNA that enables biological heredity and evolution has non‐
trivial implications for the self‐organization of DNA molecules into larger assemblies and …
trivial implications for the self‐organization of DNA molecules into larger assemblies and …
A molecular view of DNA flexibility
DNA dynamics can only be understood by taking into account its complex mechanical
behavior at different length scales. At the micrometer level, the mechanical properties of …
behavior at different length scales. At the micrometer level, the mechanical properties of …
Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions
Liquid–liquid phase separation (LLPS) is an important mechanism that helps explain the
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
membraneless compartmentalization of the nucleus. Because chromatin compaction and …
Histone dynamics mediate DNA unwrapping and sliding in nucleosomes
GA Armeev, AS Kniazeva, GA Komarova… - Nature …, 2021 - nature.com
Nucleosomes are elementary building blocks of chromatin in eukaryotes. They tightly
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …
wrap∼ 147 DNA base pairs around an octamer of histone proteins. How nucleosome …
Release of linker histone from the nucleosome driven by polyelectrolyte competition with a disordered protein
Highly charged intrinsically disordered proteins are essential regulators of chromatin
structure and transcriptional activity. Here we identify a surprising mechanism of molecular …
structure and transcriptional activity. Here we identify a surprising mechanism of molecular …
[HTML][HTML] Multiscale modeling of genome organization with maximum entropy optimization
ABSTRACT Three-dimensional (3D) organization of the human genome plays an essential
role in all DNA-templated processes, including gene transcription, gene regulation, and …
role in all DNA-templated processes, including gene transcription, gene regulation, and …
AWSEM-IDP: a coarse-grained force field for intrinsically disordered proteins
The associative memory, water-mediated, structure and energy model (AWSEM) has been
successfully used to study protein folding, binding, and aggregation problems. In this work …
successfully used to study protein folding, binding, and aggregation problems. In this work …
Extensile motor activity drives coherent motions in a model of interphase chromatin
D Saintillan, MJ Shelley… - Proceedings of the …, 2018 - National Acad Sciences
The 3D spatiotemporal organization of the human genome inside the cell nucleus remains a
major open question in cellular biology. In the time between two cell divisions, chromatin …
major open question in cellular biology. In the time between two cell divisions, chromatin …
Modulation of nucleosomal DNA accessibility via charge-altering post-translational modifications in histone core
AT Fenley, R Anandakrishnan, YH Kidane… - Epigenetics & …, 2018 - Springer
Background Controlled modulation of nucleosomal DNA accessibility via post-translational
modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs …
modifications (PTM) is a critical component to many cellular functions. Charge-altering PTMs …
Nucleosome allostery in pioneer transcription factor binding
While recent experiments revealed that some pioneer transcription factors (TFs) can bind to
their target DNA sequences inside a nucleosome, the binding dynamics of their target …
their target DNA sequences inside a nucleosome, the binding dynamics of their target …