Biology subjects

Blossey, R.

Publications and source records attributed to Blossey, R..

4 recordsLinked to original sources

bioRxiv2025

Structural basis for UDG identifying DNA damage in the nucleosome

The DNA base-excision repair (BER) pathway is initiated by a glycosylase, such as UDG, which identifies and removes a wrong base incorporated in the DNA sequence. The very early steps in the identification of the DNA damage are crucial to the correct initiation of the repair chain, and become even more complex when considering the realistic environment of damage to the DNA in the nucleosome. We performed all-atom docking and molecular dynamics computer simulations of the interaction between the glycosylase UDG and a mutated uracil. The model system is a whole nucleosome in which DNA damage is inserted at various positions along the 145-bp sequence. It is shown that damage recognition by UDG requires very strict structural conditions, unlikely to be matched by purely random search along the DNA. We propose that mechanical deformation of the DNA around the defective sites may help signaling the presence of the defect, accelerating the search process.

molecular biology↗

bioRxiv2024

The "very moment" when UDG recognizes aflipped-out uracil base in dsDNA

Uracil-DNA glycosylase (UDG) is the first enzyme in the base-excision repair (BER) pathway, acting on uracil bases in DNA. How UDG finds its targets has not been conclusively resolved yet. Based on available structural and other experimental evidence, two possible pathways are under discussion. In one, the action of UDG on the DNA bases is believed to follow a pinch-push-pull model, in which UDG generates the base-flip in an active manner. A second scenario is based on the exploitation of bases flipping out thermally from the DNA. Recent molecular dynamics (MD) studies of DNA in trinucleosome arrays have shown that base-flipping can be readily induced by the action of mechanical forces on DNA alone. This alternative mechanism could possibly enhance the probability for the second scnenario of UDG-uracil interaction via the formation of a recognition complex of UDG with flipped-out base. In this work we describe DNA structures with flipped-out uracil bases generated by MD simulations which we then subject to docking simulations with the UDG enzyme. Our results for the UDG-uracil recognition complex support the view that base-flipping induced by DNA mechanics can be a relevant mechanism of uracil base recognition by the UDG glycosylase in chromatin.

bioinformatics↗

bioRxiv2020

Pioneer transcription factors in chromatin remodeling: the kinetic proofreading view

Pioneer transcription factors are a recently defined class of transcription factors which can bind directly to nucleosomal DNA; they play a key role in gene activation in certain pathways. Here we quantify their role in the initiation of nucleosome displacement within the kinetic proofreading scenario of chromatin remodeling. The model allows to perform remodeling efficiency comparisons for scenarios involving different types of transcription factors and remodelers as a function of their binding and unbinding rates and concentrations. Our results demonstrate a novel way to fine-tune the specificity of processes that modify the chromatin structure in transcriptional initiation.

biophysics↗

bioRxiv2018

Mechanical evolution of DNA double-strand breaks in the nucleosome

Double strand breaks in the DNA backbone are the most lethal type of defect that can be induced in the cell nucleus by chemical and radiation treatments of cancer. However, little is known about the potentially large differences in the outcomes of damage between free and nucleosomal DNA, leading to corresponding differences in damage repair capability. We performed microsecond-length molecular dynamics computer simulations of nucleosomes including double-strand breaks (DSB) at various sites, to characterize the early stages of the evolution of this important DNA lesion right after its formation. We find that all DSB configurations tend to remain compact, with only the terminal bases interacting with histone proteins; the interacting molecular structures are studied by looking at the essential dynamics of the relevant DNA and histone fragments, and compared to the intact nucleosome, thus exposing key features of the interactions. Moreover, we show that the broken DNA ends at the DSB must overcome a free-energy barrier to detach from the nucleosome core, as measured by means of umbrella sampling of the potential of mean force. Finally, by using state-of-the-art calculation of the covariant mechanical stress at the molecular scale, we demonstrate that, depending on the DNA-core separation distance, the coupled bending and torsional stress stored in the detached DNA can force the free end to either stick back to the nucleosome core surface, or to open up straight, thus making it accessible to damage signalization proteins.

biophysics↗