6 research outputs found
Uncovering the forces between nucleosomes using DNA origami
Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (similar to 6 nm) attractive nucleosome pair potential with a minimum of -1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, high-erorder nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques
Uncovering the forces between nucleosomes using DNA origami
Revealing the energy landscape for nucleosome association may contribute to the understanding of higher-order chromatin structures and their impact on genome regulation. We accomplish this in a direct measurement by integrating two nucleosomes into a DNA origami-based force spectrometer, which enabled subnanometer-resolution measurements of nucleosome-nucleosome distance frequencies via single-particle electron microscopy imaging. From the data, we derived the Boltzmann-weighted distance-dependent energy landscape for nucleosome pair interactions. We find a shallow but long-range (similar to 6 nm) attractive nucleosome pair potential with a minimum of -1.6 kcal/mol close to direct contact distances. The relative nucleosome orientation had little influence, but histone H4 acetylation or removal of histone tails drastically decreased the interaction strength. Because of the weak and shallow pair potential, high-erorder nucleosome assemblies will be compliant and experience dynamic shape fluctuations in the absence of additional cofactors. Our results contribute to a more accurate description of chromatin and our force spectrometer provides a powerful tool for the direct and high-resolution study of molecular interactions using imaging techniques
Mucin Biopolymers As Broad-Spectrum Antiviral Agents
Mucus is a porous biopolymer matrix that coats all wet epithelia in the human body and serves as the first line of defense against many pathogenic bacteria and viruses. However, under certain conditions viruses are able to penetrate this infection barrier, which compromises the protective function of native mucus. Here, we find that isolated porcine gastric mucin polymers, key structural components of native mucus, can protect an underlying cell layer from infection by small viruses such as human papillomavirus (HPV), Merkel cell polyomavirus (MCV), or a strain of influenza A virus. Single particle analysis of virus mobility inside the mucin barrier reveals that this shielding effect is in part based on a retardation of virus diffusion inside the biopolymer matrix. Our findings suggest that purified mucins may be used as a broad-range antiviral supplement to personal hygiene products, baby formula or lubricants to support our immune system.National Institutes of Health (U.S.) (grant P30-ES002109)National Institutes of Health (U.S.) (grant P50-GM068763)German Academic Exchange Service (Postdoctoral fellowship
Exploring Nucleosome Unwrapping Using DNA Origami
We
establish a DNA origami based tool for quantifying conformational
equilibria of biomolecular assemblies as a function of environmental
conditions. As first application, we employed the tool to study the
salt-induced disassembly of nucleosome core particles. To extract
binding constants and energetic penalties, we integrated nucleosomes
in the spectrometer such that unwrapping of the nucleosomal template
DNA, leading from bent to more extended states was directly coupled
to the conformation of the spectrometer. Nucleosome unwrapping was
induced by increasing the ionic strength. The corresponding shifts
in conformation equilibrium of the spectrometer were followed by direct
conformation imaging using negative staining TEM and by FRET read
out after gel electrophoretic separation of conformations. We find
nucleosome dissociation constants in the picomolar range at low ionic
strength (11 mM MgCl<sub>2</sub>), in the nanomolar range at intermediate
ionic strength (11 mM MgCl<sub>2</sub> with 0.5–1 M NaCl) and
in the micromolar range at larger ionic strength (11 mM MgCl<sub>2</sub> with ≥1.5 M NaCl). Integration of up to four nucleosomes
stacked side-by-side, as it might occur within chromatin fibers, did
not appear to affect the salt-induced unwrapping of nucleosomes. Presumably,
such stacking interactions are already effectively screened at the
nucleosome unwrapping conditions. Our spectrometer provides a modular
platform with a direct read out to study conformational equilibria
for targets from small biomolecules up to large macromolecular assemblies