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Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures

This study analyzed the nuclease- and serum-driven degradation of millimeter-scale, circular DNA–histone mesostructures (DHMs). DHMs are bioengineered chromatin meshes of defined DNA and histone compositions designed as minimal mimetics of physiological extracellular chromatin structures, such as ne...

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Autores principales: Wasielewski, Midori L., Nguyen, Katherine, Yalavarthi, Srilakshmi, Ekbote, Pallavi, Weerappuli, Priyan D., Knight, Jason S., Takayama, Shuichi
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9959986/
https://www.ncbi.nlm.nih.gov/pubmed/36834634
http://dx.doi.org/10.3390/ijms24043222
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author Wasielewski, Midori L.
Nguyen, Katherine
Yalavarthi, Srilakshmi
Ekbote, Pallavi
Weerappuli, Priyan D.
Knight, Jason S.
Takayama, Shuichi
author_facet Wasielewski, Midori L.
Nguyen, Katherine
Yalavarthi, Srilakshmi
Ekbote, Pallavi
Weerappuli, Priyan D.
Knight, Jason S.
Takayama, Shuichi
author_sort Wasielewski, Midori L.
collection PubMed
description This study analyzed the nuclease- and serum-driven degradation of millimeter-scale, circular DNA–histone mesostructures (DHMs). DHMs are bioengineered chromatin meshes of defined DNA and histone compositions designed as minimal mimetics of physiological extracellular chromatin structures, such as neutrophil extracellular traps (NETs). Taking advantage of the defined circular shape of the DHMs, an automated time-lapse imaging and image analysis method was developed and used to track DHM degradation and shape changes over time. DHMs were degraded well by 10 U/mL concentrations of deoxyribonuclease I (DNase I) but not by the same level of micrococcal nuclease (MNase), whereas NETs were degraded well by both nucleases. These comparative observations suggest that DHMs have a less accessible chromatin structure compared to NETs. DHMs were degraded by normal human serum, although at a slower rate than NETs. Interestingly, time-lapse images of DHMs revealed qualitative differences in the serum-mediated degradation process compared to that mediated by DNase I. Importantly, despite their reduced susceptibility to degradation and compositional simplicity, the DHMs mimicked NETs in being degraded to a greater extent by normal donor serum compared to serum from a lupus patient with high disease activity. These methods and insights are envisioned to guide the future development and expanded use of DHMs, beyond the previously reported antibacterial and immunostimulatory analyses, to extracellular chromatin-related pathophysiological and diagnostic studies.
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spelling pubmed-99599862023-02-26 Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures Wasielewski, Midori L. Nguyen, Katherine Yalavarthi, Srilakshmi Ekbote, Pallavi Weerappuli, Priyan D. Knight, Jason S. Takayama, Shuichi Int J Mol Sci Article This study analyzed the nuclease- and serum-driven degradation of millimeter-scale, circular DNA–histone mesostructures (DHMs). DHMs are bioengineered chromatin meshes of defined DNA and histone compositions designed as minimal mimetics of physiological extracellular chromatin structures, such as neutrophil extracellular traps (NETs). Taking advantage of the defined circular shape of the DHMs, an automated time-lapse imaging and image analysis method was developed and used to track DHM degradation and shape changes over time. DHMs were degraded well by 10 U/mL concentrations of deoxyribonuclease I (DNase I) but not by the same level of micrococcal nuclease (MNase), whereas NETs were degraded well by both nucleases. These comparative observations suggest that DHMs have a less accessible chromatin structure compared to NETs. DHMs were degraded by normal human serum, although at a slower rate than NETs. Interestingly, time-lapse images of DHMs revealed qualitative differences in the serum-mediated degradation process compared to that mediated by DNase I. Importantly, despite their reduced susceptibility to degradation and compositional simplicity, the DHMs mimicked NETs in being degraded to a greater extent by normal donor serum compared to serum from a lupus patient with high disease activity. These methods and insights are envisioned to guide the future development and expanded use of DHMs, beyond the previously reported antibacterial and immunostimulatory analyses, to extracellular chromatin-related pathophysiological and diagnostic studies. MDPI 2023-02-06 /pmc/articles/PMC9959986/ /pubmed/36834634 http://dx.doi.org/10.3390/ijms24043222 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Wasielewski, Midori L.
Nguyen, Katherine
Yalavarthi, Srilakshmi
Ekbote, Pallavi
Weerappuli, Priyan D.
Knight, Jason S.
Takayama, Shuichi
Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title_full Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title_fullStr Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title_full_unstemmed Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title_short Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA–Histone Mesostructures
title_sort visualization of nuclease- and serum-mediated chromatin degradation with dna–histone mesostructures
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9959986/
https://www.ncbi.nlm.nih.gov/pubmed/36834634
http://dx.doi.org/10.3390/ijms24043222
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