{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,11]],"date-time":"2025-10-11T01:51:33Z","timestamp":1760147493393,"version":"build-2065373602"},"reference-count":29,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2023,2,6]],"date-time":"2023-02-06T00:00:00Z","timestamp":1675641600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"NIH","doi-asserted-by":"publisher","award":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"],"award-info":[{"award-number":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"NIH-sponsored Research Training Program in Immuno-engineering","doi-asserted-by":"publisher","award":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"],"award-info":[{"award-number":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"HEERF III","award":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"],"award-info":[{"award-number":["R01GM123517","T32 GM145735","R01HL134846","T32EB021962"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>This study analyzed the nuclease- and serum-driven degradation of millimeter-scale, circular DNA\u2013histone 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.<\/jats:p>","DOI":"10.3390\/ijms24043222","type":"journal-article","created":{"date-parts":[[2023,2,7]],"date-time":"2023-02-07T01:56:48Z","timestamp":1675735008000},"page":"3222","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Visualization of Nuclease- and Serum-Mediated Chromatin Degradation with DNA\u2013Histone Mesostructures"],"prefix":"10.3390","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8944-5978","authenticated-orcid":false,"given":"Midori L.","family":"Wasielewski","sequence":"first","affiliation":[{"name":"Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA"},{"name":"The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0116-2656","authenticated-orcid":false,"given":"Katherine","family":"Nguyen","sequence":"additional","affiliation":[{"name":"Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA"},{"name":"The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Srilakshmi","family":"Yalavarthi","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pallavi","family":"Ekbote","sequence":"additional","affiliation":[{"name":"Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA"},{"name":"The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Priyan D.","family":"Weerappuli","sequence":"additional","affiliation":[{"name":"Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48105, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jason S.","family":"Knight","sequence":"additional","affiliation":[{"name":"Division of Rheumatology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4385-9080","authenticated-orcid":false,"given":"Shuichi","family":"Takayama","sequence":"additional","affiliation":[{"name":"Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA 30332, USA"},{"name":"The Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2023,2,6]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"1532","DOI":"10.1126\/science.1092385","article-title":"Neutrophil Extracellular Traps Kill Bacteria","volume":"303","author":"Brinkmann","year":"2004","journal-title":"Science"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1038\/nri.2017.105","article-title":"Neutrophil Extracellular Traps in Immunity and Disease","volume":"18","author":"Papayannopoulos","year":"2018","journal-title":"Nat. Rev. Immunol."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"2186","DOI":"10.1182\/blood-2018-10-862243","article-title":"Neutrophils: Back in the Thrombosis Spotlight","volume":"133","author":"Noubouossie","year":"2019","journal-title":"Blood"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1189\/jlb.5BT0615-247R","article-title":"At the Bench: Neutrophil Extracellular Traps (NETs) Highlight Novel Aspects of Innate Immune System Involvement in Autoimmune Diseases","volume":"99","author":"Grayson","year":"2016","journal-title":"J. Leukoc. Biol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"732","DOI":"10.1111\/jth.12796","article-title":"Impaired DNase1-Mediated Degradation of Neutrophil Extracellular Traps Is Associated with Acute Thrombotic Microangiopathies","volume":"13","author":"Napirei","year":"2015","journal-title":"J. Thromb. Haemost."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"9813","DOI":"10.1073\/pnas.0909927107","article-title":"Impairment of Neutrophil Extracellular Trap Degradation Is Associated with Lupus Nephritis","volume":"107","author":"Hakkim","year":"2010","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"2130","DOI":"10.1002\/art.41460","article-title":"Anti\u2013Neutrophil Extracellular Trap Antibodies and Impaired Neutrophil Extracellular Trap Degradation in Antiphospholipid Syndrome","volume":"72","author":"Zuo","year":"2020","journal-title":"Arthritis Rheumatol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"R84","DOI":"10.1186\/ar4264","article-title":"Degradation of Neutrophil Extracellular Traps Co-Varies with Disease Activity in Patients with Systemic Lupus Erythematosus","volume":"15","author":"Leffler","year":"2013","journal-title":"Arthritis Res. Ther."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1900926","DOI":"10.1002\/adhm.201900926","article-title":"Extracellular Trap-Mimicking DNA-Histone Mesostructures Synergistically Activate Dendritic Cells","volume":"8","author":"Weerappuli","year":"2019","journal-title":"Adv. Healthc. Mater."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"1807436","DOI":"10.1002\/adma.201807436","article-title":"Antimicrobial Microwebs of DNA\u2013Histone Inspired from Neutrophil Extracellular Traps","volume":"31","author":"Song","year":"2019","journal-title":"Adv. Mater."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"2100717","DOI":"10.1002\/admi.202100717","article-title":"Dosage-Dependent Antimicrobial Activity of DNA-Histone Microwebs Against Staphylococcus Aureus","volume":"8","author":"Yang","year":"2021","journal-title":"Adv. Mater. Interfaces"},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"504","DOI":"10.1016\/0006-291X(73)90740-7","article-title":"Chromatin Sub-Structure. The Digestion of Chromatin DNA at Regularly Spaced Sites by a Nuclear Deoxyribonuclease","volume":"52","author":"Hewish","year":"1973","journal-title":"Biochem. Biophys. Res. Commun."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1016\/0020-711X(89)90100-6","article-title":"Micrococcal Nuclease: Its Specificity and Use for Chromatin Analysis","volume":"21","author":"Telford","year":"1989","journal-title":"Int. J. Biochem."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"2647","DOI":"10.4049\/jimmunol.1300436","article-title":"Macrophage Clearance of Neutrophil Extracellular Traps Is a Silent Process","volume":"191","author":"Farrera","year":"2013","journal-title":"J. Immunol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1093\/intimm\/dxn142","article-title":"Serum DNase I, Soluble Fas\/FasL Levels and Cell Surface Fas Expression in Patients with SLE: A Possible Explanation for the Lack of Efficacy of HrDNase I Treatment","volume":"21","author":"Tinazzi","year":"2009","journal-title":"Int. Immunol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"101844","DOI":"10.1016\/j.mcp.2022.101844","article-title":"Variability of Endogenous Deoxyribonuclease Activity and Its Pathophysiological Consequences","volume":"65","author":"Celec","year":"2022","journal-title":"Mol. Cell. Probes"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Santocki, M., and Kolaczkowska, E. (2020). On Neutrophil Extracellular Trap (NET) Removal: What We Know Thus Far and Why So Little. Cells, 9.","DOI":"10.3390\/cells9092079"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"6673","DOI":"10.1038\/ncomms7673","article-title":"Molecular Mechanisms of NET Formation and Degradation Revealed by Intravital Imaging in the Liver Vasculature","volume":"6","author":"Kolaczkowska","year":"2015","journal-title":"Nat. Commun."},{"key":"ref_19","doi-asserted-by":"crossref","unstructured":"Jhunjhunwala, S., Aresta-DaSilva, S., Tang, K., Alvarez, D., Webber, M.J., Tang, B.C., Lavin, D.M., Veiseh, O., Doloff, J.C., and Bose, S. (2015). Neutrophil Responses to Sterile Implant Materials. PLoS ONE, 10.","DOI":"10.1371\/journal.pone.0137550"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"3522","DOI":"10.4049\/jimmunol.1102404","article-title":"Neutrophil Extracellular Traps That Are Not Degraded in Systemic Lupus Erythematosus Activate Complement Exacerbating the Disease","volume":"188","author":"Leffler","year":"2012","journal-title":"J. Immunol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"2436","DOI":"10.1016\/j.immuni.2022.11.007","article-title":"Functional Proteomic Profiling Links Deficient DNA Clearance to Mortality in Patients with Severe COVID-19 Pneumonia","volume":"55","author":"Aramburu","year":"2022","journal-title":"Immunity"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Singhal, A., Yadav, S., Chandra, T., Mulay, S.R., Gaikwad, A.N., and Kumar, S. (2022). An Imaging and Computational Algorithm for Efficient Identification and Quantification of Neutrophil Extracellular Traps. Cells, 11.","DOI":"10.3390\/cells11020191"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Barcenilla, H., and Diaz, D. (2022). Apoptosis and Cancer: Methods and Protocols, Springer US. Methods in Molecular Biology.","DOI":"10.1007\/978-1-0716-2553-8"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1021\/bi001041a","article-title":"Characterization of Human DNase I Family Endonucleases and Activation of DNase \u03b3 during Apoptosis","volume":"40","author":"Shiokawa","year":"2001","journal-title":"Biochemistry"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"205","DOI":"10.1083\/jcb.200806072","article-title":"Histone Hypercitrullination Mediates Chromatin Decondensation and Neutrophil Extracellular Trap Formation","volume":"184","author":"Wang","year":"2009","journal-title":"J. Cell Biol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"1202","DOI":"10.1126\/science.aam8897","article-title":"Host DNases Prevent Vascular Occlusion by Neutrophil Extracellular Traps","volume":"358","author":"Rangaswamy","year":"2017","journal-title":"Science"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1165\/rcmb.2016-0193PS","article-title":"Evasion of Neutrophil Extracellular Traps by Respiratory Pathogens","volume":"56","author":"Storisteanu","year":"2017","journal-title":"Am. J. Respir. Cell Mol. Biol."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1652","DOI":"10.3899\/jrheum.190875","article-title":"Role of Neutrophil Extracellular Traps Regarding Patients at Risk of Increased Disease Activity and Cardiovascular Comorbidity in Systemic Lupus Erythematosus","volume":"47","author":"Moore","year":"2020","journal-title":"J. Rheumatol."},{"key":"ref_29","first-page":"288","article-title":"Systemic Lupus Erythematosus Disease Activity Index 2000","volume":"29","author":"Gladman","year":"2002","journal-title":"J. Rheumatol."}],"container-title":["International Journal of Molecular Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/4\/3222\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,10]],"date-time":"2025-10-10T18:25:53Z","timestamp":1760120753000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1422-0067\/24\/4\/3222"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,2,6]]},"references-count":29,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2023,2]]}},"alternative-id":["ijms24043222"],"URL":"https:\/\/doi.org\/10.3390\/ijms24043222","relation":{},"ISSN":["1422-0067"],"issn-type":[{"type":"electronic","value":"1422-0067"}],"subject":[],"published":{"date-parts":[[2023,2,6]]}}}