ACS OmegaPub Date : 2024-10-31DOI: 10.1021/acsomega.4c0821910.1021/acsomega.4c08219
David V. Russell, Luke R. Sadergaski*, Jeffrey D. Einkauf, Laetitia H. Delmau and Jonathan D. Burns*,
{"title":"Remote Sensing of Nitric Acid and Temperature via Design of Experiments, Chemometrics, and Raman Spectroscopy","authors":"David V. Russell, Luke R. Sadergaski*, Jeffrey D. Einkauf, Laetitia H. Delmau and Jonathan D. Burns*, ","doi":"10.1021/acsomega.4c0821910.1021/acsomega.4c08219","DOIUrl":"https://doi.org/10.1021/acsomega.4c08219https://doi.org/10.1021/acsomega.4c08219","url":null,"abstract":"<p >This study presents an effective method for the quantification of nitric acid (0.1–9 M) and the temperature (20–60 °C) through optimal experimental design, chemometrics, and Raman spectroscopy. Raman spectroscopy can be deployed using fiber-optic cables in hot cell environments to support processing operations in the nuclear field and industry. Chemical operations frequently use nitric acid and operate at nonambient temperatures either by design or by circumstance. Examples of Raman spectroscopy for the quantification of nitric acid with applications in the industrial field are profuse. However, the effect of temperature on quantification is often ignored and should be considered in real-world scenarios. Statistical design of experiments was used to build training sets for partial least-squares regression and support vector regression (SVR) models. The SVR model with a nonlinear kernel outperformed the top partial least-squares models with respect to temperature and resulted in percent root-mean-square error of prediction of 1.8% and 2.3% for nitric acid and temperature, respectively. The D-optimal design strategy decreased the sampling time by 75% compared to a more traditional seven-level full factorial option. The new method advances chemometric applications within and beyond the nuclear field and industry.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c08219","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-31DOI: 10.1021/acsomega.4c0482310.1021/acsomega.4c04823
Christopher Dölle*, Christoph Schmüser, Igor Quiring and Ralph Wilken,
{"title":"Near-Surfaces and Bulk Modification of Silicone Rubber under UV- and Vacuum UV-Irradiation Using Excimer and Hg Lamps","authors":"Christopher Dölle*, Christoph Schmüser, Igor Quiring and Ralph Wilken, ","doi":"10.1021/acsomega.4c0482310.1021/acsomega.4c04823","DOIUrl":"https://doi.org/10.1021/acsomega.4c04823https://doi.org/10.1021/acsomega.4c04823","url":null,"abstract":"<p >The surface properties of silicone rubber can be modified by irradiation with light from the vacuum ultraviolet (VUV) spectral range of less than 200 nm. After VUV-irradiation at 185 nm with a low-pressure mercury (Hg) lamp, a reduction in residual-dust-coverage (PA fibers) of up to 80% was found. At the same time, the long wavelength UV-radiation at 254 nm of the Hg lamp causes a reduction in the optical transmission properties of the silicone bulk. The near-surface and bulk modification of optically highly transparent silicone rubber was analyzed using XPS, ATR, transmission measurements, and investigations into the reduction of the residual-dust-coverage. A comparison was made between a Hg lamp and an excimer lamp at 172 nm. The results provide valuable information for selecting the appropriate irradiation source, depending on the desired spectral range for a given application. The results indicate that excimer lamps should be preferred for optical applications in the UV-spectral range, while Hg lamps are equally suitable for applications in the visible spectral range despite low transmission losses of less than 0.5%. The irradiation dose data were obtained using a ray tracing simulation as part of these investigations to overcome limitations of UV-sensors, such as their accelerated aging and angular dependence.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c04823","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-31DOI: 10.1021/acsomega.4c0673410.1021/acsomega.4c06734
Aidan P. Holman, Roa Elsaigh, Ragd Elsaigh, Axell Rodriguez and Dmitry Kurouski*,
{"title":"Dyed Hair and Swimming Pools: The Influence of Chlorinated and Nonchlorinated Agitated Water on Surface-Enhanced Raman Spectroscopic Analysis of Artificial Dyes on Hair","authors":"Aidan P. Holman, Roa Elsaigh, Ragd Elsaigh, Axell Rodriguez and Dmitry Kurouski*, ","doi":"10.1021/acsomega.4c0673410.1021/acsomega.4c06734","DOIUrl":"https://doi.org/10.1021/acsomega.4c06734https://doi.org/10.1021/acsomega.4c06734","url":null,"abstract":"<p >Chlorine, commonly found in pools and tap water, presents an intriguing concern in forensic hair analysis due to its sources and composition. Current forensic analysis involves optical microscopy which is subjected to advanced training where even multiple experts can deliver opposing conclusions for the same hair sample. Despite challenges in traditional analysis methods, emerging techniques like surface-enhanced Raman spectroscopy (SERS) offer promising solutions, showcasing success even in harsh environments like prolonged sunlight or stagnant water immersion. This study employs partial least-squares discriminant analysis (PLS-DA) to evaluate SERS efficacy in identifying dyes on hair immersed in chlorinated and distilled moving water for up to eight weeks. Our results demonstrated that one semipermanent colorant overwhelmingly influenced Raman signals in dyed hair exposed to both chlorinated and nonchlorinated water over an eight-week period, masking other colorants’ spectral signatures. Despite one colorant’s dominance, PLS-DA identified underlying colorants and their exposure conditions, suggesting persistent, unique interactions between original colorants and the environment. This study demonstrates the high potential for PLS-DA-based identifications of dyes on hair using SERS.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c06734","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-31DOI: 10.1021/acsomega.4c0504310.1021/acsomega.4c05043
Silja Välimets, Lorenz Schwaiger, Alexandra Bennett, Daniel Maresch, Roland Ludwig, Stephan Hann, Dolores Linde, Francisco Javier Ruiz-Dueñas and Clemens Peterbauer*,
{"title":"Dye-Decolorizing Peroxidases Maintain High Stability and Turnover on Kraft Lignin and Lignocellulose Substrates","authors":"Silja Välimets, Lorenz Schwaiger, Alexandra Bennett, Daniel Maresch, Roland Ludwig, Stephan Hann, Dolores Linde, Francisco Javier Ruiz-Dueñas and Clemens Peterbauer*, ","doi":"10.1021/acsomega.4c0504310.1021/acsomega.4c05043","DOIUrl":"https://doi.org/10.1021/acsomega.4c05043https://doi.org/10.1021/acsomega.4c05043","url":null,"abstract":"<p >Fungal enzyme systems for the degradation of plant cell wall lignin, consisting of, among others, laccases and lignin-active peroxidases, are well characterized. Additionally, fungi and bacteria contain dye-decolorizing peroxidases (DyP), which are also capable of oxidizing and modifying lignin constituents. Studying DyP activity on lignocellulose poses challenges due to the heterogeneity of the substrate and the lack of continuous kinetic methods. In this study, we report the kinetic parameters of bacterial DyP from <i>Amycolatopsis</i> 75iv2 and fungal DyP from <i>Auricularia auricula-judae</i> on insoluble plant materials and kraft lignin by monitoring the depletion of the cosubstrate of the peroxidases with a H<sub>2</sub>O<sub>2</sub> sensor. In the reactions with spruce, both enzymes showed similar kinetics. On kraft lignin, the catalytic rate of bacterial DyP reached 30 ± 2 s<sup>–1</sup>, whereas fungal DyP was nearly 3 times more active (81 ± 7 s<sup>–1</sup>). Importantly, the real-time measurement of H<sub>2</sub>O<sub>2</sub> allowed the assessment of continuous activity for both enzymes, revealing a previously unreported exceptionally high stability under turnover conditions. Bacterial DyP performed 24,000 turnovers of H<sub>2</sub>O<sub>2</sub>, whereas the fungal DyP achieved 94,000 H<sub>2</sub>O<sub>2</sub> turnovers in 1 h with a remaining activity of 40 and 80%, respectively. Using mass spectrometry, the depletion of the cosubstrate H<sub>2</sub>O<sub>2</sub> was shown to correlate with product formation, validating the amperometric method.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c05043","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609541","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-31DOI: 10.1021/acsomega.4c0570110.1021/acsomega.4c05701
Jun He, Bohao Wang* and Gang Zhang,
{"title":"Influence of Microwave-Assisted Supercritical Carbon Dioxide Treatment on the Pore Structure of Low-Rank Coal","authors":"Jun He, Bohao Wang* and Gang Zhang, ","doi":"10.1021/acsomega.4c0570110.1021/acsomega.4c05701","DOIUrl":"https://doi.org/10.1021/acsomega.4c05701https://doi.org/10.1021/acsomega.4c05701","url":null,"abstract":"<p >CO<sub>2</sub> injection into coal seams not only enhances coalbed methane (CBM) extraction but also allows for CO<sub>2</sub> sequestration. Microwave irradiation is considered to be an effective technology to enhance CBM extraction. In this paper, the effects of microwave irradiation and supercritical CO<sub>2</sub> immersion on the pore structure of low-rank coals were investigated by scanning electron microscopy (SEM), mercury-in-pressure (MIP), low-temperature nitrogen adsorption (LTN<sub>2</sub>GA), and carbon dioxide isothermal adsorption/desorption (CO<sub>2</sub>IA/D) of coal samples. The results showed that the macropores and micropores of the coal samples were more developed after microwave irradiation. After carbon dioxide immersion, the coal samples showed huge fissures, and the meso- and micropores were reduced. In contrast, microwave-assisted carbon dioxide not only reduced the specific surface area in the meso- and microporous stages and decreased the adsorption sites of methane but also enhanced the pore connectivity in the macroporous stage instead of the appearance of huge fissures. This study illustrates the potential of microwave-assisted supercritical carbon dioxide for enhanced coalbed methane extraction and carbon dioxide sequestration.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c05701","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-30DOI: 10.1021/acsomega.4c0582810.1021/acsomega.4c05828
Anastasiia Antonenko, Adam Pomorski, Avinash Kumar Singh, Katarzyna Kapczyńska and Artur Krężel*,
{"title":"Site-Specific and Fluorescently Enhanced Installation of Post-Translational Protein Modifications via Bifunctional Biarsenical Linker","authors":"Anastasiia Antonenko, Adam Pomorski, Avinash Kumar Singh, Katarzyna Kapczyńska and Artur Krężel*, ","doi":"10.1021/acsomega.4c0582810.1021/acsomega.4c05828","DOIUrl":"https://doi.org/10.1021/acsomega.4c05828https://doi.org/10.1021/acsomega.4c05828","url":null,"abstract":"<p >To understand how particular post-translational modifications (PTMs) affect the function of a target protein, it is essential to first prepare and investigate the target with the modification at the desired position. This drives the continuous development of site-specific protein modification technologies. Here, we present the chemical synthesis and application of the biarsenical linker SrtCrAsH-EDT<sub>2</sub>, which has a dual labeling functionality. This linker, containing a sortase A recognition motif, can be conjugated with any protein containing the LPXTG motif at the C terminus, such as ubiquitin and the SUMO tag, and then attached to a protein of interest (POI) containing a terminal or bipartite (intramolecularly placed) tetracysteine motif. This modification of the POI facilitates the straightforward and rapid incorporation of PTMs, which are further highlighted by the fluorescent biarsenical probe. Consequently, this directly correlates proteins’ physical properties and cellular roles under various physiological conditions or in disease states. The proposed one-pot labeling methodology can be utilized to explore the effects of PTMs on proteins, affecting their structure, function, localization, and interactions within the cellular environment. Understanding these effects is crucial for uncovering the complex mechanisms that regulate cellular function and dysfunction.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c05828","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-30DOI: 10.1021/acsomega.4c0640410.1021/acsomega.4c06404
Sanierlly da Paz Do Nascimento, Ramon Ramos Marques de Souza, Marianna Vieira Sobral, Francisco Humberto Xavier-Junior, Marcus Vinícius Santos da Silva, Marcelo Machado Viana, Fausthon Fred da Silva, Michael J. Serpe and Antonia L. de Souza*,
{"title":"Gelatin-Oxidized Alginate and Chitosan-Coated Zein Nanoparticle Hydrogel Composite to Enhance Breast Cancer Cytotoxicity in Dual-Drug Delivery","authors":"Sanierlly da Paz Do Nascimento, Ramon Ramos Marques de Souza, Marianna Vieira Sobral, Francisco Humberto Xavier-Junior, Marcus Vinícius Santos da Silva, Marcelo Machado Viana, Fausthon Fred da Silva, Michael J. Serpe and Antonia L. de Souza*, ","doi":"10.1021/acsomega.4c0640410.1021/acsomega.4c06404","DOIUrl":"https://doi.org/10.1021/acsomega.4c06404https://doi.org/10.1021/acsomega.4c06404","url":null,"abstract":"<p >This study explores the combined delivery of doxorubicin and quercetin using a gelatin-oxidized alginate-based hydrogel as a promising strategy for localized breast cancer therapy. Our approach involves the incorporation of doxorubicin within the hydrogel matrix and loading quercetin into chitosan-coated zein nanoparticles. The hydrogel exhibited self-healing properties attributed to Schiff base cross-linking and demonstrated injectability. Characterization of its microstructural, mechanical, and textural properties revealed a porous and flexible structure, demonstrating its suitability for drug release applications. Both drugs exhibited distinct in vitro release profiles at pH 6.8 (typical of tumor tissue), with doxorubicin at 81.2% and quercetin at 9.7%. After 72 h of release, the cytotoxicity against MCF-7 breast cancer cells was assessed. The hydrogel formulation containing doxorubicin increased the cytotoxic action by 4.66-fold, whereas the hydrogel composite, containing both doxorubicin and quercetin-loaded nanoparticles, enhanced it by 20.7-fold compared with doxorubicin alone. Thus, the findings of our study highlight the enhancing effect of the dual release system, thereby expanding the utility of gelatin-oxidized alginate-based hydrogels as advanced drug delivery systems, as exemplified by the combined delivery of doxorubicin and quercetin.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c06404","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609410","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-30DOI: 10.1021/acsomega.4c0741610.1021/acsomega.4c07416
Zhanwei Li, Shida Chen*, Dazhen Tang and Yuanhao Zhi,
{"title":"Genesis and Accumulation Modes of Coalbed Methane at the Eastern Margin of Ordos Basin, China: Evidence from Its Geochemistry","authors":"Zhanwei Li, Shida Chen*, Dazhen Tang and Yuanhao Zhi, ","doi":"10.1021/acsomega.4c0741610.1021/acsomega.4c07416","DOIUrl":"https://doi.org/10.1021/acsomega.4c07416https://doi.org/10.1021/acsomega.4c07416","url":null,"abstract":"<p >The genesis, occurrence, and accumulation of coalbed methane (CBM) are critical to the methane exploration and development. Combining the geological and geochemical data from CBM exploration wells and basin modeling, the genesis and accumulation characteristics of CBM in different regions and depths at the eastern margin of Ordos Basin were elucidated. Regional-scale gas content is controlled by depth and coal rank without turning depth occurs, but blocks perform variably. Three CBM genetic types, that is, secondary microbial, thermogenic, and mixed genesis, were identified based on data of gas components and isotopic composition. Under the influences of tectonic and hydrogeological conditions, secondary microbial gas is widely distributed in shallow coal seams (depth <1350 m) showing mixed gas characteristics, while secondary thermogenic gas dominates in deep coal seams. The extensive variations of carbon isotope of methane raised from desorption–diffusion induced by tectonic uplift, dissolution in flowing groundwater, secondary microbial gas generation, and rapid gas generation enhanced by magmatic thermal. Three CBM accumulation modes have been concluded depending on the depth and coal rank. The Baode mode is characterized by a high-ratio secondary microbial gas replenishment, typically occurring at lower ranks and shallow depths. The Linxing mode is distinguished by magmatic thermal influences, and the Daji mode features massive secondary thermogenetic gas associated with higher ranks and deeper depths. Every mode has the potential to form high-gas-content zones.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c07416","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609586","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-30DOI: 10.1021/acsomega.4c0677910.1021/acsomega.4c06779
Joseph Fox, Damien V. B. Batchelor, Patricia Louise Coletta, Elizabeth M.A. Valleley and Stephen D. Evans*,
{"title":"Microbubble Enhanced Delivery of Vitamin C for Treatment of Colorectal Cancer","authors":"Joseph Fox, Damien V. B. Batchelor, Patricia Louise Coletta, Elizabeth M.A. Valleley and Stephen D. Evans*, ","doi":"10.1021/acsomega.4c0677910.1021/acsomega.4c06779","DOIUrl":"https://doi.org/10.1021/acsomega.4c06779https://doi.org/10.1021/acsomega.4c06779","url":null,"abstract":"<p >During chemotherapy treatment for cancer, often only a fraction of the administered dose reaches the tumor site, with the remaining drug spreading throughout the body, producing unwanted side-effects and restricting how much drug can be safely administered. A potential solution to reduce this problem is the use of microbubbles. The interaction between microbubbles and ultrasound generates pores in the tumor cells, permitting enhanced drug uptake. This study investigates the delivery of the ascorbic acid derivative, palmitoyl ascorbate, to KRAS-mutated colorectal cancer cells in vitro. Ultrasound-triggered microbubbles enhanced the efficacy of liposomal palmitoyl ascorbate treatments by 1.7- and 2.2-fold in LS174T and HCT116 CRC cell lines, respectively. This enhancement was achieved without increasing the drug dosage, and the therapeutic effect was shown to be localized to the area that received the ultrasound pulse, aiding in the reduction of off-site toxicity.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c06779","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609299","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
ACS OmegaPub Date : 2024-10-30DOI: 10.1021/acsomega.4c0435910.1021/acsomega.4c04359
Seyedeh Hoda FatemiAbhari*, and , Rosa Di Felice*,
{"title":"Probing Electrostatic Interactions in DNA-Bound CRISPR/Cas9 Complexes by Molecular Dynamics Simulations","authors":"Seyedeh Hoda FatemiAbhari*, and , Rosa Di Felice*, ","doi":"10.1021/acsomega.4c0435910.1021/acsomega.4c04359","DOIUrl":"https://doi.org/10.1021/acsomega.4c04359https://doi.org/10.1021/acsomega.4c04359","url":null,"abstract":"<p >Engineered protein mutations may be exploited to tune molecular interactions in the cellular environment. Here, we have explored the structural consequences of different Cas9 mutations in genome-editing CRISPR/Cas9 systems by means of Molecular Dynamics simulations. We have characterized mutation-induced structural changes and their implications for changes in protein–DNA, DNA–RNA, and DNA–DNA interactions. We present the analysis of multiple trajectories over the cumulative time scale of 7.7 μs, focusing on triple mutations that have been associated with enhancement of genome editing specificity, as well as control mutations. We find that the structural changes induced by the protein mutations are consistent with decreasing the strength of the interaction between Cas9 and the nontarget DNA strand. We discuss the implications of this finding for genome editing specificity.</p>","PeriodicalId":22,"journal":{"name":"ACS Omega","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-10-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://pubs.acs.org/doi/epdf/10.1021/acsomega.4c04359","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142609406","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}