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Li X, Duan Q, Khan M, Yang D, Liu Q, Yin F, Hu Q, Yu L. Development of the viscosity biosensor for the detection of DNase I based on the flow distance on the paper with DNA mucus. Talanta 2024; 266:124994. [PMID: 37536109 DOI: 10.1016/j.talanta.2023.124994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 07/01/2023] [Accepted: 07/25/2023] [Indexed: 08/05/2023]
Abstract
Deoxyribonuclease I (DNase I) is a biomarker which has important applications in various biological processes. Thus, it is highly important to develop a user-friendly method for the detection of DNase I. Here, we present a paper-based distance sensor for the rapid detection of DNase I based on changes in the viscosity of DNA mucus. The viscosity of DNA mucus varies with different concentrations of DNase I, showing different water flow lengths on the pH test papers, this makes the quantification of DNase I possible. This method has a wide linear range (0.01-10 U/mL), excellent sensitivity, remarkable specificity and excellent reproducibility. The detection limit reaches 0.003 U/mL. Additionally, it can be well applied to detection of DNase I inhibitors, assay of DNase I in human serum and quality evaluation of nucleic acid scavengers. In general, this study offers a brief, convenient, label-free, and economical method to construct paper-based distance sensors using DNA mucus, which is very promising in the detection of DNase I in various applications.
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Affiliation(s)
- Xia Li
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China
| | - Qing Duan
- Infectious Disease Prevention and Control Section, Shandong Center for Disease Control and Prevention, Jinan, 250014, China
| | - Mashooq Khan
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, 250014, China; School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Danhong Yang
- Shandong Kehong Medical Technology Co., Ltd., 2018, Dezhou, 253011, China
| | - Qian Liu
- Shandong Kehong Medical Technology Co., Ltd., 2018, Dezhou, 253011, China
| | - Fangchao Yin
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, 250014, China; School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China
| | - Qiongzheng Hu
- Qilu University of Technology (Shandong Academy of Sciences), Shandong Analysis and Test Center, Jinan, 250014, China; School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250014, China.
| | - Li Yu
- Key Laboratory of Colloid and Interface Chemistry, Shandong University, Ministry of Education, Jinan, 250100, China.
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Williams RL, Murray RM. Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli. Nat Commun 2022; 13:6822. [PMID: 36357387 PMCID: PMC9649629 DOI: 10.1038/s41467-022-34361-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/22/2022] [Indexed: 11/12/2022] Open
Abstract
Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. Here, we show that a strategy of terminal differentiation improves the evolutionary stability of burdensome functions in a general manner by realizing a reproductive and metabolic division of labor. To implement this strategy, we develop a genetic differentiation circuit in Escherichia coli using unidirectional integrase-recombination. With terminal differentiation, differentiated cells uniquely express burdensome functions driven by the orthogonal T7 RNA polymerase, but their capacity to proliferate is limited to prevent the propagation of advantageous loss-of-function mutations that inevitably occur. We demonstrate computationally and experimentally that terminal differentiation increases duration and yield of high-burden expression and that its evolutionary stability can be improved with strategic redundancy. Further, we show this strategy can even be applied to toxic functions. Overall, this study provides an effective, generalizable approach for protecting burdensome engineered functions from evolutionary degradation.
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Affiliation(s)
- Rory L. Williams
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 US ,grid.266093.80000 0001 0668 7243Present Address: Department of Biomedical Engineering, University of California Irvine, Irvine, CA 92697 US
| | - Richard M. Murray
- grid.20861.3d0000000107068890Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125 US
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Serapinas S, Gineitytė J, Butkevičius M, Danilevičius R, Dagys M, Ratautas D. Biosensor prototype for rapid detection and quantification of DNase activity. Biosens Bioelectron 2022; 213:114475. [PMID: 35714494 DOI: 10.1016/j.bios.2022.114475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/05/2022] [Accepted: 06/08/2022] [Indexed: 11/19/2022]
Abstract
DNases are enzymes that cleave phosphodiesteric bonds of deoxyribonucleic acid molecules and are found everywhere in nature, especially in bodily fluids, i.e., saliva, blood, or sweat. Rapid and sensitive detection of DNase activity is highly important for quality control in the pharmaceutical and biotechnology industries. For clinical diagnostics, recent reports indicate that increased DNase activity could be related to various diseases, such as cancers. In this paper, we report a new bioelectronic device for the determination of nuclease activity in various fluids. The system consists of a sensor electrode, a custom design DNA target to maximize the DNase cleavage rate, a signal analysis algorithm, and supporting electronics. The developed sensor enables the determination of DNase activity in the range of 3.4 × 10-4 - 3.0 × 10-2 U mL-1 with a limit of detection of up to 3.4 × 10-4 U mL-1. The sensor was tested by measuring nuclease activity in real human saliva samples and found to demonstrate high accuracy and reproducibility compared to the industry standard DNaseAlert™️. Finally, the entire detection system was implemented as a prototype device system utilizing single-use electrodes, custom-made cells, and electronics. The developed technology can improve nuclease quality control processes in the pharmaceutical/biotechnology industry and provide new insights into the importance of nucleases for medical applications.
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Affiliation(s)
- Skomantas Serapinas
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Laboratorija 1", Pamėnkalnio g. 36, LT-01114, Vilnius, Lithuania
| | - Justina Gineitytė
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania
| | - Marius Butkevičius
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Laboratorija 1", Pamėnkalnio g. 36, LT-01114, Vilnius, Lithuania
| | | | - Marius Dagys
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania
| | - Dalius Ratautas
- Life Sciences Center, Vilnius University, Saulėtekio al. 7, LT-10257, Vilnius, Lithuania; UAB "Bioanalizės sistemos", Saulėtekio al. 15, LT-10224, Vilnius, Lithuania.
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Deoxyribonucleases and Their Applications in Biomedicine. Biomolecules 2020; 10:biom10071036. [PMID: 32664541 PMCID: PMC7407206 DOI: 10.3390/biom10071036] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/03/2020] [Accepted: 07/08/2020] [Indexed: 12/21/2022] Open
Abstract
Extracellular DNA, also called cell-free DNA, released from dying cells or activated immune cells can be recognized by the immune system as a danger signal causing or enhancing inflammation. The cleavage of extracellular DNA is crucial for limiting the inflammatory response and maintaining homeostasis. Deoxyribonucleases (DNases) as enzymes that degrade DNA are hypothesized to play a key role in this process as a determinant of the variable concentration of extracellular DNA. DNases are divided into two families-DNase I and DNase II, according to their biochemical and biological properties as well as the tissue-specific production. Studies have shown that low DNase activity is both, a biomarker and a pathogenic factor in systemic lupus erythematosus. Interventional experiments proved that administration of exogenous DNase has beneficial effects in inflammatory diseases. Recombinant human DNase reduces mucus viscosity in lungs and is used for the treatment of patients with cystic fibrosis. This review summarizes the currently available published data about DNases, their activity as a potential biomarker and methods used for their assessment. An overview of the experiments with systemic administration of DNase is also included. Whether low-plasma DNase activity is involved in the etiopathogenesis of diseases remains unknown and needs to be elucidated.
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Iron Oxide Nanoparticles Coated with a Phosphorothioate Oligonucleotide and a Cationic Peptide: Exploring Four Different Ways of Surface Functionalization. NANOMATERIALS 2015; 5:1588-1609. [PMID: 28347083 PMCID: PMC5304778 DOI: 10.3390/nano5041588] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/22/2015] [Accepted: 09/23/2015] [Indexed: 01/31/2023]
Abstract
The superparamagnetic iron oxide nanoparticles (SPIONs) have great potential in therapeutic and diagnostic applications. Due to their superparamagnetic behavior, they are used clinically as a Magnetic Resonance Imaging (MRI) contrast agent. Iron oxide nanoparticles are also recognized todays as smart drug-delivery systems. However, to increase their specificity, it is essential to functionalize them with a molecule that effectively targets a specific area of the body. Among the molecules that can fulfill this role, peptides are excellent candidates. Oligonucleotides are recognized as potential drugs for various diseases but suffer from poor uptake and intracellular degradation. In this work, we explore four different strategies, based on the electrostatic interactions between the different partners, to functionalize the surface of SPIONs with a phosphorothioate oligonucleotide (ODN) and a cationic peptide labeled with a fluorophore. The internalization of the nanoparticles has been evaluated in vitro on RAW 264.7 cells. Among these strategies, the "«one-step assembly»", i.e., the direct complexation of oligonucleotides and peptides on iron oxide nanoparticles, provides the best way of coating for the internalization of the nanocomplexes.
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