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Lin M, Yang H, Li Q, Xiao H, Jiang S, Liang J, Cui X, Zhao S. Dual lateral flow assay based on PdRu nanocages for human Papillomavirus detection. J Colloid Interface Sci 2024; 673:893-900. [PMID: 38908288 DOI: 10.1016/j.jcis.2024.06.002] [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: 03/10/2024] [Revised: 05/21/2024] [Accepted: 06/02/2024] [Indexed: 06/24/2024]
Abstract
Cervical cancer is one of the most common gynecological malignancies, with the vast majority of which being caused by persistent infection with Human Papillomavirus (HPV) 16 and 18. The current available HPV detection methods are sensitive and genotyped but are restricted by expensive instruments and skilled personnel. The development of an easy-to-use, rapid, and cost-friendly analysis method for HPV is of great need. Herein, hollow palladium-ruthenium nanocages modified with two oligonucleotides (PdRu capture probes) were constructed for genotyping and simultaneous detection of target nucleic acids HPV16 and HPV18 by dual lateral flow assay (DLFA). PdRu capture probes were endowed with bi-functions for the first time, which could be used to output signals and hybridize target nucleic acids. Under optimized conditions, the PdRu based-DLFA with detection limits of 0.93 nM and 0.19 nM, respectively, exhibited convenient operation, and high sensitivity. Meanwhile, the DLFA achieved excellent rapid detection within 20 min, which was attributed to capture probes that can be directly bound to amplification-free target nucleic acids. Therefore, the development of PdRu-based DLFA can be utilized for rapid, sensitive, and simultaneous genotyping detection of HPV16 and HPV18, showing great application for nucleic acid detection.
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Affiliation(s)
- Mingxia Lin
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Huiyi Yang
- Molecular Diagnosis and Treatment Center for Infectious Diseases, Dermatology Hospital, Southern Medical University, Guangzhou, China.
| | - Qinglan Li
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Huanxin Xiao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Shilin Jiang
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Jinhui Liang
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Xiping Cui
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
| | - Suqing Zhao
- Department of Pharmaceutical Engineering, School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, Guangzhou 510006, China.
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2
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Rosa SS, Zhang S, Sari Y, Marques MPC. A (RP)UHPLC/UV analytical method to quantify dsRNA during the mRNA vaccine manufacturing process. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:5146-5153. [PMID: 39011770 PMCID: PMC11293613 DOI: 10.1039/d4ay00560k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 07/06/2024] [Indexed: 07/17/2024]
Abstract
dsRNA is a product related impurity produced during the mRNA manufacturing process. The established immuno-based detection methods lack the flexibility and speed required to be applied throughout the manufacturing process. The RP-HPLC method developed outperforms these in terms of precision, broader detection range, LOD and LOQ, as well as in output variance. Using this method, dsRNA can be quantified in under 30 min for a single sample.
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Affiliation(s)
- Sara Sousa Rosa
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK.
- Department of Bioengineering, iBB-Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Shuran Zhang
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK.
| | - Yustika Sari
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK.
| | - Marco P C Marques
- Department of Biochemical Engineering, University College London, Gordon Street, London, WC1E 6BT, UK.
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Adak S, Rahaman SA, Karmakar S, Bandyopadhyay S. An Emission-Based Probe for the Detection and Quantification of DNA and RNA. Chem Asian J 2024; 19:e202400400. [PMID: 38779709 DOI: 10.1002/asia.202400400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Sequence-independent detection of low concentrations of nucleic acids is important for applications in forensics and diagnostics. An emission-based probe for detecting and quantifying DNA and RNA utilizing a water-soluble dicationic tetraphenylethene (TPE) derivativewas developed. The recognition is based on the electrostatic and other non-covalent interactions between the phosphate backbone of nucleic acids and the cationic probe, which cause the restriction of rotation of the aryl units of the probe, ensuing in the enhancement of the fluorescence signal. The binding was validated by different spectroscopic techniques and also by electrophoretic mobility shift assay. The probable mode of binding with the nucleic acids was studied by blind-docking studies that correlated well with the experimental results.
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Affiliation(s)
- Soumen Adak
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, WB 741246, India
| | - Sk Atiur Rahaman
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, WB 741246, India
| | - Susnata Karmakar
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, England, United Kingdom
| | - Subhajit Bandyopadhyay
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Kolkata, Mohanpur, Nadia, WB 741246, India
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Bjørstorp S, Malmstrøm J. Quantitative 31P NMR Spectroscopy Platform Method for the Assay of Oligonucleotides as Pure Drug Substances and in Drug Product Formulations Using the Internal Standard Method. Anal Chem 2024; 96:11198-11204. [PMID: 38943563 DOI: 10.1021/acs.analchem.4c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2024]
Abstract
One of the most widely used techniques for the quantification of small interfering ribonucleic acid (siRNA) is the ultraviolet (UV) spectroscopy method. However, due to uncertainties in the extinction coefficient affecting the accuracy of the method and a sample preparation including several dilution steps, the purpose of this study was to explore the possibility of determining the content of siRNA by a platform method using quantitative 31P nuclear magnetic resonance (31P-qNMR) and the internal standard method. In this paper, acquisition time, selection of a suitable internal certified reference material, signal selection used for quantification, relaxation delay, and precision are discussed. In addition, the robustness of the method and the ability to apply this platform method to both drug substance (DS) and drug product samples is also discussed. Quantifications of siRNA determined by the 31P-qNMR platform method were on average 98.5%w/w when adjusting for the sodium and water contents. The data confirmed the applicability of 31P-qNMR in siRNA content determinations. The quantifications were compared to quantifications determined by the traditional UV spectroscopy method by F- and t-tests. The statistical tests showed that the platform 31P-qNMR method provided more accurate results (mass balance close to 100% w/w) compared to the traditional UV spectroscopy method when analyzing DS samples.
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Affiliation(s)
- Simone Bjørstorp
- Department of CMC Analytical Support, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
- Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, 2100 Copenhagen Ø, Denmark
| | - Joan Malmstrøm
- Department of CMC Analytical Support, Novo Nordisk A/S, Novo Nordisk Park 1, 2760 Måløv, Denmark
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den Roover S, Aerts JL. MRNACalc: An accurate RNA quantification tool in the era of modified nucleosides. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102226. [PMID: 38868362 PMCID: PMC11166867 DOI: 10.1016/j.omtn.2024.102226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Affiliation(s)
- Sabine den Roover
- Neuro-Aging and Viro-Immunotherapy (NAVI) Research Group, Vrije Universiteit Brussel, Brussels, Belgium
| | - Joeri L. Aerts
- Neuro-Aging and Viro-Immunotherapy (NAVI) Research Group, Vrije Universiteit Brussel, Brussels, Belgium
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Cedden D, Güney G, Scholten S, Rostás M. Lethal and sublethal effects of orally delivered double-stranded RNA on the cabbage stem flea beetle, Psylliodes chrysocephala. PEST MANAGEMENT SCIENCE 2024; 80:2282-2293. [PMID: 37020381 DOI: 10.1002/ps.7494] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 03/09/2023] [Accepted: 04/06/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND The cabbage stem flea beetle (Psylliodes chrysocephala) is one of the most important insect pests of oilseed rape (Brassica napus) in northern Europe. The emergence of insecticide-resistant populations and the ban on neonicotinoid seed treatments have made the management of this pest challenging and research is needed to develop alternative strategies such as RNA interference (RNAi). We investigated lethal and sublethal effects of orally delivered double-stranded (ds)RNAs targeting P. chrysocephala orthologs of Sec23 and vacuolar adenosine triphosphatase subunit G (VatpG), which are involved in endoplasmic reticulum-Golgi transport and organelle acidification, respectively. RESULTS Feeding bioassays on P. chrysocephala adults showed that the highest concentration (200 ng/leaf disk) of dsSec23 caused mortalities of 76% and 56% in pre-aestivating and post-aestivating beetles, respectively, while the same concentration of dsVatpG led to mortality rates of ~34% in both stages. Moreover, sublethal effects, such as decreased feeding rates and attenuated locomotion were observed. Small RNA sequencing and gene expression measurements following the delivery of dsRNAs demonstrated the generation of ~21 nucleotide-long small interfering RNAs and a systemic RNAi response in P. chrysocephala. CONCLUSION We demonstrate that P. chrysocephala is a promising candidate for developing RNAi-based pest management strategies. Further research is necessary to identify more effective target genes and to assess potential non-target effects. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Doga Cedden
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Göttingen, Germany
- Department of Evolutionary Developmental Genetics, Johann-Friedrich-Blumenbach Institute, GZMB, University of Göttingen, Göttingen, Germany
| | - Gözde Güney
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Stefan Scholten
- Division of Crop Plant Genetics, Department of Crop Sciences, University of Göttingen, Göttingen, Germany
| | - Michael Rostás
- Agricultural Entomology, Department of Crop Sciences, University of Göttingen, Göttingen, Germany
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Cardoso FM, Elias A, Pereira I, Maurício I, Matos O. Improved dsRNA isolation and purification method validated by viral dsRNA detection using novel primers in Saccharomyces cerevisiae. MethodsX 2023; 11:102435. [PMID: 37876828 PMCID: PMC10591000 DOI: 10.1016/j.mex.2023.102435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023] Open
Abstract
Accurate genomic sequencing demands high-quality double-stranded RNA (dsRNA). Existing methods for dsRNA extraction from yeast, fungi, and plants primarily rely on cellulose, suitable only for small volume extractions, or the time-consuming lithium chloride precipitation. To streamline the traditional phenol-chloroform-based dsRNA extraction method, the main challenge is the reduction of mitochondrial DNA (mtDNA) and Single Stranded RNA (ssRNA) to no detectable levels after gel electrophoresis. This challenge is successfully addressed through the modified approach described here, involving phenol extraction at low pH, followed by the addition of ammonium sulfate to the aqueous buffer. The dsRNA isolated using this novel method exhibits comparable quality to that obtained through cellulose purification, and it is readily amenable to RT-PCR. Moreover, a single batch of yeast cell RNA isolation requires only 2-3 h of hands-on time, thus simplifying and expediting the process significantly.•Buffers were redesigned from [32,33,35].•No DNASE, Ribonuclease A or beads were used during the purification.•Simple and inexpensive dsRNA extraction and purification method is described.
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Affiliation(s)
- Fernando M.H. Cardoso
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | - Inês Pereira
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Isabel Maurício
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Olga Matos
- Global Health and Tropical Medicine, GHTM, Associate Laboratory in Translation and Innovation Towards Global Health, LA-REAL, Instituto de Higiene e Medicina Tropical, IHMT, Universidade NOVA de Lisboa, UNL, Rua da Junqueira 100, Lisboa 1349-008, Portugal
- Environmental Health Institute, Faculdade de Medicina da Universidade de Lisboa, Lisboa 1649-028, Portugal
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Chatterjee A, Zhang K, Parker KM. Binding of Dissolved Organic Matter to RNA and Protection from Nuclease-Mediated Degradation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:16086-16096. [PMID: 37811805 DOI: 10.1021/acs.est.3c05019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The persistence of RNA in environmental systems is an important parameter for emerging applications, including ecological surveys, wastewater-based epidemiology, and RNA interference biopesticides. RNA persistence is controlled by its rate of biodegradation, particularly by extracellular enzymes, although the specific factors determining this rate have not been characterized. Due to prior work suggesting that nucleic acids-specifically DNA-interact with dissolved organic matter (DOM), we hypothesized that DOM may bind RNA and impede its biodegradation in natural systems. We first adapted a technique previously used to assess RNA-protein binding to differentiate RNA that is bound at all sites by DOM from RNA that is unbound or partially bound by DOM. Results from this technique suggested that humic acids bound RNA more extensively than fulvic acids. At concentrations of 8-10 mgC/L, humic acids were also found to be more effective than fulvic acids at suppressing enzymatic degradation of RNA. In surface water and soil extract containing DOM, RNA degradation was suppressed by 39-46% relative to pH-adjusted controls. Due to the ability of DOM to both bind and suppress the enzymatic degradation of RNA, RNA biodegradation may be slowed in environmental systems with high DOM concentrations, which may increase its persistence.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Mwaka HS, Bauters L, Namaganda J, Marcou S, Bwesigye PN, Kubiriba J, Smagghe G, Tushemereirwe WK, Gheysen G. Transgenic East African Highland Banana Plants Are Protected against Radopholus similis through Host-Delivered RNAi. Int J Mol Sci 2023; 24:12126. [PMID: 37569502 PMCID: PMC10418933 DOI: 10.3390/ijms241512126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/22/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
The burrowing nematode Radopholus similis is considered a major problem of intensive banana cultivation. It can cause extensive root damage resulting in the toppling disease of banana, which means that plants fall to the ground. Soaking R. similis in double-stranded (ds) RNA of the nematode genes Rps13, chitin synthase (Chs-2), Unc-87, Pat-10 or beta-1,4-endoglucanase (Eng1a) suppressed reproduction on carrot discs, from 2.8-fold (Chs-2) to 7-fold (Rps13). The East African Highland Banana cultivar Nakitembe was then transformed with constructs for expression of dsRNA against the same genes, and for each construct, 30 independent transformants were tested with nematode infection. Four months after transfer from in vitro culture to the greenhouse, the banana plants were transferred to a screenhouse and inoculated with 2000 nematodes per plant, and thirteen weeks later, they were analyzed for several parameters including plant growth, root necrosis and final nematode population. Plants with dsRNA constructs against the nematode genes were on average showing lower nematode multiplication and root damage than the nontransformed controls or the banana plants expressing dsRNA against the nonendogenous gene. In conclusion, RNAi seems to efficiently protect banana against damage caused by R. similis, opening perspectives to control this pest.
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Affiliation(s)
- Henry Shaykins Mwaka
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Lander Bauters
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
| | - Josephine Namaganda
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Shirley Marcou
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
| | - Priver Namanya Bwesigye
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Jerome Kubiriba
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (J.N.); (P.N.B.); (J.K.); (W.K.T.)
| | - Guy Smagghe
- Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (S.M.)
| | | | - Godelieve Gheysen
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (L.B.)
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Luo D, Wu Z, Wang D, Zhang J, Shao F, Wang S, Cestellos-Blanco S, Xu D, Cao Y. Lateral flow immunoassay for rapid and sensitive detection of dsRNA contaminants in in vitro-transcribed mRNA products. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 32:445-453. [PMID: 37181450 PMCID: PMC10173069 DOI: 10.1016/j.omtn.2023.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 04/04/2023] [Indexed: 05/16/2023]
Abstract
High purity is essential in mRNA-based therapeutic applications. A major contaminant of in vitro-transcribed (IVT) mRNA manufacturing is double-stranded RNA (dsRNA), which can induce severe anti-viral immune responses. Detection methods, such as agarose gel electrophoresis, ELISA, and dot-blot assay, are used to detect the existence of dsRNA in IVT mRNA products. However, these methods are either not sensitive enough or time-consuming. To overcome these challenges, we develop a rapid, sensitive, and easy-to-implement colloidal gold nanoparticle-based lateral flow strip assay (LFSA) with sandwich format for the detection of dsRNA from IVT process. dsRNA contaminant can be determined visually on the test strip or quantitatively with a portable optical detector. This method allows for a 15 min detection of N1-methyl-pseudouridine (m1Ψ)-containing dsRNA with a detection limit of 69.32 ng/mL. Furthermore, we establish the correlation between the LFSA test results and the immune response caused by dsRNA in mice. The LFSA platform allows the rapid, sensitive, and quantitative monitoring of purity in massive IVT mRNA products and aids for the prevention of immunogenicity by dsRNA impurities.
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Affiliation(s)
- Dengwang Luo
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
| | - Zhanfeng Wu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Molecular Nanostructure and Nanotechnology, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daming Wang
- Academy for Engineering and Technology, Fudan University, Shanghai 200433, China
- Suzhou Institute of Biomedical Engineering and Technology (SIBET), Chinese Academy of Sciences, Suzhou, Jiangsu 215163, China
- Anbio Biotechnology Company, Xiamen, Fujian 361026, China
| | - Jieli Zhang
- Anbio Biotechnology Company, Xiamen, Fujian 361026, China
| | - Fei Shao
- University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Shuo Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Stefano Cestellos-Blanco
- Department of Materials Science and Engineering, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Dawei Xu
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- Corresponding author: Dawei Xu, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China.
| | - Yuhong Cao
- CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China
- School of Nanoscience and Technology, University of Chinese Academy of Sciences, Beijing 100049, China
- Corresponding author: Yuhong Cao, CAS Key Laboratory for Biological Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology, Chinese Academy of Sciences, Beijing 100190, China.
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11
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Wang X, Bigman LS, Greenblatt HM, Yu B, Levy Y, Iwahara J. Negatively charged, intrinsically disordered regions can accelerate target search by DNA-binding proteins. Nucleic Acids Res 2023; 51:4701-4712. [PMID: 36774964 PMCID: PMC10250230 DOI: 10.1093/nar/gkad045] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 01/03/2023] [Accepted: 01/17/2023] [Indexed: 02/14/2023] Open
Abstract
In eukaryotes, many DNA/RNA-binding proteins possess intrinsically disordered regions (IDRs) with large negative charge, some of which involve a consecutive sequence of aspartate (D) or glutamate (E) residues. We refer to them as D/E repeats. The functional role of D/E repeats is not well understood, though some of them are known to cause autoinhibition through intramolecular electrostatic interaction with functional domains. In this work, we investigated the impacts of D/E repeats on the target DNA search kinetics for the high-mobility group box 1 (HMGB1) protein and the artificial protein constructs of the Antp homeodomain fused with D/E repeats of varied lengths. Our experimental data showed that D/E repeats of particular lengths can accelerate the target association in the overwhelming presence of non-functional high-affinity ligands ('decoys'). Our coarse-grained molecular dynamics (CGMD) simulations showed that the autoinhibited proteins can bind to DNA and transition into the uninhibited complex with DNA through an electrostatically driven induced-fit process. In conjunction with the CGMD simulations, our kinetic model can explain how D/E repeats can accelerate the target association process in the presence of decoys. This study illuminates an unprecedented role of the negatively charged IDRs in the target search process.
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Affiliation(s)
- Xi Wang
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Lavi S Bigman
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Harry M Greenblatt
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Binhan Yu
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Junji Iwahara
- Department of Biochemistry and Molecular Biology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-1068, USA
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12
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Zhang K, Ho KP, Chatterjee A, Park G, Li Z, Catalano JG, Parker KM. RNA Hydrolysis at Mineral-Water Interfaces. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023. [PMID: 37216349 DOI: 10.1021/acs.est.3c01407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
As an essential biomolecule for life, RNA is ubiquitous across environmental systems where it plays a central role in biogeochemical processes and emerging technologies. The persistence of RNA in soils and sediments is thought to be limited by enzymatic or microbial degradation, which occurs on timescales that are orders of magnitude faster than known abiotic pathways. Herein, we unveil a previously unreported abiotic pathway by which RNA rapidly hydrolyzes on the timescale of hours upon adsorption to iron (oxyhydr)oxide minerals such as goethite (α-FeOOH). The hydrolysis products were consistent with iron present in the minerals acting as a Lewis acid to accelerate sequence-independent hydrolysis of phosphodiester bonds comprising the RNA backbone. In contrast to acid- or base-catalyzed RNA hydrolysis in solution, mineral-catalyzed hydrolysis was fastest at circumneutral pH, which allowed for both sufficient RNA adsorption and hydroxide concentration. In addition to goethite, we observed that RNA hydrolysis was also catalyzed by hematite (α-Fe2O3) but not by aluminum-containing minerals (e.g., montmorillonite). Given the extensive adsorption of nucleic acids to environmental surfaces, we anticipate previously overlooked mineral-catalyzed hydrolysis of RNA may be prevalent particularly in iron-rich soils and sediments, which must be considered across biogeochemical applications of nucleic acid analysis in environmental systems.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kun-Pu Ho
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Grace Park
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Zhiyao Li
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jeffrey G Catalano
- Department of Earth & Planetary Sciences, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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13
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Abdel Hakiem AF, El-Sagheir AMK, Draz ME, Mohamed NA, Aboraia AS. Assessment of binding interaction to salmon sperm DNA of two antiviral agents and ecofriendly nanoparticles: comprehensive spectroscopic study. BMC Chem 2023; 17:39. [PMID: 37076904 PMCID: PMC10114480 DOI: 10.1186/s13065-023-00952-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/05/2023] [Indexed: 04/21/2023] Open
Abstract
The direct binding of antiviral agents; Daclatasvir and valacyclovir and green synthesized nanoparticles to salmon sperm DNA have been assessed in a comparative study. The nanoparticles were synthesized by the hydrothermal autoclave method and have been fully characterized. The interactive behavior and competitive binding of the analytes to DNA in addition to the thermodynamic properties were deeply investigated by the UV-visible spectroscopy. The binding constants were monitored in the physiological pH conditions to be 1.65 × 106, 4.92 × 105 and 3.12 × 105 for daclatasvir,valacyclovir and quantum dots, respectively. The significant changes in the spectral features of all analytes have proven intercalative binding. The competitive study has confirmed that, daclatasvir, valacyclovir, and the quantum dots have exhibited groove binding. All analytes have shown good entropy and enthalpy values indicating stable interactions. The electrostatic and non-electrostatic kinetic parameters have been determined through studying the binding interactions at different concentrations of KCl solutions. A molecular modelling study has been applied to demonstrate the binding interactions and their mechanisms. The obtained results were complementary and afforded new eras for the therapeutic applications.
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Affiliation(s)
- Ahmed Faried Abdel Hakiem
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, South Valley University, Qena, 83523, Egypt.
| | | | - Mohammed E Draz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa, 11152, Egypt
| | - Niveen A Mohamed
- Department of Pharmaceutical Chemistry, Unaizah College of Pharmacy, Qassim University, Unaizah, 5888, Saudi Arabia
| | - Ahmed Safwat Aboraia
- Medicinal Chemistry Department, Faculty of Pharmacy, Assiut University, Assiut, 71516, Egypt
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14
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Asha H, Green JA, Esposito L, Martinez-Fernandez L, Santoro F, Improta R. Effect of the Thermal Fluctuations of the Photophysics of GC and CG DNA Steps: A Computational Dynamical Study. J Phys Chem B 2022; 126:10608-10621. [PMID: 36508709 DOI: 10.1021/acs.jpcb.2c05688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here we refine and assess two computational procedures aimed to include the effect of thermal fluctuations on the electronic spectra and the ultrafast excited state dynamics of multichromophore systems, focusing on DNA duplexes. Our approach is based on a fragment diabatization procedure that, from a given Quantum Mechanical (QM) reference method, can provide the parameters (energy and coupling) of the reference diabatic states on the basis of the isolated fragments, either for a purely electronic excitonic Hamiltonian (FrDEx) or a linear vibronic coupling Hamiltonian (FrD-LVC). After having defined the most cost-effective procedure for DNA duplexes on two smaller fragments, FrDEx is used to simulate the absorption and Electronic Circular Dichroism (ECD) spectra of (GC)5 sequences, including the coupling with the Charge Transfer (CT) states, on a number of structures extracted from classical Molecular Dynamics (MD) simulations. The computed spectra are close to the reference TD-DFT calculations and fully consistent with the experimental ones. We then couple MD simulations and FrD-LVC to simulate the interplay between local excitations and CT transitions, both intrastrand and interstrand, in GC and CG steps when included in a oligoGC or in oligoAT DNA sequence. We predict that for both sequences a substantial part of the photoexcited population on G and C decays, within 50-100 fs, to the corresponding intrastrand CT states. This transfer is more effective for GC steps that, on average, are more closely stacked than CG ones.
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Affiliation(s)
- Haritha Asha
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - James A Green
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 7, 60438Frankfurt am Main, Germany
| | - Luciana Esposito
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autònoma de Madrid, Campus de Excelencia UAM-CSIC, 28049Madrid, Spain
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124Pisa, Italy
| | - Roberto Improta
- Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), Via De Amicis 95,I-80145Napoli, Italy.,DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg 207, DK-2800Kongens Lyngby, Denmark
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15
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Fraga KJ, Huang YJ, Ramelot TA, Swapna GVT, Lashawn Anak Kendary A, Li E, Korf I, Montelione GT. SpecDB: A relational database for archiving biomolecular NMR spectral data. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2022; 342:107268. [PMID: 35930941 PMCID: PMC9922030 DOI: 10.1016/j.jmr.2022.107268] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/16/2022] [Accepted: 07/06/2022] [Indexed: 05/11/2023]
Abstract
NMR is a valuable experimental tool in the structural biologist's toolkit to elucidate the structures, functions, and motions of biomolecules. The progress of machine learning, particularly in structural biology, reveals the critical importance of large, diverse, and reliable datasets in developing new methods and understanding in structural biology and science more broadly. Biomolecular NMR research groups produce large amounts of data, and there is renewed interest in organizing these data to train new, sophisticated machine learning architectures and to improve biomolecular NMR analysis pipelines. The foundational data type in NMR is the free-induction decay (FID). There are opportunities to build sophisticated machine learning methods to tackle long-standing problems in NMR data processing, resonance assignment, dynamics analysis, and structure determination using NMR FIDs. Our goal in this study is to provide a lightweight, broadly available tool for archiving FID data as it is generated at the spectrometer, and grow a new resource of FID data and associated metadata. This study presents a relational schema for storing and organizing the metadata items that describe an NMR sample and FID data, which we call Spectral Database (SpecDB). SpecDB is implemented in SQLite and includes a Python software library providing a command-line application to create, organize, query, backup, share, and maintain the database. This set of software tools and database schema allow users to store, organize, share, and learn from NMR time domain data. SpecDB is freely available under an open source license at https://github.rpi.edu/RPIBioinformatics/SpecDB.
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Affiliation(s)
- Keith J Fraga
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
| | - Yuanpeng J Huang
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
| | - Theresa A Ramelot
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
| | - G V T Swapna
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA; Department of Pharmacology, Robert Wood Johnson Medical School, Rutgers The State University of New Jersey, Piscataway, NJ 08854, USA.
| | | | - Ethan Li
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
| | - Ian Korf
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
| | - Gaetano T Montelione
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180 USA.
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16
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Analysis and purification of ssRNA and dsRNA molecules using asymmetrical flow field flow fractionation. J Chromatogr A 2022; 1683:463525. [DOI: 10.1016/j.chroma.2022.463525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/30/2022] [Accepted: 09/18/2022] [Indexed: 11/20/2022]
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17
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Howard JD, Beghyn M, Dewulf N, De Vos Y, Philips A, Portwood D, Kilby PM, Oliver D, Maddelein W, Brown S, Dickman MJ. Chemically-modified dsRNA induces RNAi effects in insects in vitro and in vivo: A potential new tool for improving RNA-based plant protection. J Biol Chem 2022; 298:102311. [PMID: 35921898 PMCID: PMC9478931 DOI: 10.1016/j.jbc.2022.102311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/15/2022] [Accepted: 07/16/2022] [Indexed: 11/28/2022] Open
Abstract
Global agriculture loses over $100 billion of produce annually to crop pests such as insects. Many of these crop pests either are not currently controlled by artificial means or have developed resistance against chemical pesticides. Long dsRNAs are capable of inducing RNAi in insects and are emerging as novel, highly selective alternatives for sustainable insect management strategies. However, there are significant challenges associated with RNAi efficacy in insects. In this study, we synthesized a range of chemically modified long dsRNAs in an approach to improve nuclease resistance and RNAi efficacy in insects. Our results showed that dsRNAs containing phosphorothioate modifications demonstrated increased resistance to southern green stink bug saliva nucleases. Phosphorothioate-modified and 2′-fluoro-modified dsRNA also demonstrated increased resistance to degradation by soil nucleases and increased RNAi efficacy in Drosophila melanogaster cell cultures. In live insects, we found chemically modified long dsRNAs successfully resulted in mortality in both stink bug and corn rootworm. These results provide further mechanistic insight into the dependence of RNAi efficacy on nucleotide modifications in the sense or antisense strand of the dsRNA in insects and demonstrate for the first time that RNAi can successfully be triggered by chemically modified long dsRNAs in insect cells or live insects.
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Affiliation(s)
- John D Howard
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, United Kingdom
| | | | | | - Yves De Vos
- Syngenta, Ghent Innovation Center, Ghent, Belgium
| | | | - David Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, United Kingdom
| | | | | | - Stephen Brown
- Sheffield RNAi Screening Facility, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Mark J Dickman
- Department of Chemical & Biological Engineering, University of Sheffield, Sheffield, United Kingdom.
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18
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Chatterjee A, Zhang K, Rao Y, Sharma N, Giammar DE, Parker KM. Metal-Catalyzed Hydrolysis of RNA in Aqueous Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:3564-3574. [PMID: 35226478 DOI: 10.1021/acs.est.1c08468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The stability of RNA in aqueous systems is critical for multiple environmental applications including evaluating the environmental fate of RNA interference pesticides and interpreting viral genetic marker abundance for wastewater-based epidemiology. In addition to biological processes, abiotic reactions may also contribute to RNA loss. In particular, some metals are known to dramatically accelerate rates of RNA hydrolysis under certain conditions (i.e., 37 °C or higher temperatures, 0.15-100 mM metal concentrations). In this study, we investigated the extent to which metals catalyze RNA hydrolysis under environmentally relevant conditions. At ambient temperature, neutral pH, and ∼10 μM metal concentrations, we determined that metals that are stronger Lewis acids (i.e., lead, copper) catalyzed single-stranded (ss)RNA, whereas metals that are weaker Lewis acids (i.e., zinc, nickel) did not. In contrast, double-stranded (ds)RNA resisted hydrolysis by all metals. While lead and copper catalyzed ssRNA hydrolysis at ambient temperature and neutral pH values, other factors such as lowering the solution pH and including inorganic and organic ligands reduced the rates of these reactions. Considering these factors along with sub-micromolar metal concentrations typical of environmental systems, we determined that both ssRNA and dsRNA are unlikely to undergo significant metal-catalyzed hydrolysis in most environmental aqueous systems.
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Affiliation(s)
- Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Yue Rao
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Neha Sharma
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel E Giammar
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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19
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Ishida T, Sotani T, Sano N, Sogawa H, Sanda F. Control of Higher-Order Structures of Platinum-Containing Conjugated Polymers by Ligand Exchange Reactions: Chirality Transfer from Optically Active Ligands to Optically Inactive Polymers. Macromolecules 2022. [DOI: 10.1021/acs.macromol.1c01773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takahiro Ishida
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Taichi Sotani
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Natsuhiro Sano
- R&D Division, Nippon Chemical Industrial Co., Ltd., 9-11-1 Kameido, Koto-ku, Tokyo 136-8515, Japan
| | - Hiromitsu Sogawa
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
| | - Fumio Sanda
- Department of Chemistry and Materials Engineering, Faculty of Chemistry, Materials and Bioengineering, Kansai University, 3-3-35 Yamate-cho, Suita, Osaka 564-8680, Japan
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20
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Mwaka HS, Christiaens O, Bwesigye PN, Kubiriba J, Tushemereirwe WK, Gheysen G, Smagghe G. First Evidence of Feeding-Induced RNAi in Banana Weevil via Exogenous Application of dsRNA. INSECTS 2021; 13:40. [PMID: 35055882 PMCID: PMC8779063 DOI: 10.3390/insects13010040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/06/2023]
Abstract
Banana weevil (Cosmopolites sordidus) is the most devastating pest of banana and plantain worldwide, yet current control measures are neither effective, sustainable, nor environmentally sound, and no resistant farmer-preferred cultivars are known to date. In this paper, we examined the ability to induce RNA interference (RNAi) in the banana weevil via feeding. We first developed an agar- and banana corm (rhizome) flour-based artificial diet in a multi-well plate setup that allowed the banana weevils to complete their life cycle from egg through the larval instars to the pupal stage in an average period of 53 days. Adults emerged about 20 days later. The artificial diet allowed the tunneling and burrowing habits of the larvae and successful metamorphosis up to adult eclosion. Adding dsRNA for laccase2 to the artificial diet resulted in albino phenotypes, confirming gene-silencing. Finally, C. sordidus was fed with dsRNA against a selection of essential target genes: snf7, rps13, mad1, vha-a, vha-d, and lgl for a period of 45 days. 100% mortality within 9-16 days was realized with dssnf7, dsrps13, and dsmad1 at 200 ng/mL artificial diet, and this corresponded to a strong reduction in gene expression. Feeding the dsRNA targeting the two vha genes resulted in 100% mortality after about 3-4 weeks, while treatment with dslgl resulted in no mortality above the dsgfp-control and the water-control. Our results have implications for the development of RNAi approaches for managing important crop pests, in that banana weevils can be controlled based on the silencing of essential target genes as snf7, rps13, and mad1. They also highlight the need for research into the development of RNAi for banana protection, eventually the engineering of host-induced gene-silencing (HIGS) cultivars, given the high RNAi efficacy and its species-specific mode of action, adding the RNAi approach to the armory of integrated pest management (IPM).
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Affiliation(s)
- Henry Shaykins Mwaka
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (O.C.)
- Department of Biotechnology, Ghent University, 9000 Ghent, Belgium;
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (P.N.B.); (J.K.); (W.K.T.)
| | - Olivier Christiaens
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (O.C.)
| | - Priver Namanya Bwesigye
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (P.N.B.); (J.K.); (W.K.T.)
| | - Jerome Kubiriba
- National Agricultural Research Laboratories, Kawanda, Kampala P.O. Box 7065, Uganda; (P.N.B.); (J.K.); (W.K.T.)
| | | | | | - Guy Smagghe
- Laboratory of Agrozoology, Department of Plants and Crops, Ghent University, 9000 Ghent, Belgium; (H.S.M.); (O.C.)
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21
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Developing an Updated Strategy for Estimating the Free-Energy Parameters in RNA Duplexes. Int J Mol Sci 2021; 22:ijms22189708. [PMID: 34575896 PMCID: PMC8467000 DOI: 10.3390/ijms22189708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 09/01/2021] [Accepted: 09/02/2021] [Indexed: 12/12/2022] Open
Abstract
For the last 20 years, it has been common lore that the free energy of RNA duplexes formed from canonical Watson-Crick base pairs (bps) can be largely approximated with dinucleotide bp parameters and a few simple corrective constants that are duplex independent. Additionally, the standard benchmark set of duplexes used to generate the parameters were GC-rich in the shorter duplexes and AU-rich in the longer duplexes, and the length of the majority of the duplexes ranged between 6 and 8 bps. We were curious if other models would generate similar results and whether adding longer duplexes of 17 bps would affect the conclusions. We developed a gradient-descent fitting program for obtaining free-energy parameters-the changes in Gibbs free energy (ΔG), enthalpy (ΔH), and entropy (ΔS), and the melting temperature (Tm)-directly from the experimental melting curves. Using gradient descent and a genetic algorithm, the duplex melting results were combined with the standard benchmark data to obtain bp parameters. Both the standard (Turner) model and a new model that includes length-dependent terms were tested. Both models could fit the standard benchmark data; however, the new model could handle longer sequences better. We developed an updated strategy for fitting the duplex melting data.
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22
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A new palladium-based antiproliferative agent: synthesis, characterization, computational calculations, cytotoxicity, and DNA binding properties. Biometals 2021; 34:1173-1189. [PMID: 34363565 DOI: 10.1007/s10534-021-00335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Accepted: 07/29/2021] [Indexed: 10/20/2022]
Abstract
A new palladium(II) complex entitled [Pd(phendione)(8Q)]NO3, (PdPQ), where phendione is N,N-donor heterocyclic 1,10-phenanthroline-5,6-dion and 8Q is 8-hydroxyquinolinate, has been synthesized and then characterized by molar conductivity, CHN analysis and spectral data (UV-Vis, FT-IR, NMR). DFT/ TDDFT procedures were also performed to determine the electronic structure and the nature of the electronic transitions of PdPQ. Moreover, the affinity and binding properties of DNA to the desired complex have been studied in details using electronic absorption, fluorescence, circular dichroism spectroscopies, and viscosity measurement in combination with molecular docking technique. The obtained results exhibit relatively high DNA binding values with a static quenching mechanism, which suggest that an intercalative mode plays a peridominate role in interaction process concluded by experimental/theoretical measurements. As a result of drug exposure, in vitro cytotoxicity assay demonstrated the antiproliferative activity of the PdPQ against leukemia cancer cell line, K562.
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23
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Cheng S, Ge Y, Lee Y, Yang X. Prediction of Photolysis Kinetics of Viral Genomes under UV 254 Irradiation to Estimate Virus Infectivity Loss. WATER RESEARCH 2021; 198:117165. [PMID: 33962243 DOI: 10.1016/j.watres.2021.117165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
UV254 irradiation disinfection is a commonly used method to inactivate pathogenic viruses in water and wastewater treatment. Model prediction method can serve as a pre-screening tool to quickly estimate the effectiveness of UV254 irradiation on emerging or unculturable viruses. In this study, an improved prediction model was applied to estimate UV254 photolysis kinetics of viral genomes (kpred, genome) based on the genome sequences and their photoreactivity and to correlate with the experimental virus infectivity loss kinetics (kexp, infectivity). The UV254 inactivation data of 102 viruses (including 2 dsRNA, 65 ssRNA, 33 dsDNA and 2 ssDNA viruses) were collected from the published experimental data with kexp, infectivity ranging from 0.016 to 3.49 cm2 mJ-1. The model had fairly good performance in predicting the virus susceptibility to UV254 irradiation except dsRNA viruses (Pearson's correlation coefficient = 0.64) and 70% of kpred, genome fell in the range of 1/2 to 2 times of kexp, infectivity. The positive deviation of the model often occurred for photoresistant viruses with low kexp, infectivity less than 0.20 cm2 mJ-1 (e.g., Adenovirus, Papovaviridae and Retroviridae). We also applied this model to predict the UV254 inactivation rate of SARS-CoV-2 (kpred, genome = 3.168 cm2 mJ-1) and a UV dose of 3 mJ cm-2 seemed to be able to achieve a 2-log removal by conservative calculation using 1/2kpred, genome value. This prediction method can be used as a prescreening tool to assess the effectiveness of UV254 irradiation for emerging/unculturable viruses in water or wastewater treatment.
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Affiliation(s)
- Shuangshuang Cheng
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuexian Ge
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology (GIST), Gwangju 61005, Republic of Korea
| | - Xin Yang
- School of Environmental Science and Engineering, Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, China.
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24
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Zhang K, Hodge J, Chatterjee A, Moon TS, Parker KM. Duplex Structure of Double-Stranded RNA Provides Stability against Hydrolysis Relative to Single-Stranded RNA. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:8045-8053. [PMID: 34033461 DOI: 10.1021/acs.est.1c01255] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Phosphodiester bonds in the backbones of double-stranded (ds)RNA and single-stranded (ss)RNA are known to undergo alkaline hydrolysis. Consequently, dsRNA agents used in emerging RNA interference (RNAi) products have been assumed to exhibit low chemical persistence in solutions. However, the impact of the duplex structure of dsRNA on alkaline hydrolysis has not yet been evaluated. In this study, we demonstrated that dsRNA undergoes orders-of-magnitude slower alkaline hydrolysis than ssRNA. Furthermore, we observed that dsRNA remains intact for multiple months at neutral pH, challenging the assumption that dsRNA is chemically unstable. In systems enabling both enzymatic degradation and alkaline hydrolysis of dsRNA, we found that increasing pH effectively attenuated enzymatic degradation without inducing alkaline hydrolysis that was observed for ssRNA. Overall, our findings demonstrated, for the first time, that key degradation pathways of dsRNA significantly differ from those of ssRNA. Consideration of the unique properties of dsRNA will enable greater control of dsRNA stability during the application of emerging RNAi technology and more accurate assessment of its fate in environmental and biological systems, as well as provide insights into broader application areas including dsRNA isolation, detection and inactivation of dsRNA viruses, and prebiotic molecular evolution.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph Hodge
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Anamika Chatterjee
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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25
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Quantification of azacitidine incorporation into human DNA/RNA by accelerator mass spectrometry as direct measure of target engagement. J Pharm Biomed Anal 2021; 202:114152. [PMID: 34051483 DOI: 10.1016/j.jpba.2021.114152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 05/14/2021] [Accepted: 05/17/2021] [Indexed: 11/22/2022]
Abstract
We report an accelerator mass spectrometry (AMS) assay to quantify azacitidine (Aza) incorporation into DNA and RNA from human acute myeloid leukemia (AML) cells, mouse bone marrow (BM) and peripheral blood mononuclear cells (PBMCs). Aza, a cytidine nucleoside analogue, is a disease modifying pharmacological agent used for treatment of myelodysplastic syndromes (MDS) and AML. Our assay was able to directly quantify the complex of Aza incorporated into DNA/RNA, via isolation of DNA/RNA from matrix (i.e., cancer cells, BM and PBMC) and subsequent measurement of total radioactivity (i.e., 14C-Aza) by using AMS. The sensitivity of the method was able to quantify as little as a single Aza molecule incorporated into DNA with approximately 2 × 107 nucleotides from PBMCs. An in vivo mouse model was used for establishing the lower limits of quantification (LLOQs) for Aza incorporated into DNA/RNA in mouse PBMCs (∼ 3.7 × 105) and BM (∼27.8 mg) collected 24 h post-dose after total exposure of 18 nCi/mouse (Aza 1 mg/kg). The LLOQs for PBMC analysis were 2.5 picogram equivalents per microgram (pgEq/μg) DNA and 0.22 pgEq/μg RNA, and for BM analysis were 1.7 pgEq/μg DNA and 0.22 pgEq/μg RNA. A linear relationship (i.e., ∼10-fold) was established of radioactive dose from 14C-Aza 17 nCi/mouse to 188 nCi/mouse and AMS response (i.e., 14C/12C ratio ranging from 2.45 × 10-11 to 2.50 × 10-10), as Aza was incorporated into DNA in mouse BM. The current method enables the direct measurement of Aza incorporation into DNA and RNA from patient PBMCs and BM to provide dosing optimization, and to assess target engagement with as little as ∼5 mL whole blood and ∼3 mL of BM from patients.
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Majikes JM, Patrone PN, Kearsley AJ, Zwolak M, Liddle JA. Failure Mechanisms in DNA Self-Assembly: Barriers to Single-Fold Yield. ACS NANO 2021; 15:3284-3294. [PMID: 33565312 PMCID: PMC11005093 DOI: 10.1021/acsnano.0c10114] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Understanding the folding process of DNA origami is a critical stepping stone to the broader implementation of nucleic acid nanofabrication technology but is notably nontrivial. Origami are formed by several hundred cooperative hybridization events-folds-between spatially separate domains of a scaffold, derived from a viral genome, and oligomeric staples. Individual events are difficult to detect. Here, we present a real-time probe of the unit operation of origami assembly, a single fold, across the scaffold as a function of hybridization domain separation-fold distance-and staple/scaffold ratio. This approach to the folding problem elucidates a predicted but previously unobserved blocked state that acts as a limit on yield for single folds, which may manifest as a barrier in whole origami assembly.
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Affiliation(s)
- Jacob M. Majikes
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Paul N. Patrone
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Anthony J. Kearsley
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - Michael Zwolak
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
| | - J. Alexander Liddle
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899-6203, United States
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Santos IC, Brodbelt JS. Recent developments in the characterization of nucleic acids by liquid chromatography, capillary electrophoresis, ion mobility, and mass spectrometry (2010-2020). J Sep Sci 2021; 44:340-372. [PMID: 32974962 PMCID: PMC8378248 DOI: 10.1002/jssc.202000833] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/25/2022]
Abstract
The development of new strategies for the analysis of nucleic acids has gained momentum due to the increased interest in using these biomolecules as drugs or drug targets. The application of new mass spectrometry ion activation techniques and the optimization of separation methods including liquid chromatography, capillary electrophoresis, and ion mobility have allowed more detailed characterization of nucleic acids and oligonucleotide therapeutics including confirmation of sequence, localization of modifications and interaction sites, and structural analysis as well as identification of failed sequences and degradation products. This review will cover tandem mass spectrometry methods as well as the recent developments in liquid chromatography, capillary electrophoresis, and ion mobility coupled to mass spectrometry for the analysis of nucleic acids and oligonucleotides.
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Affiliation(s)
- Inês C Santos
- Department of Chemistry, University of Texas at Austin, Austin, Texas, USA
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Zhang Y, Liu Z, Wang Y, Kuang X, Ma H, Wei Q. Directly assembled electrochemical sensor by combining self-supported CoN nanoarray platform grown on carbon cloth with molecularly imprinted polymers for the detection of Tylosin. JOURNAL OF HAZARDOUS MATERIALS 2020; 398:122778. [PMID: 32470771 DOI: 10.1016/j.jhazmat.2020.122778] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 03/14/2020] [Accepted: 04/16/2020] [Indexed: 05/23/2023]
Abstract
Molecularly imprinted polymers (MIPs) based on electrochemical sensors (MIP-EC sensors) have obtained ideal achievements in recent years. However, some challenges are still need to be addressed, such as adjustable preparation, unstable sensing interface and great signal-to-noise ratio. Here, based on the ingenious combination of the MIP and the self-supported CoN nanowire arrays grown on carbon cloth (CoN NWs/CC), a robust MIP-EC sensor was developed, in which the MIP film was uniformly coated on the CoN NWs/CC via a bulk polymerization crosslinking process. Especially, CoN NWs/CC were prepared via in-situ transformation of their oxide precursors and then directly as a candidate of EC electrode. Under the optimal conditions, the MIP-EC sensor can detect Tylosin (TS) in the concentration range from 8.6 × 10-11 to 6.7 × 10-5 mol L-1, and the low detection limit (LOD) is 5.5 × 10-12 mol L-1 (S/N = 3). Furthermore, the MIP-EC sensor showed high selectivity, reproducibility and stability. The practicability of the MIP-EC sensor was tested in the actual samples of surface water and soil with the comparison of the traditional ELISA method. The developed MIP-EC sensor with simple and fabrication process can provide a versatile and reliable method, which has great potential application value for the detection of small hazardous molecules.
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Affiliation(s)
- Yong Zhang
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China.
| | - Zhaoyi Liu
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Yaoguang Wang
- Shandong Provincial Key Laboratory of Molecular Engineering, School of Chemistry and Pharmaceutical Engineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan, 250353, PR China
| | - Xuan Kuang
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Hongmin Ma
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
| | - Qin Wei
- Collaborative Innovation Center for Green Chemical Manufacturing and Accurate Detection, Key Laboratory of Interfacial Reaction & Sensing Analysis in Universities of Shandong, School of Chemistry and Chemical Engineering, University of Jinan, Jinan, 250022, PR China
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Obianyor C, Newnam G, Clifton BE, Grover MA, Hud NV. Towards Efficient Nonenzymatic DNA Ligation: Comparing Key Parameters for Maximizing Ligation Rates and Yields with Carbodiimide Activation**. Chembiochem 2020; 21:3359-3370. [DOI: 10.1002/cbic.202000335] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/21/2020] [Indexed: 01/14/2023]
Affiliation(s)
- Chiamaka Obianyor
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Gary Newnam
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Bryce E. Clifton
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
| | - Martha A. Grover
- Georgia Institute of Technology School of Chemical and Biomolecular Engineering Atlanta Georgia 30332-0400 USA
| | - Nicholas V. Hud
- Georgia Institute of Technology, Chemistry and Biochemistry 311 Ferst Drive Atlanta Georgia 30332-0400 USA
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30
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Kline MC, Duewer DL. Evaluating digital PCR for the quantification of human nuclear DNA: determining target strandedness. Anal Bioanal Chem 2020; 412:4749-4760. [PMID: 32474725 DOI: 10.1007/s00216-020-02733-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 01/28/2023]
Abstract
Digital polymerase chain reaction (dPCR) methodology has been asserted to be a "potentially primary" analytical approach for assigning DNA concentration. The essence of dPCR measurements is the independent dispersal of fragments into multiple reaction partitions, amplifying fragments containing a target nucleotide sequence until the signal from all partitions containing at least one such fragment rises above threshold, and then determining the proportion of partitions with an above-threshold signal. Should originally double-stranded DNA (dsDNA) fragments be converted into two single strands (ssDNA) prior to dispersal, the dPCR measurements could be biased high by as much as a factor of two. Realizing dPCR's metrological potential therefore requires analytical methods for determining the proportion of ssDNA in nominally dsDNA samples. To meet this need, we have investigated several approaches to this determination: A260 ratio, dPCR ratio, cdPCR staircase, and ddPCR enzyme. In our hands, only the endonuclease-based approach provides adequately accurate estimates for relatively small ssDNA proportions. We present four (enzyme, assay) pairs that provide self-consistent results for human nuclear DNA extracts. However, the proportion of ssDNA differs by as much as 50% between assays, apparently related to the guanine-cytosine (GC) content of the fragment near the assay's target sequence. While materials extracted by us have no more than 6% ssDNA content even after long storage, a commercially obtained PCR assay calibrant contains ≈18% ssDNA. Graphical abstract.
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Affiliation(s)
- Margaret C Kline
- Biomolecular Measurement Division, Material Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, 20899-8314, USA
| | - David L Duewer
- Chemical Sciences Division, Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8390, Gaithersburg, MD, 20899-8390, USA.
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Zhang K, Wei J, Huff Hartz KE, Lydy MJ, Moon TS, Sander M, Parker KM. Analysis of RNA Interference (RNAi) Biopesticides: Double-Stranded RNA (dsRNA) Extraction from Agricultural Soils and Quantification by RT-qPCR. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:4893-4902. [PMID: 32212649 DOI: 10.1021/acs.est.9b07781] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Double-stranded RNA (dsRNA) molecules are used as a novel class of biopesticides. To enable assessments of the ecological risk associated with their release to receiving environments, we developed an approach to quantify dsRNA in agricultural soils using quantitative reverse transcription-polymerase chain reaction (RT-qPCR). To allow quantification of dsRNA adsorbed to particles, we also developed a protocol to transfer dsRNA from particles to the extraction buffer by changing particle surface charge and adding constituents to compete with dsRNA for adsorption sites. Our approach could quantify dsRNA amounts as low as 0.003 ngdsRNA/gsoil. This approach is the first available field-applicable approach able to quantify dsRNA biopesticides down to environmentally relevant concentrations. We applied this approach to investigate dsRNA dissipation (including dilution, degradation, and adsorption) in two agricultural soils. When we applied a low amount of dsRNA (1 ngdsRNA/gsoil) to the soils, we observed that a greater fraction of dsRNA was adsorbed to and extractable from soil particles in a silty clay loam soil than in a fine sandy loam soil. In both soils, dsRNA dissipated on the timescale of hours. Overall, these results demonstrate that our approach can be applied to assess the environmental fate of dsRNA biopesticides at concentrations relevant to their release to soils.
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Affiliation(s)
- Ke Zhang
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Jingmiao Wei
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Kara E Huff Hartz
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Michael J Lydy
- Center for Fisheries, Aquaculture, and Aquatic Sciences, Department of Zoology, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Tae Seok Moon
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Michael Sander
- Department of Environmental Systems Science (DUSYS), ETH Zurich, 8092 Zurich, Switzerland
| | - Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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Nwokeoji AO, Kumar S, Kilby PM, Portwood DE, Hobbs JK, Dickman MJ. Analysis of long dsRNA produced in vitro and in vivo using atomic force microscopy in conjunction with ion-pair reverse-phase HPLC. Analyst 2019; 144:4985-4994. [PMID: 31328735 DOI: 10.1039/c9an00954j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Long double-stranded (ds) RNA is emerging as a novel alternative to chemical and genetically-modified insect and fungal management strategies. The ability to produce large quantities of dsRNA in either bacterial systems, by in vitro transcription, in cell-free systems or in planta for RNA interference applications has generated significant demand for the development and application of analytical tools for analysis of dsRNA. We have utilised atomic force microscopy (AFM) in conjunction with ion-pair reverse-phase high performance liquid chromatography (IP-RP-HPLC) to provide novel insight into dsRNA for RNAi applications. The AFM analysis enabled direct structural characterisation of the A-form duplex dsRNA and accurate determination of the dsRNA duplex length. Moreover, further analysis under non-denaturing conditions revealed the presence of heterogeneous dsRNA species. IP-RP-HPLC fractionation and AFM analysis revealed that these alternative RNA species do not arise from different lengths of individual dsRNA molecules in the product, but represent misannealed RNA species that present as larger assemblies or multimeric forms of the RNA. These results for the first time provide direct structural insight into dsRNA produced both in vivo in bacterial systems and in vitro, highlighting the structural heterogeneity of RNA produced. These results are the first example of detailed characterisation of the different forms of dsRNA from two production systems and establish atomic force microscopy as an important tool for the characterisation of long dsRNA.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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Yang B, Qin C, Hu X, Xia K, Lu C, Gudda FO, Ma Z, Gao Y. Enzymatic degradation of extracellular DNA exposed to chlorpyrifos and chlorpyrifos-methyl in an aqueous system. ENVIRONMENT INTERNATIONAL 2019; 132:105087. [PMID: 31430607 DOI: 10.1016/j.envint.2019.105087] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 07/30/2019] [Accepted: 08/07/2019] [Indexed: 05/25/2023]
Abstract
The persistence of extracellular DNA (eDNA) is crucial for ensuring species diversity and ecological function in aquatic systems. However, scarce information exists about the impact of pesticides on eDNA, although they often co-exist in the aquatic environment. Using a variety of spectroscopic analyses, eDNA degradation and the associated alterations in DNA secondary structure was investigated by exposing DNase I to tested DNA in the presence of chlorpyrifos, a commonly used organophosphate pesticide. Molecular dynamics simulation was used to explore the weak interactions between the tested DNA and chlorpyrifos. The results indicated that chlorpyrifos significantly enhanced DNA degradation without affecting the enzyme activity of DNase I in an aqueous system. Spectroscopic experiments confirmed that chlorpyrifos and the analog chlorpyrifos-methyl could bind with DNA to cause the bases noncovalent stacking interaction. Molecular simulations further demonstrated that pesticide binding with DNA molecules caused widening of the DNA grooves and destruction of the hydrated layer, which enhanced DNA degradation. The findings presented herein provide novel insight into the genotoxicity and ecotoxicity of chlorpyrifos and chlorpyrifos-methyl, as well as their impacts on DNA persistence in aquatic environments.
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Affiliation(s)
- Bing Yang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Chao Qin
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Kang Xia
- School of Plant and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, United States
| | - Chao Lu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Fredrick Owino Gudda
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Zhao Ma
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, P.R. China.
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Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 PMCID: PMC7421392 DOI: 10.1186/s42490-019-0008-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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Markwalter C, Kantor AG, Moore CP, Richardson KA, Wright DW. Inorganic Complexes and Metal-Based Nanomaterials for Infectious Disease Diagnostics. Chem Rev 2019; 119:1456-1518. [PMID: 30511833 PMCID: PMC6348445 DOI: 10.1021/acs.chemrev.8b00136] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Indexed: 12/12/2022]
Abstract
Infectious diseases claim millions of lives each year. Robust and accurate diagnostics are essential tools for identifying those who are at risk and in need of treatment in low-resource settings. Inorganic complexes and metal-based nanomaterials continue to drive the development of diagnostic platforms and strategies that enable infectious disease detection in low-resource settings. In this review, we highlight works from the past 20 years in which inorganic chemistry and nanotechnology were implemented in each of the core components that make up a diagnostic test. First, we present how inorganic biomarkers and their properties are leveraged for infectious disease detection. In the following section, we detail metal-based technologies that have been employed for sample preparation and biomarker isolation from sample matrices. We then describe how inorganic- and nanomaterial-based probes have been utilized in point-of-care diagnostics for signal generation. The following section discusses instrumentation for signal readout in resource-limited settings. Next, we highlight the detection of nucleic acids at the point of care as an emerging application of inorganic chemistry. Lastly, we consider the challenges that remain for translation of the aforementioned diagnostic platforms to low-resource settings.
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Affiliation(s)
| | | | | | | | - David W. Wright
- Department of Chemistry, Vanderbilt
University, Nashville, Tennessee 37235, United States
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Nwokeoji AO, Earll ME, Kilby PM, Portwood DE, Dickman MJ. High resolution fingerprinting of single and double-stranded RNA using ion-pair reverse-phase chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2018; 1104:212-219. [PMID: 30530113 PMCID: PMC6329874 DOI: 10.1016/j.jchromb.2018.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/23/2018] [Accepted: 11/27/2018] [Indexed: 02/07/2023]
Abstract
The emergence of new sustainable approaches for insect management using RNA interference (RNAi) based insecticides has created the demand for high throughput analytical techniques to fully characterise and accurately quantify double stranded RNA (dsRNA) prior to downstream RNAi applications. In this study we have developed a method for the rapid characterisation of single stranded and double stranded RNA using high resolution RNase mapping in conjunction with ion-pair reverse-phase chromatography utilising a column with superficially porous particles. The high resolution oligoribonucleotide map provides an important 'fingerprint' for identity testing and bioprocess monitoring. Reproducible RNA mapping chromatograms were generated from replicate analyses. Moreover, this approach was used to provide a method to rapidly distinguish different RNA sequences of the same size, based on differences in the resulting chromatograms. Principal components analysis of the high resolution RNA mapping data enabled us to rapidly compare multiple HPLC chromatograms and distinguish two dsRNA sequences of different size which share 72% sequence homology. We used the high resolution RNase mapping method to rapidly fingerprint biomanufactured dsRNA across a number of different batches. The resulting chromatograms in conjunction with principal components analysis demonstrated high similarity in the dsRNA produced across the different batches highlighting the potential ability of this method to provide information for batch release in a high throughput manner.
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Affiliation(s)
- Alison O Nwokeoji
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK
| | - Mark E Earll
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire RG42 6EY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, S1 3JD, UK.
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Tankovskaia SA, Kotb OM, Dommes OA, Paston SV. Application of spectral methods for studying DNA damage induced by gamma-radiation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 200:85-92. [PMID: 29674243 DOI: 10.1016/j.saa.2018.04.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Spectral methods can provide a variety of possibilities to determine several types of radiation-induced DNA damage, such as nucleobase destruction and local denaturation. DNA UV absorption and CD spectra measured at room temperature undergo noticeable alteration under the action of γ-radiation. We have applied the Spirin method of total nucleobases determination, and have measured the molar extinction coefficient of DNA and DNA CD spectra for solutions with different NaCl concentrations (3mM-3.2M) and containing MgCl2, exposed to γ-radiation with the doses of 0-103Gy. The melting temperatures of DNA in irradiated solutions at the doses of 0-50Gy were obtained with the help of spectrophotometric melting. It was found that the amount of destructed nucleobases and radiation-induced loss of DNA helicity significantly decreases with the rise of the ionic strength of the irradiated solution. Substitution of a portion of Na+ ions on Mg2+ while keeping the total ionic strength constant (μ=5mM) does not affect the considered radiation effects. The role of the structure and composition of the DNA secondary hydration layer in the radiation-induced damages is discussed.
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Affiliation(s)
- Svetlana A Tankovskaia
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia
| | - Omar M Kotb
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia; Department of Physics, Faculty of Science, Zagazig University, Sharkia Gov, Zagazig 44519, Egypt
| | - Olga A Dommes
- Institute of Macromolecular Compounds, Bolshoy pr. 31, 199004 Saint-Petersburg, Russia
| | - Sofia V Paston
- Department of Molecular Biophysics and Polymer Physics, Faculty of Physics, Saint-Petersburg State University, Ulyanovskaya, 3, St. Petersburg 198504, Russia.
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Kung AW, Kilby PM, Portwood DE, Dickman MJ. Quantification of dsRNA using stable isotope labeling dilution liquid chromatography/mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:590-596. [PMID: 29397006 DOI: 10.1002/rcm.8074] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 01/26/2018] [Accepted: 01/26/2018] [Indexed: 06/07/2023]
Abstract
RATIONALE Recent developments in RNA interference (RNAi) have created a need for cost-effective and large-scale synthesis of double-stranded RNA (dsRNA), in conjunction with high-throughput analytical techniques to fully characterise and accurately quantify dsRNA prior to downstream RNAi applications. METHODS Stable isotope labeled dsRNA was synthesised both in vivo (15 N) and in vitro (13 C,15 N-guanosine-containing dsRNA) prior to purification and quantification. The stable isotope labeled dsRNA standards were subsequently spiked into total RNA extracted from E. coli engineered to express dsRNA. RNase mass mapping approaches were subsequently performed using liquid chromatography/electrospray ionisation mass spectrometry (LC/ESI-MS) for both the identification and absolute quantification of the dsRNA using the ratios of the light and heavy oligonucleotide pairs. RESULTS Absolute quantification was performed based on the resulting light and heavy oligoribonucleotides identified using MS. Using this approach we determined that 624.6 ng/μL and 466.5 ng/μL of dsRNA was present in 80 μL total RNA extracted from 108 E. coli cells expressing 765 bp and 401 bp dsRNAs, respectively. CONCLUSIONS Stable isotope labeling of dsRNA in conjunction with MS enabled the characterisation and quantification of dsRNA in complex total RNA mixtures.
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Affiliation(s)
- An-Wen Kung
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, Sheffield, S1 3JD, UK
| | - Peter M Kilby
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - David E Portwood
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK
| | - Mark J Dickman
- Department of Chemical and Biological Engineering, Mappin Street, University of Sheffield, Sheffield, S1 3JD, UK
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