1
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Kaur J, Sharma A, Mundlia P, Sood V, Pandey A, Singh G, Barnwal RP. RNA-Small-Molecule Interaction: Challenging the "Undruggable" Tag. J Med Chem 2024. [PMID: 38498010 DOI: 10.1021/acs.jmedchem.3c01354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases. A deeper understanding of RNA biology reveals that RNA molecules can adopt a variety of structures, carrying defined binding pockets that can accommodate small-molecule drugs. Due to its functional diversity and structural complexity, RNA can be perceived as a prospective target for therapeutic intervention. This perspective highlights the proof of concept of RNA-small-molecule interactions, exemplified by targeting of various transcripts with functional modulators. The advent of RNA-oriented knowledge would help expedite drug discovery.
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Affiliation(s)
- Jaskirat Kaur
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Akanksha Sharma
- Department of Biophysics, Panjab University, Chandigarh 160014, India
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
| | - Poonam Mundlia
- Department of Biophysics, Panjab University, Chandigarh 160014, India
| | - Vikas Sood
- Department of Biochemistry, Jamia Hamdard, New Delhi 110062, India
| | - Ankur Pandey
- Department of Chemistry, Panjab University, Chandigarh 160014, India
| | - Gurpal Singh
- University Institute of Pharmaceutical Sciences, Panjab University, Chandigarh 160014, India
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Xie S, Yang H, Teng L, Liang S, Zhang J, Tang Y, Xu Y. A dual-mode of electrochemical-colorimetric biosensing platform for kanamycin detection based on self-sacrifice beacon and magnetic separation technique. Anal Chim Acta 2022; 1236:340590. [DOI: 10.1016/j.aca.2022.340590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 10/28/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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3
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Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. THE PLANT CELL 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
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Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
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4
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Das R, Rauf A, Mitra S, Emran TB, Hossain MJ, Khan Z, Naz S, Ahmad B, Meyyazhagan A, Pushparaj K, Wan CC, Balasubramanian B, Rengasamy KR, Simal-Gandara J. Therapeutic potential of marine macrolides: An overview from 1990 to 2022. Chem Biol Interact 2022; 365:110072. [PMID: 35952775 DOI: 10.1016/j.cbi.2022.110072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 01/05/2023]
Abstract
The sea is a vast ecosystem that has remained primarily unexploited and untapped, resulting in numerous organisms. Consequently, marine organisms have piqued the interest of scientists as an abundant source of natural resources with unique structural features and fascinating biological activities. Marine macrolide is a top-class natural product with a heavily oxygenated polyene backbone containing macrocyclic lactone. In the last few decades, significant efforts have been made to isolate and characterize macrolides' chemical and biological properties. Numerous macrolides are extracted from different marine organisms such as marine microorganisms, sponges, zooplankton, molluscs, cnidarians, red algae, tunicates, and bryozoans. Notably, the prominent macrolide sources are fungi, dinoflagellates, and sponges. Marine macrolides have several bioactive characteristics such as antimicrobial (antibacterial, antifungal, antimalarial, antiviral), anti-inflammatory, antidiabetic, cytotoxic, and neuroprotective activities. In brief, marine organisms are plentiful in naturally occurring macrolides, which can become the source of efficient and effective therapeutics for many diseases. This current review summarizes these exciting and promising novel marine macrolides in biological activities and possible therapeutic applications.
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Affiliation(s)
- Rajib Das
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Abdur Rauf
- Department of Chemistry, University of Swabi, Swabi, 94640, Pakistan.
| | - Saikat Mitra
- Department of Pharmacy, Faculty of Pharmacy, University of Dhaka, Dhaka, 1000, Bangladesh.
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, 4381, Bangladesh; Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh.
| | - Md Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka, 1205, Bangladesh.
| | - Zidan Khan
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, 4318, Bangladesh.
| | - Saima Naz
- Department of Biotechnology, Bacha Khan University, Charsadda, KPK, Pakistan.
| | - Bashir Ahmad
- Department of Biotechnology, Bacha Khan University, Charsadda, KPK, Pakistan.
| | - Arun Meyyazhagan
- Department of Life Science, CHRIST (Deemed to be University), Bengaluru, Karnataka, 560076, India.
| | - Karthika Pushparaj
- Department of Zoology, School of Biosciences, Avinashilingam Institute for Home Science and Higher Education for Women, Coimbatore, 641 043, Tamil Nadu, India.
| | - Chunpeng Craig Wan
- Jiangxi Key Laboratory for Postharvest Technology and Nondestructive Testing of Fruit &Vegetables, Collaborative Innovation Center of Postharvest Key Technology and Quality Safety of Fruit & Vegetables, College of Agronomy, Jiangxi Agricultural University Nanchang, 330045, Jiangxi, China.
| | | | - Kannan Rr Rengasamy
- Centre for Transdisciplinary Research, Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical Sciences (SIMATS), Chennai, 600077, India.
| | - Jesus Simal-Gandara
- Universidade de Vigo, Nutrition and Bromatology Group, Department of Analytical Chemistry and Food Science, Faculty of Science, E-32004 Ourense, Spain.
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5
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Liu Y, Deng Y, Li S, Wang-Ngai Chow F, Liu M, He N. Monitoring and detection of antibiotic residues in animal derived foods: Solutions using aptamers. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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6
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Kumar N, Sharma S, Kaushal PS. Protein synthesis in Mycobacterium tuberculosis as a potential target for therapeutic interventions. Mol Aspects Med 2021; 81:101002. [PMID: 34344520 DOI: 10.1016/j.mam.2021.101002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 07/11/2021] [Accepted: 07/16/2021] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) causes one of humankind's deadliest diseases, tuberculosis. Mtb protein synthesis machinery possesses several unique species-specific features, including its ribosome that carries two mycobacterial specific ribosomal proteins, bL37 and bS22, and ribosomal RNA segments. Since the protein synthesis is a vital cellular process that occurs on the ribosome, a detailed knowledge of the structure and function of mycobacterial ribosomes is essential to understand the cell's proteome by translation regulation. Like in many bacterial species such as Bacillus subtilis and Streptomyces coelicolor, two distinct populations of ribosomes have been identified in Mtb. Under low-zinc conditions, Mtb ribosomal proteins S14, S18, L28, and L33 are replaced with their non-zinc binding paralogues. Depending upon the nature of physiological stress, species-specific modulation of translation by stress factors and toxins that interact with the ribosome have been reported. In addition, about one-fourth of messenger RNAs in mycobacteria have been reported to be leaderless, i.e., without 5' UTR regions. However, the mechanism by which they are recruited to the Mtb ribosome is not understood. In this review, we highlight the mycobacteria-specific features of the translation apparatus and propose exploiting these features to improve the efficacy and specificity of existing antibiotics used to treat tuberculosis.
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Affiliation(s)
- Niraj Kumar
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Shivani Sharma
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India
| | - Prem S Kaushal
- Structural Biology & Translation Regulation Laboratory, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, 121 001, India.
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7
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Gu B, Chen D, Gao B, Liu Z, Wang Z, Wang T, Yang Y, Guo Q, Wang G. Ultrasensitive Fluorescent Detection of Tetracycline Based on Selective Supramolecular Interaction of Nitrogen Chlorine Co–Doped Graphene Quantum Dots. ChemistrySelect 2020. [DOI: 10.1002/slct.202000816] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Bingli Gu
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
| | - Da Chen
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
- Division of Physics and Applied PhysicsSchool of Physical and Mathematical Sciences, Nanyang Technological University Singapore 637371
| | - Bo Gao
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
| | - Zhiduo Liu
- State Key Laboratory of Integrated OptoelectronicsInstitute of Semiconductors, Chinese Academy of Sciences Beijing 100083 P. R. China
| | - Zihao Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
| | - Ting Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
| | - Yongsheng Yang
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
| | - Qinglei Guo
- Center of Nanoelectronics and School of MicroelectronicsShandong University Jinan 250100 P. R. China
| | - Gang Wang
- Department of Microelectronic Science and Engineering, School of Physical Science and TechnologyNingbo University Ningbo 315211 P. R. China
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8
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Liu X, Zhou Z, Wang T, Xu Y, Lu K, Yan Y. Molecularly imprinted polymers-captivity ZnO nanorods for sensitive and selective detecting environmental pollutant. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 228:117785. [PMID: 31767418 DOI: 10.1016/j.saa.2019.117785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
To develop the semiconductor of ZnO nanomaterials as the fluorescence sensor without leakage toxicity. Here, a molecularly imprinted polymer captivity ZnO nanorods (NRs) (MIPs-captivity ZnO NRs) was fabricated by precipitation polymerization. Such traditional technology was not only achieved the specific recognition for direct fluorescent quantification of the target tetracycline (TC) through fluorescence quenching, but also formed the shield to reduce the toxic effects of ZnO towards organisms. Under the optimized experimental conditions, the MIPs-captivity ZnO NRs were effectively applied to the direct fluorescence quantification of TC with excellent stability. Moreover, the practical analytical performance of the MIPs-captivity ZnO NRs was assayed by appraising the detection effects of TC in water sample from the Yangtze River with satisfactory results.
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Affiliation(s)
- Xiqing Liu
- School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhiping Zhou
- School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Tao Wang
- Institute of Green Chemistry and Chemical Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yeqing Xu
- Institute of Green Chemistry and Chemical Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Kai Lu
- Institute of Green Chemistry and Chemical Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongsheng Yan
- Institute of Green Chemistry and Chemical Technology, School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, China.
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9
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Wei W, He J, Wang Y, Kong M. Ratiometric method based on silicon nanodots and Eu3+ system for highly-sensitive detection of tetracyclines. Talanta 2019; 204:491-498. [DOI: 10.1016/j.talanta.2019.06.036] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 06/05/2019] [Accepted: 06/09/2019] [Indexed: 10/26/2022]
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10
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Jia L, Guo S, Xu J, Chen X, Zhu T, Zhao T. A Ratiometric Fluorescent Nano-Probe for Rapid and Specific Detection of Tetracycline Residues Based on a Dye-Doped Functionalized Nanoscaled Metal-Organic Framework. NANOMATERIALS 2019; 9:nano9070976. [PMID: 31277413 PMCID: PMC6669437 DOI: 10.3390/nano9070976] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 06/23/2019] [Accepted: 06/27/2019] [Indexed: 11/16/2022]
Abstract
Tetracycline (TC) residues are harmful to the environment and human body, so it is necessary to develop a highly sensitive probe for rapid detection of tetracycline residues. In the present paper, a novel dye-doped porous metal–organic framework (UiO-66)-based multi-color fluorescent nano-probe was designed for sensitive ratiometric detection of tetracycline (TC). In this probe, dye-molecules doped UiO-66 was used as a fluorescent internal standard, and the externally grafted lanthanide Eu3+ complex was used as response signals. The fluorescence of the Eu3+ complex was selectively enhanced with increasing concentrations of TC, which was accompanied by a visual blue-to-red color switch. The nano-probe had a linear response between 0.1 and 6 μM with a lowest detection limit of 17.9 nM, which was much lower than the maximum residue limits set by the United States Food and Drug Administration (676 nM) and the European Union (225 nM). The applicability of this method in the analysis of actual samples was evaluated by the determination of TC in honey and milk samples, indicating satisfactory recovery and good reproducibility. In addition, a cost-effective paper-based probe for rapid and visual detection of TC was developed by fixing the nano-probe on filter papers. With the help of a smartphone camera to capture the fluorescence color, and chromaticity analysis software, the calculation and analysis of red (R) and blue (B) values can be realized, which has the potential for real-time visual detection of TC.
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Affiliation(s)
- Lei Jia
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Shengli Guo
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Jun Xu
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China.
| | - Xiangzhen Chen
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Tinghui Zhu
- College of Chemistry and Chemical Engineering, Henan Polytechnic University, Jiaozuo 454000, China
| | - Tongqian Zhao
- Institute of Resources & Environment, Henan Polytechnic University, Jiaozuo 454000, China.
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Wang D, Li J, Xu Z, Zhu Y, Chen G. Preparation of novel flower-like BiVO4/Bi2Ti2O7/Fe3O4 for simultaneous removal of tetracycline and Cu2+: Adsorption and photocatalytic mechanisms. J Colloid Interface Sci 2019; 533:344-357. [DOI: 10.1016/j.jcis.2018.08.089] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 08/20/2018] [Accepted: 08/26/2018] [Indexed: 10/28/2022]
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12
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Yao Y, Jiang C, Ping J. Flexible freestanding graphene paper-based potentiometric enzymatic aptasensor for ultrasensitive wireless detection of kanamycin. Biosens Bioelectron 2018; 123:178-184. [PMID: 30174273 DOI: 10.1016/j.bios.2018.08.048] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/20/2018] [Accepted: 08/21/2018] [Indexed: 10/28/2022]
Abstract
Flexible sensing devices have drawn tremendous attention in the past decades due to their potential applications in future hand-held, potable consumer, and wearable electronics. Here, we firstly developed an ultrasensitive wireless potentiometric aptasensor based on flexible freestanding graphene paper for kanamycin detection. Flexible graphene paper made from a simple vacuum filtration method was used as a biocompatible platform for effective immobilization of aptamer. A nuclease-assisted amplification strategy was introduced into this potentiometric biosensing system in order to significantly improve the detection sensitivity through a classic catalytic recycling reaction of target induced by the nuclease (DNase I). As expected, an ultra-low detection limit of 30.0 fg/mL for kanamycin was achieved. Furthermore, the developed potentiometric enzymatic aptasensor exhibits high selectivity, favorable flexibility, excellent stability and reproducibility, which holds great promising for its routine sensing application.
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Affiliation(s)
- Yao Yao
- School of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China
| | - Chengmei Jiang
- School of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China
| | - Jianfeng Ping
- School of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou 310058, PR China.
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Li W, Zhu J, Xie G, Ren Y, Zheng YQ. Ratiometric system based on graphene quantum dots and Eu 3+ for selective detection of tetracyclines. Anal Chim Acta 2018; 1022:131-137. [DOI: 10.1016/j.aca.2018.03.018] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 03/05/2018] [Indexed: 11/28/2022]
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14
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A dual-signal amplification strategy for kanamycin based on ordered mesoporous carbon-chitosan/gold nanoparticles-streptavidin and ferrocene labelled DNA. Anal Chim Acta 2018; 1033:185-192. [PMID: 30172325 DOI: 10.1016/j.aca.2018.05.070] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/23/2018] [Accepted: 05/26/2018] [Indexed: 01/21/2023]
Abstract
An ultrasensitive electrochemical aptasensor for kanamycin (KAN) detection was constructed with a dual-signal amplification strategy. The aptasensor achieved greatly amplified sensitivity due to the excellent electrical conductivity of the ordered mesoporous carbon-chitosan (OMC-CS)/gold nanoparticles-streptavidin (AuNPs-SA) and DNA2 labelled with ferrocene (Fc-DNA2). The AuNPs-SA was used to immobilize the DNA strand (biotin labelled) with the biotin-streptavidin system. The DNA2 strand containing the KAN aptamer was labelled with ferrocene to increase the current signal on the electrode surface when bound to KAN. Some factors that affect the performance of the aptasensor were optimized, and the proposed aptasensor provided a wide linear range from 1 × 10-10 M to 4 × 10-6 M, with a detection limit as low as 35.69 pM for KAN under the optimized conditions. This aptasensor had satisfactory electrochemical performance with good stability, sensitivity and reproducibility. Additionally, it also displayed a good specificity for KAN without interference from competitive analogues. Furthermore, the constructed aptasensor was successfully used to detect KAN in a real milk sample. The proposed method for KAN detection has great potential for the detection of other antibiotics.
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15
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Frank J. The translation elongation cycle-capturing multiple states by cryo-electron microscopy. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2016.0180. [PMID: 28138066 DOI: 10.1098/rstb.2016.0180] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2016] [Indexed: 12/17/2022] Open
Abstract
During the work cycle of elongation, the ribosome, a molecular machine of vast complexity, exists in a large number of states distinguished by constellation of its subunits, its subunit domains and binding partners. Single-particle cryogenic electron microscopy (cryo-EM), developed over the past 40 years, is uniquely suited to determine the structure of molecular machines in their native states. With the emergence, 10 years ago, of unsupervised clustering techniques in the analysis of single-particle data, it has been possible to determine multiple structures from a sample containing ribosomes equilibrating in different thermally accessible states. In addition, recent advances in detector technology have made it possible to reach near-atomic resolution for some of these states. With these capabilities, single-particle cryo-EM has been at the forefront of exploring ribosome dynamics during its functional cycle, along with single-molecule fluorescence resonance energy transfer and molecular dynamics computations, offering insights into molecular architecture uniquely honed by evolution to capitalize on thermal energy in the ambient environment.This article is part of the themed issue 'Perspectives on the ribosome'.
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Affiliation(s)
- Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA .,Howard Hughes Medical Institute, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA.,Department of Biological Sciences, Columbia University, Black Building, 650 W. 168th Street, New York, NY 10032, USA
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16
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Burkhart BJ, Schwalen CJ, Mann G, Naismith JH, Mitchell DA. YcaO-Dependent Posttranslational Amide Activation: Biosynthesis, Structure, and Function. Chem Rev 2017; 117:5389-5456. [PMID: 28256131 DOI: 10.1021/acs.chemrev.6b00623] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
With advances in sequencing technology, uncharacterized proteins and domains of unknown function (DUFs) are rapidly accumulating in sequence databases and offer an opportunity to discover new protein chemistry and reaction mechanisms. The focus of this review, the formerly enigmatic YcaO superfamily (DUF181), has been found to catalyze a unique phosphorylation of a ribosomal peptide backbone amide upon attack by different nucleophiles. Established nucleophiles are the side chains of Cys, Ser, and Thr which gives rise to azoline/azole biosynthesis in ribosomally synthesized and posttranslationally modified peptide (RiPP) natural products. However, much remains unknown about the potential for YcaO proteins to collaborate with other nucleophiles. Recent work suggests potential in forming thioamides, macroamidines, and possibly additional post-translational modifications. This review covers all knowledge through mid-2016 regarding the biosynthetic gene clusters (BGCs), natural products, functions, mechanisms, and applications of YcaO proteins and outlines likely future research directions for this protein superfamily.
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Affiliation(s)
| | | | - Greg Mann
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom
| | - James H Naismith
- Biomedical Science Research Complex, University of St Andrews , BSRC North Haugh, St Andrews KY16 9ST, United Kingdom.,State Key Laboratory of Biotherapy, Sichuan University , Sichuan, China
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17
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Malik AH, Iyer PK. Conjugated Polyelectrolyte Based Sensitive Detection and Removal of Antibiotics Tetracycline from Water. ACS APPLIED MATERIALS & INTERFACES 2017; 9:4433-4439. [PMID: 28094507 DOI: 10.1021/acsami.6b13949] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new conjugated polyelectrolyte poly[5,5'-(((2-phenyl-9H-fluorene-9,9-diyl)bis(hexane-6,1-diyl))bis(oxy))diisophthalate] sodium (PFPT) was synthesized via the palladium-catalyzed Suzuki cross-coupling polymerization method and successfully applied for the rapid, real time, and highly sensitive detection of antibiotics tetracycline (Tc) in 100% aqueous media via photoinduced electron transfer with detection limit in the ppb level. Remarkably, PFPT could also be applied for the trace analysis of Tc in serum samples having recoveries well in the range 92-97% with relative standard deviations (RSD) of 1.01-1.14%, confirming reliability of the present method for the analysis of Tc. Additionally, PFPT was blended with the abundant natural polysaccharide chitosan to form CS-PFPT composite films and developed as a biopolymer based membrane for the removal of Tc from water samples with a good adsorption capacity of 3.12 mg g-1, thus finding vital application in the treatment of antibiotic infested wastewater.
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Affiliation(s)
- Akhtar Hussain Malik
- Department of Chemistry and ‡Centre for Nanotechnology, Indian Institute of Technology Guwahati , Guwahati 781039, India
| | - Parameswar Krishnan Iyer
- Department of Chemistry and ‡Centre for Nanotechnology, Indian Institute of Technology Guwahati , Guwahati 781039, India
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18
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Ma L, Sun N, Tu C, Zhang Q, Diao A. Design of an aptamer – based fluorescence displacement biosensor for selective and sensitive detection of kanamycin in aqueous samples. RSC Adv 2017. [DOI: 10.1039/c7ra07052g] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
A label-free detection method for kanamycin A using an aptamer-based displacement biosensor has been developed.
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Affiliation(s)
- Long Ma
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Nana Sun
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Chunhao Tu
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
| | - Qian Zhang
- College of Chemical Engineering and Materials Science
- Tianjin University of Science & Technology
- Tianjin 300457
- China
| | - Aipo Diao
- Key Laboratory of Industrial Fermentation Microbiology
- Ministry of Education
- School of Biotechnology
- Tianjin University of Science & Technology
- Tianjin 300457
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19
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rRNA Binding Sites and the Molecular Mechanism of Action of the Tetracyclines. Antimicrob Agents Chemother 2016; 60:4433-41. [PMID: 27246781 DOI: 10.1128/aac.00594-16] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The tetracycline antibiotics are known to be effective in the treatment of both infectious and noninfectious disease conditions. The 16S rRNA binding mechanism currently held for the antibacterial action of the tetracyclines does not explain their activity against viruses, protozoa that lack mitochondria, and noninfectious conditions. Also, the mechanism by which the tetracyclines selectively inhibit microbial protein synthesis against host eukaryotic protein synthesis despite conservation of ribosome structure and functions is still questionable. Many studies have investigated the binding of the tetracyclines to the 16S rRNA using the small ribosomal subunit of different bacterial species, but there seems to be no agreement between various reports on the exact binding site on the 16S rRNA. The wide range of activity of the tetracyclines against a broad spectrum of bacterial pathogens, viruses, protozoa, and helminths, as well as noninfectious conditions, indicates a more generalized effect on RNA. In the light of recent evidence that the tetracyclines bind to various synthetic double-stranded RNAs (dsRNAs) of random base sequences, suggesting that the double-stranded structures may play a more important role in the binding of the tetracyclines to RNA than the specific base pairs, as earlier speculated, it is imperative to consider possible alternative binding modes or sites that could help explain the mechanisms of action of the tetracyclines against various pathogens and disease conditions.
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20
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Hermann T. Small molecules targeting viral RNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2016; 7:726-743. [PMID: 27307213 PMCID: PMC7169885 DOI: 10.1002/wrna.1373] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 04/29/2016] [Accepted: 05/23/2016] [Indexed: 02/06/2023]
Abstract
Highly conserved noncoding RNA (ncRNA) elements in viral genomes and transcripts offer new opportunities to expand the repertoire of drug targets for the development of antiinfective therapy. Ligands binding to ncRNA architectures are able to affect interactions, structural stability or conformational changes and thereby block processes essential for viral replication. Proof of concept for targeting functional RNA by small molecule inhibitors has been demonstrated for multiple viruses with RNA genomes. Strategies to identify antiviral compounds as inhibitors of ncRNA are increasingly emphasizing consideration of drug‐like properties of candidate molecules emerging from screening and ligand design. Recent efforts of antiviral lead discovery for RNA targets have provided drug‐like small molecules that inhibit viral replication and include inhibitors of human immunodeficiency virus (HIV), hepatitis C virus (HCV), severe respiratory syndrome coronavirus (SARS CoV), and influenza A virus. While target selectivity remains a challenge for the discovery of useful RNA‐binding compounds, a better understanding is emerging of properties that define RNA targets amenable for inhibition by small molecule ligands. Insight from successful approaches of targeting viral ncRNA in HIV, HCV, SARS CoV, and influenza A will provide a basis for the future exploration of RNA targets for therapeutic intervention in other viral pathogens which create urgent, unmet medical needs. Viruses for which targeting ncRNA components in the genome or transcripts may be promising include insect‐borne flaviviruses (Dengue, Zika, and West Nile) and filoviruses (Ebola and Marburg). WIREs RNA 2016, 7:726–743. doi: 10.1002/wrna.1373 This article is categorized under:
RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Small Molecule–RNA Interactions Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
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Affiliation(s)
- Thomas Hermann
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA. .,Center for Drug Discovery Innovation, University of California, San Diego, La Jolla, CA, USA.
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21
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An aptasensor for tetracycline using a glassy carbon modified with nanosheets of graphene oxide. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1810-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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22
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Glassford I, Teijaro CN, Daher SS, Weil A, Small MC, Redhu SK, Colussi DJ, Jacobson MA, Childers WE, Buttaro B, Nicholson AW, MacKerell AD, Cooperman BS, Andrade RB. Ribosome-Templated Azide-Alkyne Cycloadditions: Synthesis of Potent Macrolide Antibiotics by In Situ Click Chemistry. J Am Chem Soc 2016; 138:3136-44. [PMID: 26878192 PMCID: PMC4785600 DOI: 10.1021/jacs.5b13008] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Over half of all antibiotics target the bacterial ribosome-nature's complex, 2.5 MDa nanomachine responsible for decoding mRNA and synthesizing proteins. Macrolide antibiotics, exemplified by erythromycin, bind the 50S subunit with nM affinity and inhibit protein synthesis by blocking the passage of nascent oligopeptides. Solithromycin (1), a third-generation semisynthetic macrolide discovered by combinatorial copper-catalyzed click chemistry, was synthesized in situ by incubating either E. coli 70S ribosomes or 50S subunits with macrolide-functionalized azide 2 and 3-ethynylaniline (3) precursors. The ribosome-templated in situ click method was expanded from a binary reaction (i.e., one azide and one alkyne) to a six-component reaction (i.e., azide 2 and five alkynes) and ultimately to a 16-component reaction (i.e., azide 2 and 15 alkynes). The extent of triazole formation correlated with ribosome affinity for the anti (1,4)-regioisomers as revealed by measured Kd values. Computational analysis using the site-identification by ligand competitive saturation (SILCS) approach indicated that the relative affinity of the ligands was associated with the alteration of macrolactone+desosamine-ribosome interactions caused by the different alkynes. Protein synthesis inhibition experiments confirmed the mechanism of action. Evaluation of the minimal inhibitory concentrations (MIC) quantified the potency of the in situ click products and demonstrated the efficacy of this method in the triaging and prioritization of potent antibiotics that target the bacterial ribosome. Cell viability assays in human fibroblasts confirmed 2 and four analogues with therapeutic indices for bactericidal activity over in vitro mammalian cytotoxicity as essentially identical to solithromycin (1).
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Affiliation(s)
- Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | | | - Samer S. Daher
- Department of Chemistry, Temple University, Philadelphia, PA 19122
| | - Amy Weil
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Meagan C. Small
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Shiv K. Redhu
- Department of Biology, Temple University, Philadelphia, PA 19122
| | - Dennis J. Colussi
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Marlene A. Jacobson
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Wayne E. Childers
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, Pennsylvania, 19140, United States
| | - Bettina Buttaro
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, PA 19140
| | | | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, MD 21201
| | - Barry S. Cooperman
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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23
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Proteomic analysis of tylosin-resistant Mycoplasma gallisepticum reveals enzymatic activities associated with resistance. Sci Rep 2015; 5:17077. [PMID: 26584633 PMCID: PMC4653647 DOI: 10.1038/srep17077] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/18/2015] [Indexed: 01/18/2023] Open
Abstract
Mycoplasma gallisepticum is a significant pathogenic bacterium that infects poultry, causing chronic respiratory disease and sinusitis in chickens and turkeys, respectively. M. gallisepticum infection poses a substantial economic threat to the poultry industry, and this threat is made worse by the emergence of antibiotic-resistant strains. The mechanisms of resistance are often difficult to determine; for example, little is known about antibiotic resistance of M. gallisepticum at the proteome level. In this study, we performed comparative proteomic analyses of an antibiotic (tylosin)-resistant M. gallisepticum mutant and a susceptible parent strain using a combination of two-dimensional differential gel electrophoresis and nano-liquid chromatography-quadrupole-time of flight mass spectrometry. Thirteen proteins were identified as differentially expressed in the resistant strain compared to the susceptible strain. Most of these proteins were related to catalytic activity, including catalysis that promotes the formylation of initiator tRNA and energy production. Elongation factors Tu and G were over-expressed in the resistant strains, and this could promote the binding of tRNA to ribosomes and catalyze ribosomal translocation, the coordinated movement of tRNA, and conformational changes in the ribosome. Taken together, our results indicate that M. gallisepticum develops resistance to tylosin by regulating associated enzymatic activities.
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24
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Guo W, Sun N, Qin X, Pei M, Wang L. A novel electrochemical aptasensor for ultrasensitive detection of kanamycin based on MWCNTs-HMIMPF6 and nanoporous PtTi alloy. Biosens Bioelectron 2015. [PMID: 26208174 DOI: 10.1016/j.bios.2015.06.081] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A novel aptasensor based on a novel composite film consisting of multi-walled carbon nanotubes (MWCNTs), ionic liquid (IL) of 1-hexyl-3-methylimidazolium hexafluorophosphate (HMIMPF6), and nanoporous PtTi (NP-PtTi) alloy was constructed for ultrasensitive detection of kanamycin. The NP-PtTi alloy was successfully fabricated by a simple dealloying of PtTiAl source alloy in HCl solution. The NP-PtTi alloy has uniform interconnected network structure with specific surface area and was used to immobilize aptamer. After modified with the composite material, current signal was amplified obviously, which attributed to the larger specific surface area and excellent electrical conductivity of NP-PtTi and MWCNTs. A number of factors affecting the activity of the aptasensor have been discussed and optimized. Under the optimized conditions, the proposed aptasensor provided a linear range of 0.05-100 ng mL(-1) with a low detection limit of 3.7 pg mL(-1). This aptasensor displayed high sensitivity, stability and reproducibility. In addition, the as-prepared aptasensor was successfully used for the determination of kanamycin in a real sample.
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Affiliation(s)
- Wenjuan Guo
- Shandong Provincial Key Laboratory of Chemical Sensing & Analysis, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Na Sun
- Environmental Protection Monitoring Station, Jining 272045, China
| | - Xiaoli Qin
- Shandong Provincial Key Laboratory of Chemical Sensing & Analysis, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
| | - Meishan Pei
- Shandong Provincial Key Laboratory of Chemical Sensing & Analysis, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China.
| | - Luyan Wang
- Shandong Provincial Key Laboratory of Chemical Sensing & Analysis, School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China
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25
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Investigating Bacterial Protein Synthesis Using Systems Biology Approaches. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 883:21-40. [PMID: 26621460 DOI: 10.1007/978-3-319-23603-2_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Protein synthesis is essential for bacterial growth and survival. Its study in Escherichia coli helped uncover features conserved among bacteria as well as universally. The pattern of discovery and the identification of some of the longest-known components of the protein synthesis machinery, including the ribosome itself, tRNAs, and translation factors proceeded through many stages of successively more refined biochemical purifications, finally culminating in the isolation to homogeneity, identification, and mapping of the smallest unit required for performing the given function. These early studies produced a wealth of information. However, many unknowns remained. Systems biology approaches provide an opportunity to investigate protein synthesis from a global perspective, overcoming the limitations of earlier ad hoc methods to gain unprecedented insights. This chapter reviews innovative systems biology approaches, with an emphasis on those designed specifically for investigating the protein synthesis machinery in E. coli.
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26
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Abstract
A convergent synthesis of macrolide natural product (−)-A26771B starting from d-glucal is reported. Key features of this synthesis involve Ferrier rearrangement, cross metathesis of chiral fragments 3 and 4 and Yamaguchi macrolactonization.
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Affiliation(s)
- Puli Saidhareddy
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute (CDRI)
- Lucknow-226031
- India
| | - Arun K. Shaw
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute (CDRI)
- Lucknow-226031
- India
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27
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Arabidopsis protein arginine methyltransferase 3 is required for ribosome biogenesis by affecting precursor ribosomal RNA processing. Proc Natl Acad Sci U S A 2014; 111:16190-5. [PMID: 25352672 DOI: 10.1073/pnas.1412697111] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Ribosome biogenesis is a fundamental and tightly regulated cellular process, including synthesis, processing, and assembly of rRNAs with ribosomal proteins. Protein arginine methyltransferases (PRMTs) have been implicated in many important biological processes, such as ribosome biogenesis. Two alternative precursor rRNA (pre-rRNA) processing pathways coexist in yeast and mammals; however, how PRMT affects ribosome biogenesis remains largely unknown. Here we show that Arabidopsis PRMT3 (AtPRMT3) is required for ribosome biogenesis by affecting pre-rRNA processing. Disruption of AtPRMT3 results in pleiotropic developmental defects, imbalanced polyribosome profiles, and aberrant pre-rRNA processing. We further identify an alternative pre-rRNA processing pathway in Arabidopsis and demonstrate that AtPRMT3 is required for the balance of these two pathways to promote normal growth and development. Our work uncovers a previously unidentified function of PRMT in posttranscriptional regulation of rRNA, revealing an extra layer of complexity in the regulation of ribosome biogenesis.
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28
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Glassford I, Lee M, Wagh B, Velvadapu V, Paul T, Sandelin G, DeBrosse C, Klepacki D, Small MC, MacKerell AD, Andrade RB. Desmethyl macrolides: synthesis and evaluation of 4-desmethyl telithromycin. ACS Med Chem Lett 2014; 5:1021-6. [PMID: 25221660 DOI: 10.1021/ml5002097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 07/16/2014] [Indexed: 12/15/2022] Open
Abstract
Novel sources of antibiotics are needed to address the serious threat of bacterial resistance. Accordingly, we have launched a structure-based drug design program featuring a desmethylation strategy wherein methyl groups have been replaced with hydrogens. Herein we report the total synthesis, molecular modeling, and biological evaluation of 4-desmethyl telithromycin (6), a novel desmethyl analogue of the third-generation ketolide antibiotic telithromycin (2) and our final analogue in this series. While 4-desmethyl telithromycin (6) was found to be equipotent with telithromycin (2) against wild-type bacteria, it was 4-fold less potent against the A2058G mutant. These findings reveal that strategically replacing the C4-methyl group with hydrogen (i.e., desmethylation) did not address this mechanism of resistance. Throughout the desmethyl series, the sequential addition of methyls to the 14-membered macrolactone resulted in improved bioactivity. Molecular modeling methods indicate that changes in conformational flexibility dominate the increased biological activity; moreover, they reveal 6 adopts a different conformation once bound to the A2058G ribosome, thus impacting noncovalent interactions reflected in a lower MIC value. Finally, fluorescence polarization experiments of 6 with E. coli ribosomes confirmed 6 is indeed binding the ribosome.
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Affiliation(s)
- Ian Glassford
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Miseon Lee
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Bharat Wagh
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Venkata Velvadapu
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tapas Paul
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Gary Sandelin
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Charles DeBrosse
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Dorota Klepacki
- Center
for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, United States
| | - Meagan C. Small
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201, United States
| | - Rodrigo B. Andrade
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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29
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Hong W, Zeng J, Xie J. Antibiotic drugs targeting bacterial RNAs. Acta Pharm Sin B 2014; 4:258-65. [PMID: 26579393 PMCID: PMC4629089 DOI: 10.1016/j.apsb.2014.06.012] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 06/04/2014] [Accepted: 06/20/2014] [Indexed: 10/26/2022] Open
Abstract
RNAs have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. The recent increase in structural and functional information related to RNAs has put them in the limelight as a drug target for small molecule therapy. In addition, the recognition of the marked difference between prokaryotic and eukaryotic rRNA has led to the development of antibiotics that specifically target bacterial rRNA, reduce protein translation and thereby inhibit bacterial growth. To facilitate the development of new antibiotics targeting RNA, we here review the literature concerning such antibiotics, mRNA, riboswitch and tRNA and the key methodologies used for their screening.
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Affiliation(s)
| | | | - Jianping Xie
- Institute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource of the Three Gorges Area, Key Laboratory of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing 400715, China
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30
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Moshiri H, Mehta V, Salavati R. RNA catalyst as a reporter for screening drugs against RNA editing in trypanosomes. J Vis Exp 2014. [PMID: 25079143 DOI: 10.3791/51712] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Substantial progress has been made in determining the mechanism of mitochondrial RNA editing in trypanosomes. Similarly, considerable progress has been made in identifying the components of the editosome complex that catalyze RNA editing. However, it is still not clear how those proteins work together. Chemical compounds obtained from a high-throughput screen against the editosome may block or affect one or more steps in the editing cycle. Therefore, the identification of new chemical compounds will generate valuable molecular probes for dissecting the editosome function and assembly. In previous studies, in vitro editing assays were carried out using radio-labeled RNA. These assays are time consuming, inefficient and unsuitable for high-throughput purposes. Here, a homogenous fluorescence-based "mix and measure" hammerhead ribozyme in vitro reporter assay to monitor RNA editing, is presented. Only as a consequence of RNA editing of the hammerhead ribozyme a fluorescence resonance energy transfer (FRET) oligoribonucleotide substrate undergoes cleavage. This in turn results in separation of the fluorophore from the quencher thereby producing a signal. In contrast, when the editosome function is inhibited, the fluorescence signal will be quenched. This is a highly sensitive and simple assay that should be generally applicable to monitor in vitro RNA editing or high throughput screening of chemicals that can inhibit the editosome function.
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Affiliation(s)
- Houtan Moshiri
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University
| | - Vaibhav Mehta
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University
| | - Reza Salavati
- Department of Biochemistry, McGill University; Institute of Parasitology, McGill University; McGill Centre for Bioinformatics, McGill University;
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31
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Hayat A, Marty JL. Aptamer based electrochemical sensors for emerging environmental pollutants. Front Chem 2014; 2:41. [PMID: 25019067 PMCID: PMC4071757 DOI: 10.3389/fchem.2014.00041] [Citation(s) in RCA: 88] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 06/09/2014] [Indexed: 12/30/2022] Open
Abstract
Environmental contaminants monitoring is one of the key issues in understanding and managing hazards to human health and ecosystems. In this context, aptamer based electrochemical sensors have achieved intense significance because of their capability to resolve a potentially large number of problems and challenges in environmental contamination. An aptasensor is a compact analytical device incorporating an aptamer (oligonulceotide) as the sensing element either integrated within or intimately associated with a physiochemical transducer surface. Nucleic acid is well known for the function of carrying and passing genetic information, however, it has found a key role in analytical monitoring during recent years. Aptamer based sensors represent a novelty in environmental analytical science and there are great expectations for their promising performance as alternative to conventional analytical tools. This review paper focuses on the recent advances in the development of aptamer based electrochemical sensors for environmental applications with special emphasis on emerging pollutants.
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Affiliation(s)
- Akhtar Hayat
- BIOMEM, Université de Perpignan Perpignan, France ; Interdisciplinary Research Centre in Biomedical Materials, COMSATS Institute of Information Technology Lahore, Pakistan
| | - Jean L Marty
- BIOMEM, Université de Perpignan Perpignan, France
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32
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Wang S, Yong W, Liu J, Zhang L, Chen Q, Dong Y. Development of an indirect competitive assay-based aptasensor for highly sensitive detection of tetracycline residue in honey. Biosens Bioelectron 2014; 57:192-8. [PMID: 24583691 DOI: 10.1016/j.bios.2014.02.032] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2013] [Revised: 02/08/2014] [Accepted: 02/11/2014] [Indexed: 10/25/2022]
Abstract
Tetracycline (TC) is widely used for prevention and control of animal diseases for its broad spectrum antimicrobial activity and low cost, but its abuse can seriously affect human health and may result in trade loss. Thus there is an imperative need to develop high-performing analytical technique for TC detection. In this study, we developed a biosensor based on an indirect competitive enzyme-linked aptamer assay (ic-ELAA). A 76mer single-stranded DNA (ssDNA) aptamer, selected by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), was applied for the recognition and detection of TC in honey. The limit of detection was 9.6×10(-3) ng/mL with a linear working range from 0.01 to 100 ng/mL toward TC in honey, and a mean recovery rate of 93.23% in TC-spiked honey was obtained. This aptasensor can be applied to detect TC residue in food with high sensitivity and simplicity, and it is prospective to develop useful ELAA Kits for TC determination in food.
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Affiliation(s)
- Sai Wang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Wei Yong
- Institute of Food Safety, Chinese Academy of Inspection and Quarantine, Beijing 100123, PR China
| | - Jiahui Liu
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Liya Zhang
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Qilong Chen
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China
| | - Yiyang Dong
- Beijing Key Laboratory of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, PR China.
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33
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Wu J, Zhu Y, Xue F, Mei Z, Yao L, Wang X, Zheng L, Liu J, Liu G, Peng C, Chen W. Recent trends in SELEX technique and its application to food safety monitoring. Mikrochim Acta 2014; 181:479-491. [PMID: 25419005 DOI: 10.1007/s00604-013-1156-7] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The method referred to as "systemic evolution of ligands by exponential enrichment" (SELEX) was introduced in 1990 and ever since has become an important tool for the identification and screening of aptamers. Such nucleic acids can recognize and bind to their corresponding targets (analytes) with high selectivity and affinity, and aptamers therefore have become attractive alternatives to traditional antibodies not the least because they are much more stable. Meanwhile, they have found numerous applications in different fields including food quality and safety monitoring. This review first gives an introduction into the selection process and to the evolution of SELEX, then covers applications of aptamers in the surveillance of food safety (with subsections on absorptiometric, electrochemical, fluorescent and other methods), and then gives conclusions and perspectives. The SELEX method excels by its features of in vitro, high throughput and ease of operation. This review contains 86 references.
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Affiliation(s)
- Jingjing Wu
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Yingyue Zhu
- School of Biotechnology and Food Engineering, Changshu Institute of Technology, Changshu 215500, People's Republic of China
| | - Feng Xue
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Zhanlong Mei
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Li Yao
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Xin Wang
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Lei Zheng
- School of Medical Engineering, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Jian Liu
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
| | - Guodong Liu
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, ND 58108, USA
| | - Chifang Peng
- School Food Science & Technology, Jiangnan University, Wuxi 214122, People's Republic of China
| | - Wei Chen
- School of Biotechnology and Food Engineering, Anhui Provincial Key Lab of Functional Materials & Devices, Hefei University of Technology, Hefei 230009, People's Republic of China
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Wagh B, Paul T, DeBrosse C, Klepacki D, Small MC, MacKerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,8,10-Tridesmethyl Cethromycin. ACS Med Chem Lett 2013; 4:1114-1118. [PMID: 24470840 DOI: 10.1021/ml400337t] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Antibiotic-resistant bacteria are emerging at an alarming rate in both hospital and community settings. Motivated by this issue, we have prepared desmethyl (i.e., replacing methyl groups with hydrogens) analogues of third-generation macrolide drugs telithromycin (TEL, 2) and cethromycin (CET, 6), both of which are semi-synthetic derivatives of flagship macrolide antibiotic erythromycin (1). Herein, we report the total synthesis, molecular modeling, and biological evaluation of 4,8,10-tridesmethyl cethromycin (7). In MIC assays, CET analogue 7 was found to be equipotent with TEL (2) against a wild-type E. coli strain, more potent than previously disclosed desmethyl TEL congeners 3, 4, and 5, but fourfold less potent than TEL (2) against a mutant E. coli A2058G strain.
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Affiliation(s)
- Bharat Wagh
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tapas Paul
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Charles DeBrosse
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Dorota Klepacki
- Center
for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, United States
| | - Meagan C. Small
- Department
of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Alexander D. MacKerell
- Department
of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Rodrigo B. Andrade
- Department
of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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35
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Burnett BJ, Altman RB, Ferrao R, Alejo JL, Kaur N, Kanji J, Blanchard SC. Elongation factor Ts directly facilitates the formation and disassembly of the Escherichia coli elongation factor Tu·GTP·aminoacyl-tRNA ternary complex. J Biol Chem 2013; 288:13917-28. [PMID: 23539628 DOI: 10.1074/jbc.m113.460014] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Aminoacyl-tRNA (aa-tRNA) enters the ribosome in a ternary complex with the G-protein elongation factor Tu (EF-Tu) and GTP. RESULTS EF-Tu·GTP·aa-tRNA ternary complex formation and decay rates are accelerated in the presence of the nucleotide exchange factor elongation factor Ts (EF-Ts). CONCLUSION EF-Ts directly facilitates the formation and disassociation of ternary complex. SIGNIFICANCE This system demonstrates a novel function of EF-Ts. Aminoacyl-tRNA enters the translating ribosome in a ternary complex with elongation factor Tu (EF-Tu) and GTP. Here, we describe bulk steady state and pre-steady state fluorescence methods that enabled us to quantitatively explore the kinetic features of Escherichia coli ternary complex formation and decay. The data obtained suggest that both processes are controlled by a nucleotide-dependent, rate-determining conformational change in EF-Tu. Unexpectedly, we found that this conformational change is accelerated by elongation factor Ts (EF-Ts), the guanosine nucleotide exchange factor for EF-Tu. Notably, EF-Ts attenuates the affinity of EF-Tu for GTP and destabilizes ternary complex in the presence of non-hydrolyzable GTP analogs. These results suggest that EF-Ts serves an unanticipated role in the cell of actively regulating the abundance and stability of ternary complex in a manner that contributes to rapid and faithful protein synthesis.
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Affiliation(s)
- Benjamin J Burnett
- Departments of Physiology and Biophysics, Weill Cornell Medical College, New York, New York 10065, USA
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36
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Annoni C, Nakata E, Tamura T, Liew FF, Nakano S, Gelmi ML, Morii T. Construction of ratiometric fluorescent sensors by ribonucleopeptides. Org Biomol Chem 2013; 10:8767-9. [PMID: 23069733 DOI: 10.1039/c2ob26722e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Ratiometric fluorescent sensors were constructed from RNA aptamers by generating modular ribonucleopeptide complexes. Fluorescent ribonucleopeptides containing fluorophore seminaphthorhodafluor tethered to their peptide subunit revealed a dual emission property, which permitted a ratiometric fluorescent measurement of a substrate-binding event. The strategy successfully afforded ratiometric fluorescent sensors for biologically active small ligands, tetracycline, dopamine and streptomycin.
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Affiliation(s)
- Chiara Annoni
- Dipartimento di Scienze Farmaceutiche Pietro Pratesi, Sezione Chimica Generale Organica A. Marchesini, Universita` degli Studi di Milano, via Venezian 21, 20133 Milan, Italy
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37
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Wagh B, Paul T, Glassford I, DeBrosse C, Klepacki D, Small MC, MacKerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,8-Didesmethyl Telithromycin. ACS Med Chem Lett 2012; 3:1013-1018. [PMID: 24015325 DOI: 10.1021/ml300230h] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
There is an urgent need for novel sources of antibiotics to address the incessant and inevitable onset of bacterial resistance. To this end, we have initiated a structure-based drug design program that features a desmethylation strategy (i.e., replacing methyl groups with hydrogens). Herein we report the total synthesis, molecular modeling and biological evaluation of 4,8-didesmethyl telithromycin (5), a novel desmethyl analogue of the third-generation ketolide antibiotic telithromycin (2), which is an FDA-approved semisynthetic derivative of erythromycin (1). We found 4,8-didesmethyl telithromycin (5) to be eight times more active than previously prepared 4,8,10-tridesmethyl congener (3) and two times more active than 4,10-didesmethyl regioisomer (4) in MIC assays. While less potent than telithromycin (2) and paralleling the observations made in the previous study of 4,10-didesmethyl analogue (4), the inclusion of a single methyl group improves biological activity thus supporting its role in antibiotic activity.
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Affiliation(s)
- Bharat Wagh
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Tapas Paul
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Charles DeBrosse
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Dorota Klepacki
- Center for
Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, United
States
| | - Meagan C. Small
- Department of Pharmaceutical
Sciences, University of Maryland, Baltimore,
Maryland 21201,
United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical
Sciences, University of Maryland, Baltimore,
Maryland 21201,
United States
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
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38
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Blaha GM, Polikanov YS, Steitz TA. Elements of ribosomal drug resistance and specificity. Curr Opin Struct Biol 2012; 22:750-8. [PMID: 22981944 DOI: 10.1016/j.sbi.2012.07.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Revised: 07/19/2012] [Accepted: 07/19/2012] [Indexed: 10/27/2022]
Abstract
The structures of ribosomes in complex with inhibitors of translation have not only shed light on the interactions of antibiotics with the ribosome but also on the underlying mechanisms by which they interfere with the ribosome function. Several recent papers [1(•),2(••),3,4] have correlated the available ribosome structures with the wealth of biochemical data [5(•)]. In this review we shall focus on the lessons learned for drug specificity rather than presenting a comprehensive survey of the known structures of ribosome complexes with antibiotics.
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Affiliation(s)
- Gregor M Blaha
- Department of Biochemistry, University of California, Riverside, CA 92521, USA
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39
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Velvadapu V, Glassford I, Lee M, Paul T, DeBrosse C, Klepacki D, Small MC, MacKerell AD, Andrade RB. Desmethyl Macrolides: Synthesis and Evaluation of 4,10-Didesmethyl Telithromycin. ACS Med Chem Lett 2012; 3:211-215. [PMID: 22708010 DOI: 10.1021/ml200254h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Novel sources of antibiotics are required to keep pace with the inevitable onset of bacterial resistance. Continuing with our macrolide desmethylation strategy as a source of new antibiotics, we report the total synthesis, molecular modeling and biological evaluation of 4,10-didesmethyl telithromycin (4), a novel desmethyl analogue of the 3rd-generation drug telithromycin (2). Telithromycin is an FDA-approved ketolide antibiotic derived from erythromycin (1). We found 4,10-didesmethyl telithromycin (4) to be four times more active than previously prepared 4,8,10-tridesmethyl congener (3) in MIC assays. While less potent than telithromycin (2), the inclusion of the C-8 methyl group has improved biological activity suggesting it plays an important role in antibiotic function.
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Affiliation(s)
- Venkata Velvadapu
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Ian Glassford
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Miseon Lee
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Tapas Paul
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Charles DeBrosse
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
| | - Dorota Klepacki
- Center for
Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, United
States
| | - Meagan C. Small
- Department of Pharmaceutical
Sciences, University of Maryland, Baltimore,
Maryland 21201,
United States
| | - Alexander D. MacKerell
- Department of Pharmaceutical
Sciences, University of Maryland, Baltimore,
Maryland 21201,
United States
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122,
United States
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40
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Sett A, Das S, Sharma P, Bora U. Aptasensors in Health, Environment and Food Safety Monitoring. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ojab.2012.12002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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41
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Walter JD, Hunter M, Cobb M, Traeger G, Spiegel PC. Thiostrepton inhibits stable 70S ribosome binding and ribosome-dependent GTPase activation of elongation factor G and elongation factor 4. Nucleic Acids Res 2011; 40:360-70. [PMID: 21908407 PMCID: PMC3245911 DOI: 10.1093/nar/gkr623] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Thiostrepton, a macrocyclic thiopeptide antibiotic, inhibits prokaryotic translation by interfering with the function of elongation factor G (EF-G). Here, we have used 70S ribosome binding and GTP hydrolysis assays to study the effects of thiostrepton on EF-G and a newly described translation factor, elongation factor 4 (EF4). In the presence of thiostrepton, ribosome-dependent GTP hydrolysis is inhibited for both EF-G and EF4, with IC(50) values equivalent to the 70S ribosome concentration (0.15 µM). Further studies indicate the mode of thiostrepton inhibition is to abrogate the stable binding of EF-G and EF4 to the 70S ribosome. In support of this model, an EF-G truncation variant that does not possess domains IV and V was shown to possess ribosome-dependent GTP hydrolysis activity that was not affected by the presence of thiostrepton (>100 µM). Lastly, chemical footprinting was employed to examine the nature of ribosome interaction and tRNA movements associated with EF4. In the presence of non-hydrolyzable GTP, EF4 showed chemical protections similar to EF-G and stabilized a ratcheted state of the 70S ribosome. These data support the model that thiostrepton inhibits stable GTPase binding to 70S ribosomal complexes, and a model for the first step of EF4-catalyzed reverse-translocation is presented.
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Affiliation(s)
- Justin D Walter
- Department of Chemistry, Western Washington University, 516 High Street, MS 9150, Bellingham, WA 98225-9150, USA
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42
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Duke SO, Dayan FE. Modes of action of microbially-produced phytotoxins. Toxins (Basel) 2011; 3:1038-1064. [PMID: 22069756 PMCID: PMC3202864 DOI: 10.3390/toxins3081038] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Revised: 08/15/2011] [Accepted: 08/17/2011] [Indexed: 01/17/2023] Open
Abstract
Some of the most potent phytotoxins are synthesized by microbes. A few of these share molecular target sites with some synthetic herbicides, but many microbial toxins have unique target sites with potential for exploitation by the herbicide industry. Compounds from both non-pathogenic and pathogenic microbes are discussed. Microbial phytotoxins with modes of action the same as those of commercial herbicides and those with novel modes of action of action are covered. Examples of the compounds discussed are tentoxin, AAL-toxin, auscaulitoxin aglycone, hydantocidin, thaxtomin, and tabtoxin.
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Affiliation(s)
- Stephen O. Duke
- United States Department of Agriculture, Agricultural Research Service, Natural Products Utilization Research Unit, P. O. Box 8048, MS 38677, USA;
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43
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Song KM, Cho M, Jo H, Min K, Jeon SH, Kim T, Han MS, Ku JK, Ban C. Gold nanoparticle-based colorimetric detection of kanamycin using a DNA aptamer. Anal Biochem 2011; 415:175-81. [PMID: 21530479 DOI: 10.1016/j.ab.2011.04.007] [Citation(s) in RCA: 282] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 03/30/2011] [Accepted: 04/04/2011] [Indexed: 02/07/2023]
Abstract
A selective kanamycin-binding single-strand DNA (ssDNA) aptamer (TGGGGGTTGAGGCTAAGCCGA) was discovered through in vitro selection using affinity chromatography with kanamycin-immobilized sepharose beads. The selected aptamer has a high affinity for kanamycin and also for kanamycin derivatives such as kanamycin B and tobramycin. The dissociation constants (K(d) [kanamycin]=78.8 nM, K(d) [kanamycin B]=84.5 nM, and K(d) [tobramycin]=103 nM) of the new aptamer were determined by fluorescence intensity analysis using 5'-fluorescein amidite (FAM) modification. Using this aptamer, kanamycin was detected down to 25 nM by the gold nanoparticle-based colorimetric method. Because the designed colorimetric method is simple, easy, and visible to the naked eye, it has advantages that make it useful for the detection of kanamycin. Furthermore, the selected new aptamer has many potential applications as a bioprobe for the detection of kanamycin, kanamycin B, and tobramycin in pharmaceutical preparations and food products.
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Affiliation(s)
- Kyung-Mi Song
- Department of Chemistry, Pohang University of Science and Technology, Pohang, Gyungbuk 790-784, South Korea
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44
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Velvadapu V, Paul T, Wagh B, Klepacki D, Guvench O, MacKerell A, Andrade RB. Desmethyl Macrolide Analogues to Address Antibiotic Resistance: Total Synthesis and Biological Evaluation of 4,8,10-Tridesmethyl Telithromycin. ACS Med Chem Lett 2011; 2:68-72. [PMID: 21643527 DOI: 10.1021/ml1002184] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
There is an urgent need to discover new drugs to address the pressing problem of antibiotic-resistance. Macrolide antibiotics such as erythromycin (1) are safe, broad-spectrum antibiotics used in the clinic since 1954. Herein we report the synthesis and evaluation of 4,8,10-tridesmethyl telithromycin (3), a novel desmethyl analogue of the 3rd-generation drug telithromycin (2), which is a semisynthetic derivative of 1. Analogue 3 was found to possess antibiotic activity and was superior to telithromycin (2) when tested against resistant strains of S. aureus possessing an A→T mutation at position 2058 (E. coli numbering).
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Affiliation(s)
- Venkata Velvadapu
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Tapas Paul
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Bharat Wagh
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Dorota Klepacki
- Center for Pharmaceutical Biotechnology, University of Illinois, Chicago, Illinois 60607, United States
| | - Olgun Guvench
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Alexander MacKerell
- Department of Pharmaceutical Sciences, University of Maryland, Baltimore, Maryland 21201, United States
| | - Rodrigo B. Andrade
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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45
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McCoy LS, Xie Y, Tor Y. Antibiotics that target protein synthesis. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 2:209-32. [DOI: 10.1002/wrna.60] [Citation(s) in RCA: 95] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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46
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Padilla IMG, Burgos L. Aminoglycoside antibiotics: structure, functions and effects on in vitro plant culture and genetic transformation protocols. PLANT CELL REPORTS 2010; 29:1203-13. [PMID: 20644935 DOI: 10.1007/s00299-010-0900-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Revised: 07/06/2010] [Accepted: 07/06/2010] [Indexed: 05/12/2023]
Abstract
Plant transformation protocols generally involve the use of selectable marker genes for the screening of transgenic material. The bacterial gene nptII, coding for a neomycin phosphotransferase, and the hpt gene, coding for a hygromycin phosphotransferase, are frequently used. These enzymes detoxify aminoglycoside antibiotics by phosphorylation, thereby permitting cell growth in the presence of antibiotics. Nevertheless, the screening for transgenic regenerated shoots is often partial and difficult due to regeneration of escapes and chimeras. These difficulties can be caused, in part, by an incorrect assumption about the mode of action of antibiotics in bacterial and eukaryotic cells and in in vitro tissue culture. The information contained in this review could be useful to establish better selection strategies by taking into account factors such as explant complexity, transformation and selection protocols that allow better accessibility to cells of Agrobacterium and antibiotics, and faster regeneration methods that avoid collateral effects of antibiotics on recovered, putative transgenic shoots.
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Affiliation(s)
- I M G Padilla
- Grupo de Biotecnología de Frutales, Departamento de Mejora, CEBAS-CSIC, Campus Universitario de Espinardo, Apartado de correos 164, 30100, Murcia, Spain.
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47
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Abstract
This essay is a reflection on the ways the X-ray structures of the ribosome are helping in the interpretation of cryogenic electron microscopy (cryo-EM) density maps showing the translating ribosome in motion. Through advances in classification methods, cryo-EM and single-particle reconstruction methods have recently evolved to the point where they can yield an array of structures from a single sample ("story in a sample"), providing snapshots of an entire subprocess of translation, such as translocation or decoding.
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Affiliation(s)
- Joachim Frank
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA and Department of Biological Sciences, Columbia University, 1212 Amsterdam Ave., New York, NY 10027, USA, phone: +1 (0)212 305 9510, fax: +1 (0)212 305 9500
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48
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Wu S, Fu Y, Yan R, Wu Y, Lei X, Ye XS. Synthesis of neamine–carboline conjugates for RNA binding and their antibacterial activities. Tetrahedron 2010. [DOI: 10.1016/j.tet.2010.03.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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49
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Starosta AL, Karpenko VV, Shishkina AV, Mikolajka A, Sumbatyan NV, Schluenzen F, Korshunova GA, Bogdanov AA, Wilson DN. Interplay between the Ribosomal Tunnel, Nascent Chain, and Macrolides Influences Drug Inhibition. ACTA ACUST UNITED AC 2010; 17:504-14. [DOI: 10.1016/j.chembiol.2010.04.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 03/22/2010] [Accepted: 04/02/2010] [Indexed: 12/01/2022]
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50
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András CD, Csajági C, Orbán CK, Albert C, Ábrahám B, Miklóssy I. A possible explanation of the germicide effect of carbon dioxide in supercritical state based on molecular-biological evidence. Med Hypotheses 2010; 74:325-9. [DOI: 10.1016/j.mehy.2009.08.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Accepted: 08/24/2009] [Indexed: 12/01/2022]
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