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Düzel A, Bora B, Özgen GÖ, Evran S. Selection of DNA aptamers for the aptamer-assisted magnetic capture of the purified xylanase from Aspergillus niger. Int J Biol Macromol 2024; 257:128540. [PMID: 38061523 DOI: 10.1016/j.ijbiomac.2023.128540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/12/2023] [Accepted: 11/30/2023] [Indexed: 01/26/2024]
Abstract
Xylanases are a group of enzymes that catalyze the hydrolysis of xylan. Xylanases have wide industrial applications, and they can produced by various organisms. In this study, we aimed to develop aptamers for the capture of xylanase produced by a wild-type Aspergillus niger strain. Xylanase was produced by Aspergillus niger in a 5-liter stirred-tank bioreactor and then purified by column chromatography. Magnetic bead-based SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was performed to select DNA aptamers specific to the purified xylanase. After nine rounds of selection, next-generation sequencing (NGS) analysis was performed. Four aptamers, namely AXYL-1, AXYL-2, AXYL-3, and AXYL-4, were identified for further characterization. The binding properties of the selected aptamers were characterized by fluorescence quenching (FQ) analysis and an enzyme-linked aptamer assay (ELAA). The Kd values were found to be in the low μM range. Then, each aptamer was immobilized on streptavidin-coated magnetic particles, and the recovery ratio of xylanase was determined. Although AXYL-1 wasn't effective, AXYL-2, AXYL-3, and AXYL-4 were proven to capture the xylanase. The maximum recovery rate of xylanase was found to be approximately 54 %.
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Affiliation(s)
- Ahmet Düzel
- Department of Bioengineering, Faculty of Engineering and Architecture, Sinop University, 57000 Sinop, Türkiye.
| | - Burhan Bora
- Department of Biochemistry, Faculty of Science, Ege University, 35100 İzmir, Türkiye
| | - Gaye Öngen Özgen
- Department of Bioengineering, Faculty of Engineering, Ege University, 35100 İzmir, Türkiye
| | - Serap Evran
- Department of Biochemistry, Faculty of Science, Ege University, 35100 İzmir, Türkiye
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Feng T, Liu J, Chen G, Wu L, Ren F, Yang Y, Zhu J, Shen F, Wang L, Chen Q. The fluorescent aptasensor based on CRISPR-Cas12a combined with TdT for highly sensitive detection of cocaine. Anal Bioanal Chem 2022; 414:7291-7297. [PMID: 36029324 DOI: 10.1007/s00216-022-04280-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/09/2022] [Indexed: 11/01/2022]
Abstract
Ultrasensitive and specific detection of cocaine is of great significance for monitoring cocaine abuse. Herein, a fluorescent aptasensor via coupling CRISPR-Cas12a, with magnetic nanoparticles (MNPs), split-aptamer, and terminal deoxynucleotidyl transferase (TdT), was developed for the detection of cocaine. In short, the complete cocaine aptamer is split into two parts, one is modified on magnetic nanoparticles (MNPs) and the other is free. The presence of cocaine will mediate the binding of these two segments. Then TdT will mediate the extension to form an ultra-long sequence that can bind with multiple CRISPR-Cas12a resulting in the trans-cleavage activity of CRISPR-Cas12a being triggered. Thence, the DNA reporter which is bi-labeled with fluorophore and quencher is cleaved resulting in the generation of a fluorescence signal. The developed fluorescent aptasensor realizes the detection of cocaine with excellent sensitivity and specificity. The detection limit is low down to 33 pM, and the linear range is from 330 to 1.65 × 105 pM. Most importantly, this fluorescent aptasensor can be successfully applied to the determination of cocaine in human plasma samples.
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Affiliation(s)
- Tao Feng
- Department of Anesthesiology, Affiliated Baoan Central Hospital of Guangdong Medical University, Shenzhen, 518101, China
| | - Jingjian Liu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, China
| | - Gong Chen
- Department of Anesthesiology, Affiliated Baoan Central Hospital of Guangdong Medical University, Shenzhen, 518101, China
| | - Lun Wu
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, China
| | - Fangling Ren
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, China
| | - Yang Yang
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Jing Zhu
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China
| | - Feng Shen
- Sinopharm Dongfeng General Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, China
| | - Linhai Wang
- Department of Pharmacy, Renmin Hospital, Hubei University of Medicine, Shiyan, 442008, Hubei, China.
| | - Qinhua Chen
- Shenzhen Baoan Authentic TCM Therapy Hospital, Shenzhen, 518101, China.
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Bulut H, Yuksel B, Gul M, Eren M, Karatas E, Kara N, Yilmazer B, Kocyigit A, Labrou NE, Binay B. Conserved Amino Acid Residues that Affect Structural Stability of Candida boidinii Formate Dehydrogenase. Appl Biochem Biotechnol 2020; 193:363-376. [PMID: 32974869 DOI: 10.1007/s12010-020-03429-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 09/18/2020] [Indexed: 10/23/2022]
Abstract
The NAD+-dependent formate dehydrogenase (FDH; EC 1.2.1.2) from Candida boidinii (CboFDH) has been extensively used in NAD(H)-dependent industrial biocatalysis as well as in the production of renewable fuels and chemicals from carbon dioxide. In the present work, the effect of amino acid residues Phe285, Gln287, and His311 on structural stability was investigated by site-directed mutagenesis. The wild-type and mutant enzymes (Gln287Glu, His311Gln, and Phe285Thr/His311Gln) were cloned and expressed in Escherichia coli. Circular dichroism (CD) spectroscopy was used to determine the effect of each mutation on thermostability. The results showed the decisive roles of Phe285, Gln287, and His311 on enhancing the enzyme's thermostability. The melting temperatures for the wild-type and the mutant enzymes Gln287Glu, His311Gln, and Phe285Thr/His311Gln were 64, 70, 77, and 73 °C, respectively. The effects of pH and temperature on catalytic activity of the wild-type and mutant enzymes were also investigated. Interestingly, the mutant enzyme His311Gln exhibits a large shift of pH optimum at the basic pH range (1 pH unit) and substantial increase of the optimum temperature (25 °C). The present work supports the multifunctional role of the conserved residues Phe285, Gln287, and His311 and further underlines their pivotal roles as targets in protein engineering studies.
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Affiliation(s)
- Huri Bulut
- Medical Biochemistry Department, Faculty of Medicine, Istinye University, 34010, Istanbul, Turkey.,Medical Biochemistry Department, School of Medicine, Bezmialem Vakif University, 34093, Istanbul, Turkey
| | - Busra Yuksel
- Molecular Biology and Genetics Department, Istanbul Technical University, 34467, Istanbul, Turkey
| | - Mehmet Gul
- Molecular Biology and Genetics Department, Istanbul Technical University, 34467, Istanbul, Turkey
| | - Meryem Eren
- Molecular Biology and Genetics Department, Istanbul Technical University, 34467, Istanbul, Turkey
| | - Ersin Karatas
- Molecular Biology and Genetics Department, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Nazli Kara
- Medical Biochemistry Department, Faculty of Medicine, Istinye University, 34010, Istanbul, Turkey
| | - Berin Yilmazer
- Molecular Biology and Genetics Department, Gebze Technical University, 41400, Kocaeli, Turkey
| | - Abdurrahim Kocyigit
- Medical Biochemistry Department, School of Medicine, Bezmialem Vakif University, 34093, Istanbul, Turkey
| | - Nikolaos E Labrou
- Laboratory of Enzyme Technology, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, Gr-11855, Athens, Greece
| | - Baris Binay
- Department of Bioengineering, Gebze Technical University, 41400, Kocaeli, Turkey.
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