1
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Lee M, Kang S, Kim S, Park N. Advances and Trends in miRNA Analysis Using DNAzyme-Based Biosensors. BIOSENSORS 2023; 13:856. [PMID: 37754090 PMCID: PMC10526965 DOI: 10.3390/bios13090856] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
miRNAs are endogenous small, non-coding RNA molecules that function in post-transcriptional regulation of gene expression. Because miRNA plays a pivotal role in maintaining the intracellular environment, and abnormal expression has been found in many cancer diseases, detection of miRNA as a biomarker is important for early diagnosis of disease and study of miRNA function. However, because miRNA is present in extremely low concentrations in cells and many types of miRNAs with similar sequences are mixed, traditional gene detection methods are not suitable for miRNA detection. Therefore, in order to overcome this limitation, a signal amplification process is essential for high sensitivity. In particular, enzyme-free signal amplification systems such as DNAzyme systems have been developed for miRNA analysis with high specificity. DNAzymes have the advantage of being more stable in the physiological environment than enzymes, easy to chemically synthesize, and biocompatible. In this review, we summarize and introduce the methods using DNAzyme-based biosensors, especially with regard to various signal amplification methods for high sensitivity and strategies for improving detection specificity. We also discuss the current challenges and trends of these DNAzyme-based biosensors.
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Affiliation(s)
- Minhyuk Lee
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea (S.K.)
| | - Seungjae Kang
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
| | - Sungjee Kim
- Department of Chemistry, Pohang University of Science and Technology, Pohang 37673, Republic of Korea (S.K.)
| | - Nokyoung Park
- Department of Chemistry and the Natural Science Research Institute, Myongji University, 116 Myongji-ro, Yongin-si 17058, Republic of Korea
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2
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Celebi Torabfam G, K. Demir G, Demir D. Quantum tunneling time delay investigation of [Formula: see text] ion in human telomeric G-quadruplex systems. J Biol Inorg Chem 2023; 28:213-224. [PMID: 36656371 PMCID: PMC9851595 DOI: 10.1007/s00775-022-01982-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/24/2022] [Indexed: 01/20/2023]
Abstract
Guanine-rich quadruplex DNA (G-quadruplex) is of interest both in cell biology and nanotechnology. Its biological functions necessitate a G-quadruplex to be stabilized against escape of the monovalent metal cations. The potassium ion ([Formula: see text]) is particularly important as it experiences a potential energy barrier while it enters and exits the G-quadruplex systems which are normally found in human telomere. In the present work, we analyzed the time it takes for the [Formula: see text] cations to get in and out of the G-quadruplex. Our time estimate is based on entropic tunneling time-a time formula which gave biologically relevant results for DNA point mutation by proton tunneling. The potential energy barrier experienced by [Formula: see text] ions is determined from a quantum mechanical simulation study, Schrodinger equation is solved using MATLAB, and the computed eigenfunctions and eigenenergies are used in the entropic tunneling time formula to compute the time delay and charge accumulation rate during the tunneling of [Formula: see text] in G-quadruplex. The computations have shown that ion tunneling takes picosecond times. In addition, average [Formula: see text] accumulation rate is found to be in the picoampere range. Our results show that time delay during the [Formula: see text] ion tunneling is in the ballpark of the conformational transition times in biological systems, and it could be an important parameter for understanding its biological role in human DNA as well as for the possible applications in biotechnology. To our knowledge, for the first time in the literature, time delay during the ion tunneling from and into G-quadruplexes is computed.
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Affiliation(s)
- Gizem Celebi Torabfam
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, 34956 Istanbul, Turkey
| | - Güleser K. Demir
- Department of Electrical and Electronics Engineering, Dokuz Eylül University, Buca, 35390 İzmir, Turkey
| | - Durmuş Demir
- Faculty of Engineering and Natural Sciences, Sabancı University, Tuzla, 34956 Istanbul, Turkey
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3
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Gorbenko DA, Shkodenko LA, Rubel MS, Slita AV, Nikitina EV, Martens EA, Kolpashchikov DM. DNA nanomachine for visual detection of structured RNA and double stranded DNA. Chem Commun (Camb) 2022; 58:5395-5398. [PMID: 35415727 DOI: 10.1039/d2cc00325b] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Visual detection of ssRNA and dsDNA amplicons was achieved at room temperature without the need for a probe-analyte annealing stage. This approach uses a DNA nanostructure equipped with two analyte-binding arms. Highly selective binding of the third arm leads to the formation of a G-quadruplex structure capable of changing the solution color.
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Affiliation(s)
- Daria A Gorbenko
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation. .,Ioffe Institute, 26 Politekhnicheskaya, St. Petersburg, 194021, Russian Federation
| | - Liubov A Shkodenko
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation.
| | - Maria S Rubel
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation.
| | - Aleksandr V Slita
- St. Petersburg Pasteur Institute, 14 Mira Str., St. Petersburg, 197101, Russian Federation
| | - Ekaterina V Nikitina
- Pediatric Research and Clinical Center for Infectious Diseases, 9 Prof. Popova Str, Saint Petersburg, 197022, Russian Federation
| | - Elvira A Martens
- Pediatric Research and Clinical Center for Infectious Diseases, 9 Prof. Popova Str, Saint Petersburg, 197022, Russian Federation
| | - Dmitry M Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials, SCAMT Institute, ITMO University, Saint-Petersburg, Russia, 9 Lomonosova Str., St. Petersburg, 191002, Russian Federation. .,Chemistry Department, University of Central Florida, 4000 Central Florida Blvd., Orlando, FL 32816, USA.,Burnett School of Biomedical Sciences, University of Central Florida, Orlando, Florida, USA.,National Center for Forensic Science, University of Central Florida, Orlando, FL, USA
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4
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Santiago-McRae E, Oh SW, Carlo AM, Bar O, Guan E, Zheng D, Grgicak C, Fu J. Rapid Nucleic Acid Reaction Circuits for Point-Of-Care Diseases Diagnosis. Curr Top Med Chem 2022; 22:686-698. [PMID: 35139798 DOI: 10.2174/1570163819666220207114148] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/28/2021] [Accepted: 01/05/2022] [Indexed: 11/22/2022]
Abstract
An urgent need exists for a rapid, cost-effective, facile, and reliable nucleic acid assay for mass screening to control and prevent the spread of emerging pandemic diseases. This urgent need is not fully met by current diagnostic tools. In this review, we summarize the current state-of-the-art research in novel nucleic acid amplification and detection that could be applied to point-of-care (POC) diagnosis and mass screening of diseases. The critical technological breakthroughs will be discussed for their advantages and disadvantages. Finally, we will discuss the future challenges of developing nucleic acid-based POC diagnosis.
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Affiliation(s)
| | - Sung Won Oh
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Anthony Monte Carlo
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Omri Bar
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | | | - Doris Zheng
- Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Catherine Grgicak
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
| | - Jinglin Fu
- Center for Computational and Integrative Biology,Camden, NJ 08102, USA.,Department of Chemistry and, Rutgers University-Camden, Camden, NJ 08102, USA
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5
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Antiviral Effects of 5-Aminolevulinic Acid Phosphate against Classical Swine Fever Virus: In Vitro and In Vivo Evaluation. Pathogens 2022; 11:pathogens11020164. [PMID: 35215109 PMCID: PMC8877771 DOI: 10.3390/pathogens11020164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/04/2023] Open
Abstract
The inhibitory effects of 5-aminolevulinic acid phosphate (5-ALA), an important amino acid for energy production in the host, against viral infections were previously reported. Here, the antiviral effects of 5-ALA against classical swine fever virus (CSFV) belonging to the genus Pestivirus in the Flaviviridae family and its possible mechanisms were investigated. CSFV replication was suppressed in swine cells supplemented with 5-ALA or its metabolite, protoporphyrin IX (PPIX). The infectivity titer of CSFV was decreased after mixing with PPIX extracellularly. In addition, the activities of the replication cycle were decreased in the presence of PPIX based on the CSFV replicon assay. These results showed that PPIX exerted antiviral effects by inactivating virus particles and inhibiting the replication cycle. To evaluate the in vivo efficacy of 5-ALA, pigs were supplemented daily with 5-ALA for 1 week before virus inoculation and then inoculated with a virulent CSFV strain at the 107.0 50% tissue culture infectious dose. The clinical scores of the supplemented group were significantly lower than those of the nonsupplemented group, whereas the virus growth was not. Taken together, 5-ALA showed antiviral effects against CSFV in vitro, and PPIX played a key role by inactivating virus particles extracellularly and inhibiting the replication cycle intracellularly.
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Zhang Y, Ma X, Zhang J, Luo F, Wang W, Cui X. Design of a High-Sensitivity Dimeric G-Quadruplex/Hemin DNAzyme Biosensor for Norovirus Detection. Molecules 2021; 26:7352. [PMID: 34885931 PMCID: PMC8659037 DOI: 10.3390/molecules26237352] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 11/16/2022] Open
Abstract
G-quadruplexes can bind with hemin to form peroxidase-like DNAzymes that are widely used in the design of biosensors. However, the catalytic activity of G-quadruplex/hemin DNAzyme is relatively low compared with natural peroxidase, which hampers its sensitivity and, thus, its application in the detection of nucleic acids. In this study, we developed a high-sensitivity biosensor targeting norovirus nucleic acids through rationally introducing a dimeric G-quadruplex structure into the DNAzyme. In this strategy, two separate molecular beacons each having a G-quadruplex-forming sequence embedded in the stem structure are brought together through hybridization with a target DNA strand, and thus forms a three-way junction architecture and allows a dimeric G-quadruplex to form, which, upon binding with hemin, has a synergistic enhancement of catalytic activities. This provides a high-sensitivity colorimetric readout by the catalyzing H2O2-mediated oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline -6-sulfonic acid) diammonium salt (ABTS). Up to 10 nM of target DNA can be detected through colorimetric observation with the naked eye using our strategy. Hence, our approach provides a non-amplifying, non-labeling, simple-operating, cost-effective colorimetric biosensing method for target nucleic acids, such as norovirus-conserved sequence detection, and highlights the further implication of higher-order multimerized G-quadruplex structures in the design of high-sensitivity biosensors.
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Affiliation(s)
- Yun Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Xinao Ma
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Jingtian Zhang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
| | - Feixian Luo
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
| | - Wenshu Wang
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
| | - Xiaojie Cui
- College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; (Y.Z.); (X.M.); (J.Z.); (F.L.); (W.W.)
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing 100081, China
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7
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Chen X, Wang L, He F, Chen G, Bai L, He K, Zhang F, Xu X. Label-Free Colorimetric Method for Detection of Vibrio parahaemolyticus by Trimming the G-Quadruplex DNAzyme with CRISPR/Cas12a. Anal Chem 2021; 93:14300-14306. [PMID: 34645259 DOI: 10.1021/acs.analchem.1c03468] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Vibrio parahaemolyticus (V. parahaemolyticus), which may cause gastrointestinal disorders in humans, is a pathogen commonly found in seafood. There are many methods for detecting V. parahaemolyticus, yet they have some shortcomings, such as high cost, labor-intensiveness, and complicated operation, which are impractical for resource-limited settings. Herein, we present a sequence-specific, label-free, and colorimetric method for visual detection of V. parahaemolyticus. This method utilizes CRISPR/Cas12a to specifically recognize the loop-mediated isothermal amplification (LAMP) products for further trans-cleaving the G-quadruplex DNAzyme and depriving its peroxidase-mimicking activity. In this way, the results can be directly observed with the naked eyes via the color development of 2,2'-azino-di-(3-ethylbenzthiazoline-6-sulfonic acid) (ABTS2-), which displays colorless for positive samples while green for target-free samples. We term such Cas12a-crRNA preventing ABTS2- from developing color by trimming the G-quadruplex DNAzyme as Cascade. The proposed method can detect 9.8 CFU (per reaction) of pure cultured V. parahaemolyticus, and the sensitivity is comparable to real-time LAMP. It has been applied for practical use and showed the capability to detect 6.1 × 102 CFU/mL V. parahaemolyticus in shrimp samples. Based on this, the newly established Cascade method can be employed as a universal biosensing strategy for pathogenic bacterial testing in the field.
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Affiliation(s)
- Xueyun Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Liu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fang He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Ganghui Chen
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Linlin Bai
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China.,State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Kaiyu He
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou 350108, China
| | - Xiahong Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products; Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs; Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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8
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Comparison of Duplex and Quadruplex Folding Structure Adenosine Aptamers for Carbon Nanotube Field Effect Transistor Aptasensors. NANOMATERIALS 2021; 11:nano11092280. [PMID: 34578596 PMCID: PMC8468449 DOI: 10.3390/nano11092280] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 12/24/2022]
Abstract
Carbon nanotube field effect transistor (CNT FET) aptasensors have been investigated for the detection of adenosine using two different aptamer sequences, a 35-mer and a 27-mer. We found limits of detection for adenosine of 100 pM and 320 nM for the 35-mer and 27-mer aptamers, with dissociation constants of 1.2 nM and 160 nM, respectively. Upon analyte recognition the 35-mer adenosine aptamer adopts a compact G-quadruplex structure while the 27-mer adenosine aptamer changes to a folded duplex. Using the CNT FET aptasensor platform adenosine could be detected with high sensitivity over the range of 100 pM to 10 µM, highlighting the suitability of the CNT FET aptasensor platform for high performance adenosine detection. The aptamer restructuring format is critical for high sensitivity with the G-quadraplex aptasensor having a 130-fold smaller dissociation constant than the duplex forming aptasensor.
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9
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Li T, Hu R, Xia J, Xu Z, Chen D, Xi J, Liu BF, Zhu J, Li Y, Yang Y, Liu M. G-triplex: A new type of CRISPR-Cas12a reporter enabling highly sensitive nucleic acid detection. Biosens Bioelectron 2021; 187:113292. [PMID: 33991961 DOI: 10.1016/j.bios.2021.113292] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/19/2021] [Accepted: 04/27/2021] [Indexed: 12/20/2022]
Abstract
CRISPR-Cas12a (Cpf1) trans-cleaves ssDNA and this feature has been widely harnessed for nucleic acid detection. Herein, we introduce a new type of Cas12a reporter, G-triplex (G3), and a highly sensitive biosensor termed G-CRISPR. We proved that Cas12a trans-cleaves G3 structures in about 10 min and G3 can serve as an excellent reporter based on the cleavage-induced high-order structure disruption. G3 reporter improves the analytical sensitivity up to 20 folds, enabling the detection of unamplified and amplified DNA as low as 50 pmol and 0.1 amol (one copy/reaction), respectively. G-CRISPR has been utilized for the analysis of 27 PCR-amplified patient samples with HPV infection risk based on both fluorescence and lateral flow assays, resulting in 100% concordance between the two. In comparison with the clinical results, it achieved overall specificity and sensitivity of 100% and 94.7%, respectively. These results suggest that G-CRISPR can serve as a rapid, sensitive, and reliable biosensor, and could further expand the CRISPR toolbox in biomedical diagnostics.
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Affiliation(s)
- Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jianbo Xia
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Zhichen Xu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Dongjuan Chen
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Jinou Xi
- Department of Laboratory Medicine, Maternal and Child Health Hospital of Hubei Province, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China; University of Chinese Academy of Sciences, Beijing, 10049, China.
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10
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Abstract
This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.
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Affiliation(s)
- Erin M McConnell
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4K1, Canada.
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11
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Small Molecule Receptor Binding Inhibitors with In Vivo Efficacy against Botulinum Neurotoxin Serotypes A and E. Int J Mol Sci 2021; 22:ijms22168577. [PMID: 34445283 PMCID: PMC8395308 DOI: 10.3390/ijms22168577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/04/2021] [Accepted: 08/05/2021] [Indexed: 12/20/2022] Open
Abstract
Botulinum neurotoxins (BoNTs) are the most poisonous substances in nature. Currently, the only therapy for botulism is antitoxin. This therapy suffers from several limitations and hence new therapeutic strategies are desired. One of the limitations in discovering BoNT inhibitors is the absence of an in vitro assay that correlates with toxin neutralization in vivo. In this work, a high-throughput screening assay for receptor-binding inhibitors against BoNT/A was developed. The assay is composed of two chimeric proteins: a receptor-simulating protein, consisting of the fourth luminal loop of synaptic vesicle protein 2C fused to glutathione-S-transferase, and a toxin-simulating protein, consisting of the receptor-binding domain of BoNT/A fused to beta-galactosidase. The assay was applied to screen the LOPAC1280 compound library. Seven selected compounds were evaluated in mice exposed to a lethal dose of BoNT/A. The compound aurintricarboxylic acid (ATA) conferred 92% protection, whereas significant delayed time to death (p < 0.005) was observed for three additional compounds. Remarkably, ATA was also fully protective in mice challenged with a lethal dose of BoNT/E, which also uses the SV2 receptor. This study demonstrates that receptor-binding inhibitors have the potential to serve as next generation therapeutics for botulism, and therefore the assay developed may facilitate discovery of new anti-BoNT countermeasures.
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12
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Highly-sensitive and fast detection of human telomeric G-Quadruplex DNA based on a hemin-conjugated fluorescent metal-organic framework platform. Biosens Bioelectron 2021; 178:112999. [PMID: 33493897 DOI: 10.1016/j.bios.2021.112999] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/06/2021] [Accepted: 01/10/2021] [Indexed: 02/02/2023]
Abstract
The formation of G-quadruplex (G4) structures in Human telomeric DNA (H-Telo) has been demonstrated to inhibit the activity of telomerase enzyme that is associated with the proliferation of many cancer cells. Accordingly, G-quadruplex structures have become one of the well-established targets in anticancer therapeutic strategies. And, the development of simple and selective detection platforms for G4 structures has become a significant focus of research in recent years. In this study, a simple "off-on" fluorometric method was developed for the selective detection of picomolar quantities of H-Telo G4 DNA based on a fluorescent cerium-based metal organic framework (Ce-MOF) conjugated with hemin to form the sensing probe, Hemin@Ce-MOF. The solvothermal synthesis of the Ce-MOF took advantage of 5-aminoisophtlalic acid (5AIPA) as the organic bridging ligand, (Ce2(5AIPA)3(DMF)2). Characterization of Ce-MOF and Hemin@Ce-MOF was performed by XRD, XPS, TEM, SEM, BET and FTIR techniques. The detection and quantification of the H-Telo was carried out through the adsorption/incorporation of hemin molecules on the pores and surface of Ce-MOF resulting in the fluorescent quenching of the system followed by the restoration of the fluorescence upon addition of H-Telo probably due to a competition between H-Telo and Ce-MOF to bind to hemin. The impact of the key variables including MOF quantity, hemin concentration and detection time was investigated and optimized. Under the optimized conditions, the developed probe provides a limit of detection (LOD) of 665 pM, linear dynamic range (LDR) of 1.6-39.7 nM and excellent selectivity towards H-Telo. Taken together, these results present a simple, novel and superior platform for the selective detection of H-Telo G4 DNA.
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Kovtunov EA, Shkodenko LA, Goncharova EA, Nedorezova DD, Sidorenko SV, Koshel EI, Kolpashchikov DM. Towards Point of Care Diagnostics: Visual Detection of Meningitis Pathogens Directly from Cerebrospinal Fluid. ChemistrySelect 2020. [DOI: 10.1002/slct.202003869] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Evgeny A. Kovtunov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Liubov A. Shkodenko
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Ekaterina A. Goncharova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- Saint-Petersburg Pasteur Institute Mira st.14, St. Petersburg 197101 Russian Federation
| | - Daria D. Nedorezova
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Sergey V. Sidorenko
- Department of Medical Microbiology and Molecular Epidemiology Pediatric Research and Clinical Center for Infectious Diseases Saint Petersburg 197022 Russian Federation
- North Western State Medical University named after I.I. Mechnikov Kirochnaya Str. 41, St. Petersburg Russia 191015
| | - Elena I. Koshel
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
| | - Dmitry M. Kolpashchikov
- Laboratory of Molecular Robotics and Biosensor Materials Chemistry Department SCAMT Institute ITMO University 9 Lomonosova Str. Saint Petersburg 191002 Russian Federation
- University of Central Florida Chemistry Department 4111 Libra Drive, Physical Sciences 255 Orlando FL USA 32816-2366
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14
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Platform- and label-free detection of lead ions in environmental and laboratory samples using G-quadraplex probes by circular dichroism spectroscopy. Sci Rep 2020; 10:20461. [PMID: 33235290 PMCID: PMC7686487 DOI: 10.1038/s41598-020-77449-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/13/2020] [Indexed: 12/15/2022] Open
Abstract
Guanine-rich quadruplex (G-QD) are formed by conversion of nucleotides with specific sequences by stabilization of positively charged K+ or Na+. These G-QD structures differentially absorb two-directional (right- and left-handed) circularly polarized light, which can discriminate the parallel or anti-parallel structures of G-QDs. In this study, G-QDs stabilized by Pb2+ were analyzed by a circular dichroism (CD) spectroscopy to determine Pb2+ concentration in water samples. Thrombin aptamer (TBA), PS2.M, human telomeric DNA (HTG), AGRO 100, and telomeric related sequence (T2) were studied to verify their applicability as probes for platform- and label-free detection of Pb2+ in environmental as well as laboratory samples. Among these nucleotides, TBA and PS2.M exhibited higher binding constants for Pb2+, 1.20-2.04 × 106/M at and 4.58 × 104-1.09 × 105/M at 100 micromolar and 100 mM K+ concentration, respectively. They also exhibited excellent selectivity for Pb2+ than for Al3+, Cu2+, Ni2+, Fe3+, Co2+, and Cr2+. When Pb2+ was spiked into an effluent sample from a wastewater treatment plant (WWTP), its existence was detected by CD spectroscopy following a simple addition of TBA or PS2.M. By the addition of TBA and PS2.M, the Pb2+ signals were observed in effluent samples over 0.5 micromolar (100 ppb) concentration. Furthermore, PS2.M caused a Pb2+-specific absorption band in the effluent sample without spiking of Pb2+, and could be induced to G-QD structure by the background Pb2+ concentration in the effluent, 0.159 micromolar concentration (3.30 ppb). Taken together, we propose that TBA and PS2.M are applicable as platform- and label-free detection probes for monitoring Pb2+ in environmental samples such as discharged effluent from local WWTPs, using CD spectroscopy.
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15
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Li Y, Li T, Liu BF, Hu R, Zhu J, He T, Zhou X, Li C, Yang Y, Liu M. CRISPR-Cas12a trans-cleaves DNA G-quadruplexes. Chem Commun (Camb) 2020; 56:12526-12529. [PMID: 32966423 DOI: 10.1039/d0cc05540a] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
We for the first time report that the activated CRISPR-Cas12a system trans-cleaves DNA G-quadruplexes (G4). The cleavage activity on human telomere G4 and TBA G4 was investigated and verified by FRET, CD, gel electrophoresis and NMR. We believe that this finding will pave a new avenue for advancing the applications of CRISPR-Cas12a and G4 in biosensing and biochemistry.
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Affiliation(s)
- Ying Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Tao Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Bi-Feng Liu
- The Key Laboratory for Biomedical Photonics of MOE at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Rui Hu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Jiang Zhu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China.
| | - Ting He
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China.
| | - Xin Zhou
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Conggang Li
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Yunhuang Yang
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
| | - Maili Liu
- State Key Laboratory of Magnetic Resonance and Atomic Molecular Physics, Wuhan National Laboratory for Optoelectronics, National Centre for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences - Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430071, China. and University of Chinese Academy of Sciences, Beijing, 10049, China
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16
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Nishio T, Sugino K, Yoshikawa Y, Matsumoto M, Oe Y, Sadakane K, Yoshikawa K. K+ promotes the favorable effect of polyamine on gene expression better than Na. PLoS One 2020; 15:e0238447. [PMID: 32881909 PMCID: PMC7470421 DOI: 10.1371/journal.pone.0238447] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/10/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Polyamines are involved in a wide variety of biological processes including a marked effect on the structure and function of DNA. During our study on the interaction of polyamines with DNA, we found that K+ enhanced in vitro gene expression in the presence of polyamine more strongly than Na+. Thus, we sought to clarify the physico-chemical mechanism underlying this marked difference between the effects of K+ and Na+. PRINCIPAL FINDINGS It was found that K+ enhanced gene expression in the presence of spermidine, SPD(3+), much more strongly than Na+, through in vitro experiments with a Luciferase assay on cell extracts. Single-DNA observation by fluorescence microscopy showed that Na+ prevents the folding transition of DNA into a compact state more strongly than K+. 1H NMR measurement revealed that Na+ inhibits the binding of SPD to DNA more strongly than K+. Thus, SPD binds to DNA more favorably in K+-rich medium than in Na+-rich medium, which leads to favorable conditions for RNA polymerase to access DNA by decreasing the negative charge. CONCLUSION AND SIGNIFICANCE We found that Na+ and K+ exhibit markedly different effects through competitive binding with a cationic polyamine, SPD, to DNA, which causes a large difference in the higher-order structure of genomic DNA. It is concluded that the larger favorable effect of Na+ than K+ on in vitro gene expression observed in this study is well attributable to the significant difference between Na+ and K+ on the competitive binding inducing conformational transition of DNA.
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Affiliation(s)
- Takashi Nishio
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kaito Sugino
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | | | - Yohei Oe
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Koichiro Sadakane
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan
- Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan
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17
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18
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Peeters B, Safdar S, Daems D, Goos P, Spasic D, Lammertyn J. Solid-Phase PCR-Amplified DNAzyme Activity for Real-Time FO-SPR Detection of the MCR-2 Gene. Anal Chem 2020; 92:10783-10791. [PMID: 32638586 DOI: 10.1021/acs.analchem.0c02241] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The polymerase chain reaction (PCR) has been the gold standard molecular analysis technique for decades and has seen quite some evolution in terms of reaction components, methodology, and readout mechanisms. Nucleic acid enzymes (NAzymes) have been used to further exploit the applications of PCR, but so far the work was limited to the colorimetric G-quadruplex or fluorescent substrate cleaving NAzymes. In this study, a solid-phase, fiber optic surface plasmon resonance (FO-SPR) technique is presented as an alternative readout for PCR utilizing NAzymes. First, the surface cleavage activity of DNAzyme-extended amplicons (DNAzyme-amps) is established, followed by optimization of the PCR conditions, which are required for compatibility with the FO-SPR system. Next, by integrating the complement of a 10-23 DNAzyme into the primer pair, PCR-amplified DNAzyme-amps were generated, tested, and validated on qPCR for the detection of the antimicrobial resistance gene MCR-2. Once validated, this primer concept was developed as a one-step assay, driven by PCR-amplified DNAzymes, for FO-SPR-based sensitive and specific detection. Using gold nanoparticle labeled RNA-DNA hybrid strands as substrate for the DNAzyme, PCR-amplified DNAzyme-amps generated in the presence of MCR-2 gene were monitored in real-time, which resulted in an experimental limit of detection of 4 × 105 copy numbers or 6.6 fM. In addition, the DNAzyme-based FO-PCR assay was able to discriminate between the MCR-1 and MCR-2 genes, to further prove the specificity of this assay. Henceforth, this DNAzyme-based fiber optic PCR assay provides a universally applicable, real-time system for the detection of virtually any target NA, in a specific and sensitive manner.
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Affiliation(s)
- Bernd Peeters
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Saba Safdar
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Devin Daems
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Peter Goos
- Department of Biosystems, Biostatistics Group, KU Leuven, Kasteelpark Arenberg 30, Leuven B-3001, Belgium
| | - Dragana Spasic
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
| | - Jeroen Lammertyn
- Department of Biosystems, Biosensors Group, KU Leuven, Willem de Croylaan 42, Leuven B-3001, Belgium
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19
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Price DA, Kartje ZJ, Hughes JA, Hill TD, Loth TM, Watts JK, Gagnon KT, Moran SD. Infrared Spectroscopy Reveals the Preferred Motif Size and Local Disorder in Parallel Stranded DNA G-Quadruplexes. Chembiochem 2020; 21:2792-2804. [PMID: 32372560 DOI: 10.1002/cbic.202000136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 05/04/2020] [Indexed: 12/23/2022]
Abstract
Infrared spectroscopy detects the formation of G-quadruplexes in guanine-rich nucleic acid sequences through shifts in the guanine C=O stretch mode. Here, we use ultrafast 2D infrared (IR) spectroscopy and isotope substitution to show that these shifts arise from vibrational delocalization among stacked G-quartets. This provides a direct measure of the sizes of locally ordered motifs in heterogeneous samples with substantial disordered regions. We find that parallel-stranded, potassium-bound DNA G-quadruplexes are limited to five consecutive G-quartets and 3-4 consecutive layers are preferred for longer polyguanine tracts. The resulting potassium-dependent G-quadruplex assembly landscape reflects the polyguanine tract lengths found in genomes, the ionic conditions prevalent in healthy mammalian cells, and the onset of structural disorder in disease states. Our study describes spectral markers that can be used to probe other G-quadruplex structures and provides insight into the fundamental limits of their formation in biological and artificial systems.
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Affiliation(s)
- David A Price
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Joanna A Hughes
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Tayler D Hill
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Taylor M Loth
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Jonathan K Watts
- RNA Therapeutics Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA.,Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, 1245 Lincoln Drive, Carbondale, IL 62901, USA
| | - Sean D Moran
- Department of Chemistry and Biochemistry, Southern Illinois University Carbondale, 1245 Lincoln Drive, Carbondale, IL 62901, USA
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20
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Sitte E, Senge MO. The Red Color of Life Transformed - Synthetic Advances and Emerging Applications of Protoporphyrin IX in Chemical Biology. European J Org Chem 2020; 2020:3171-3191. [PMID: 32612451 PMCID: PMC7319466 DOI: 10.1002/ejoc.202000074] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Indexed: 01/10/2023]
Abstract
Protoporphyrin IX (PPIX) is the porphyrin scaffold of heme b, a ubiquitous prosthetic group of proteins responsible for oxygen binding (hemoglobin, myoglobin), electron transfer (cytochrome c) and catalysis (cytochrome P450, catalases, peroxidases). PPIX and its metallated derivatives frequently find application as therapeutic agents, imaging tools, catalysts, sensors and in light harvesting. The vast toolkit of accessible porphyrin functionalization reactions enables easy synthetic modification of PPIX to meet the requirements for its multiple uses. In the past few years, particular interest has arisen in exploiting the interaction of PPIX and its synthetic derivatives with biomolecules such as DNA and heme-binding proteins to evolve molecular devices with new functions as well as to uncover potential therapeutic toeholds. This review strives to shine a light on the most recent developments in the synthetic chemistry of PPIX and its uses in selected fields of chemical biology.
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Affiliation(s)
- Elisabeth Sitte
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
| | - Mathias O. Senge
- School of ChemistryTrinity College DublinThe University of DublinTrinity Biomedical Sciences Institute152‐160 Pearse Street2DublinIreland
- Institute for Advanced Study (TUM‐IAS)Technische Universität MünchenLichtenberg‐Str. 2a85748GarchingGermany
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21
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Su Y, Edwards PJB, Stetsenko DA, Filichev VV. The Importance of Phosphates for DNA G-Quadruplex Formation: Evaluation of Zwitterionic G-Rich Oligodeoxynucleotides. Chembiochem 2020; 21:2455-2466. [PMID: 32281223 DOI: 10.1002/cbic.202000110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/09/2020] [Indexed: 12/21/2022]
Abstract
A quaternary ammonium butylsulfonyl phosphoramidate group (N+) was designed to replace all the phosphates in a G-rich oligodeoxynucleotide d(TG4 T), resulting in a formally charge-neutral zwitterionic N+TG4 T sequence. We evaluated the effects of N+phosphate modifications on the structural, thermodynamic and kinetic properties of the parallel G-quadruplexes (G4) formed by TG4 T and compared them to the properties of the recently published phosphoryl guanidine d(TG4 T) (PG-TG4 T). Using size-exclusion chromatography, we established that, unlike PG-TG4 T, which exists as a mixture of complexes of different molecularity in solution, N+TG4 T forms an individual tetramolecular complex. In contrast to PG modifications that destabilized G4s, the presence of N+ modifications increased thermal stability relative to unmodified [d(TG4 T)]4 . The initial stage of assembly of N+TG4 T proceeded faster in the presence of Na+ than K+ ions and, similarly to PG-TG4 T, was independent of the salt concentration. However, after complex formation exceeded 75 %, N+TG4 T in solution with Na+ showed slower association than with K+ . N+TG4 T could also form G4s in solution with Li+ ions at a very low strand concentration (10 μM); something that has never been reported for the native d(TG4 T). Charge-neutral PG-G4s can invade preformed native G4s, whereas no invasion was observed between N+and native G4s, possibly due to the increased thermal stability of [N+TG4 T]4 . The N+ modification makes d(TG4 T) fully resistant to enzymatic digestion, which could be useful for intracellular application of N+-modified DNA or RNA.
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Affiliation(s)
- Yongdong Su
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Patrick J B Edwards
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand
| | - Dmitry A Stetsenko
- Novosibirsk State University, 2 Pirogov Street, Novosibirsk, 630090, Russia.,Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 10 Lavrentiev Avenue, Novosibirsk, 630090, Russia
| | - Vyacheslav V Filichev
- School of Fundamental Sciences, Massey University, Private Bag 11-222, 4442, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, Auckland, 1142, New Zealand
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22
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Wang J, Cheng M, Chen J, Ju H, Monchaud D, Mergny JL, Zhou J. An oxidatively damaged G-quadruplex/hemin DNAzyme. Chem Commun (Camb) 2020; 56:1839-1842. [PMID: 31950946 DOI: 10.1039/c9cc09237d] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Oxidative damage of guanine to 8-oxoguanine triggers a partial and variable loss of G-quadruplex/hemin DNAzyme activity and provides clues to the mechanistic origins of DNAzyme deactivation, which originates from an interplay between decreased G-quadruplex stability, lower hemin affinity and a modification of the nature of hemin binding sites.
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Affiliation(s)
- Jiawei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Mingpan Cheng
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Jielin Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Huangxian Ju
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - David Monchaud
- Institut de Chimie Moléculaire, Université de Bourgogne (ICMUB), CNRS UMR6302, UBFC Dijon 21000, France
| | - Jean-Louis Mergny
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
| | - Jun Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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23
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Structural Features of Nucleoprotein CST/Shelterin Complex Involved in the Telomere Maintenance and Its Association with Disease Mutations. Cells 2020; 9:cells9020359. [PMID: 32033110 PMCID: PMC7072152 DOI: 10.3390/cells9020359] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/29/2022] Open
Abstract
Telomere comprises the ends of eukaryotic linear chromosomes and is composed of G-rich (TTAGGG) tandem repeats which play an important role in maintaining genome stability, premature aging and onsets of many diseases. Majority of the telomere are replicated by conventional DNA replication, and only the last bit of the lagging strand is synthesized by telomerase (a reverse transcriptase). In addition to replication, telomere maintenance is principally carried out by two key complexes known as shelterin (TRF1, TRF2, TIN2, RAP1, POT1, and TPP1) and CST (CDC13/CTC1, STN1, and TEN1). Shelterin protects the telomere from DNA damage response (DDR) and regulates telomere length by telomerase; while, CST govern the extension of telomere by telomerase and C strand fill-in synthesis. We have investigated both structural and biochemical features of shelterin and CST complexes to get a clear understanding of their importance in the telomere maintenance. Further, we have analyzed ~115 clinically important mutations in both of the complexes. Association of such mutations with specific cellular fault unveils the importance of shelterin and CST complexes in the maintenance of genome stability. A possibility of targeting shelterin and CST by small molecule inhibitors is further investigated towards the therapeutic management of associated diseases. Overall, this review provides a possible direction to understand the mechanisms of telomere borne diseases, and their therapeutic intervention.
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24
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An ultrasensitive electrochemical DNA sensing strategy free from pre-immobilization via G-quadruplex based homogenous proximity hybridization. Talanta 2019; 210:120628. [PMID: 31987201 DOI: 10.1016/j.talanta.2019.120628] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 12/02/2019] [Accepted: 12/07/2019] [Indexed: 01/10/2023]
Abstract
Motivated by the desire for simple, rapid and highly sensitive DNA detection, we presented a signal-on electrochemical DNA (E-DNA) sensing strategy utilizing cooperative proximity hybridization based on a G-quadruplex (G4) probe labeled with the SH, which could specifically hybridize with its target DNA in homogenous solution. In the presence of target DNA, proximity hybridization was triggered to form a Y-shaped complex and the SH was released from G4 probe stem, companied by chemisorption on the electrode surface through Au-S binding when applied a positive potential, which brought Fc labeled on the signal probe close to the electrode surface. Thus, electrochemical signal dramatically increased, ensuring the highly sensitive "signal-on" assay. Such an E-DNA sensing strategy allows for ultrasensitive DNA detection with a detection limit as low as 2.82 × 10-15 M and a wide linear response from 1.0 × 10-9 to 1.0 × 10-15 M. In addition, the powerful discriminating ability of the mismatched DNA from the perfect matched target DNA was also demonstrated. More importantly, this homogenous proximity hybridization strategy could expand to colorimetric assay by incorporating G4 probe with hemin to form DNAzyme, which could effectively catalyze ABTS to generate a visual color change. Taking the joint advantages of G4 stem-loop probe and homogenous proximity hybridization, this sensing strategy exhibits greatly enhanced sensitivity and excellent specificity, making it a promising strategy for point-of-care testing.
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