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Chen K, Zhu L, Li J, Zhang Y, Yu Y, Wang X, Wei W, Huang K, Xu W. High-content tailoring strategy to improve the multifunctionality of functional nucleic acids. Biosens Bioelectron 2024; 261:116494. [PMID: 38901394 DOI: 10.1016/j.bios.2024.116494] [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: 05/08/2024] [Revised: 05/30/2024] [Accepted: 06/11/2024] [Indexed: 06/22/2024]
Abstract
Functional nucleic acids (FNAs) have attracted increasing attention in recent years due to their diverse physiological functions. The understanding of their conformational recognition mechanisms has advanced through nucleic acid tailoring strategies and sequence optimization. With the development of the FNA tailoring techniques, they have become a methodological guide for nucleic acid repurposing. Therefore, it is necessary to systematize the relationship between FNA tailoring strategies and the development of nucleic acid multifunctionality. This review systematically categorizes eight types of FNA multifunctionality, and introduces the traditional FNA tailoring strategy from five aspects, including deletion, substitution, splitting, fusion and elongation. Based on the current state of FNA modification, a new generation of FNA tailoring strategy, called the high-content tailoring strategy, was unprecedentedly proposed to improve FNA multifunctionality. In addition, the multiple applications of rational tailoring-driven FNA performance enhancement in various fields were comprehensively summarized. The limitations and potential of FNA tailoring and repurposing in the future are also explored in this review. In summary, this review introduces a novel tailoring theory, systematically summarizes eight FNA performance enhancements, and provides a systematic overview of tailoring applications across all categories of FNAs. The high-content tailoring strategy is expected to expand the application scenarios of FNAs in biosensing, biomedicine and materials science, thus promoting the synergistic development of various fields.
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Affiliation(s)
- Keren Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Jie Li
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Yongxia Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China
| | - Xiaofu Wang
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Wei Wei
- Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Kunlun Huang
- Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing, 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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2
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Wang Y, Xiong Y, Shi K, Effah CY, Song L, He L, Liu J. DNA nanostructures for exploring cell-cell communication. Chem Soc Rev 2024; 53:4020-4044. [PMID: 38444346 DOI: 10.1039/d3cs00944k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability. Herein, this review is dedicated to offering a new perspective on using DNA nanostructures to explore the progress of cell-cell communication. After briefly outlining the anchoring strategy of DNA nanostructures on cell membranes and the subsequent dynamic regulation of DNA nanostructures, this paper highlights the significant contribution of DNA nanostructures in monitoring cell-cell communication and regulating its interactions. Finally, we provide a quick overview of the current challenges and potential directions for the application of DNA nanostructures in cellular communication and interactions.
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Affiliation(s)
- Ya Wang
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Yamin Xiong
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Kangqi Shi
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Clement Yaw Effah
- The First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, Zhengzhou 450003, China
| | - Lulu Song
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Leiliang He
- College of Public Health, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianbo Liu
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha 410082, China.
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Wu Y, Liang R, Chen W, Wang C, Xing D. The development of biosensors for alkaline phosphatase activity detection based on a phosphorylated DNA probe. Talanta 2024; 270:125622. [PMID: 38215586 DOI: 10.1016/j.talanta.2024.125622] [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: 09/15/2023] [Revised: 12/21/2023] [Accepted: 01/03/2024] [Indexed: 01/14/2024]
Abstract
Alkaline phosphatase (ALP) is a zinc-containing metalloprotein that shows very great significance in clinical diagnosis, which can catalyze the hydrolysis of phosphorylated species. ALP has the potential to serve as a valuable biomarker for detecting liver dysfunction and bone diseases. On the other hand, ALP is an efficient biocatalyst to amplify detection signals in the enzyme-linked assay. It has always been a major research focus to develop novel biosensors that can detect ALP activity with high selectivity and sensitivity. There have been numerous reports on the development of biosensors to determine ALP activity using a phosphorylated DNA probe. Among them, various beneficial strategies, such as λ exonuclease-mediated cleavage reaction, terminal deoxynucleotidyl transferase-triggered DNA polymerization, and Klenow fragment polymerase-catalyzed elongation, are employed to generate amplified and more intuitive signal. This review discusses and summarizes the development and advances of biosensors for ALP activity detection that use a well-designed phosphorylated DNA probe, aiming to provide some guidelines for the design of more sophisticated sensing strategies that exhibit improved sensitivity, selectivity, and adaptability in detecting ALP activity.
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Affiliation(s)
- Yudong Wu
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China
| | - Rongxiang Liang
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Wujun Chen
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China
| | - Chao Wang
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China.
| | - Dongming Xing
- The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China.
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Xu X, Li T, Liu Y, Zhou L, Li Y, Luo Y, Xu Y, Zhao L, Song W, Jiang D, He P, Zhou H. Engineering Assembly of Plasmonic Virus-Like Gold SERS Nanoprobe Guided by Intelligent Dual-Machine Nanodevice for High-Performance Analysis of Tetracycline. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2309502. [PMID: 38282176 DOI: 10.1002/smll.202309502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/10/2024] [Indexed: 01/30/2024]
Abstract
Accurate detection of trace tetracyclines (TCs) in complex matrices is of great significance for food and environmental safety monitoring. However, traditional recognition and amplification tools exhibit poor specificity and sensitivity. Herein, a novel dual-machine linkage nanodevice (DMLD) is proposed for the first time to achieve high-performance analysis of TC, with a padlock aptamer component as the initiation command center, nucleic acid-encoded multispike virus-like Au nanoparticles (nMVANs) as the signal indicator, and cascade walkers circuit as the processor. The existence of spike vertices and interspike nanogaps in MVANs enables intense electromagnetic near-field focusing, allowing distinct surface-enhanced Raman scattering (SERS) activity. Moreover, through the sequential activation between multistage walker catalytic circuits, the DLMD system converts the limited TC recognition into massive engineering assemblies of SERS probes guided by DNA amplicons, resulting in synergistic enhancement of bulk plasmonic hotspot entities. The continuously guaranteed target recognition and progressively promoted signal enhancement ensure highly specific amplification analysis of TC, with a detection limit as low as 7.94 × 10-16 g mL-1 . Furthermore, the reliable recoveries in real samples confirm the practicability of the proposed sensing platform, highlighting the enormous potential of intelligent nanomachines for analyzing the trace hazards in the environment and food.
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Affiliation(s)
- Xinlin Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Tiantian Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Yue Liu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Luxiao Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Yingying Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Yu Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Yang Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Lin Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Weiling Song
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Degang Jiang
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Peng He
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
| | - Hong Zhou
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Ministry of Education, Shandong Key Laboratory of Biochemical Analysis, and College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology, Qingdao, 266042, P. R. China
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Ma Z, Chen H, Yang Y, Gao S, Yang J, Cui S, Zhou S, Jiang B, Zou B, Sun M, Wang L. Characterization of an ssDNA ligase and its application in aptamer circularization. Anal Biochem 2024; 685:115409. [PMID: 38006953 DOI: 10.1016/j.ab.2023.115409] [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: 08/24/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 11/27/2023]
Abstract
Aptamers are widely used in various biomedical areas as novel molecular recognition elements, however, short single-stranded DNA (ssDNA) or RNA oligonucleotides are easily degraded by nucleases in biological fluids. This problem can be solved by circularizing aptamers with circular ligases. Herein, a moderately thermostable ssDNA ligase was expressed and purified. The purified ligase showed good circularization activity for different length substrates and much higher circularization efficiency than T4 RNA ligase 1. Biochemical characterization revealed that the enzyme showed optimal circularization activity at pH 7.5 and 50 ᵒC. Mn2+ and Mg2+ increased enzyme circularization activity, with Mn2+ having higher activity than Mg2+. The optimal concentrations of Mn2+ and ligase were 1.25-2.5 mM and 0.02 nM, respectively. The kinetic parameters Km, Vmax and Kcat of ssDNA ligase were 1.16 μM, 10.71 μM/min, and 10.7 min-1, respectively. The ssDNA ligase efficiency was nucleotide-dependent, and 5'-G and 3'-T were the most ligase-favored terminal nucleotides. In addition, the affinity and stability of the circular aptamer were determined. The affinity constant (KD) was 4.9 μM, and the stability increased compared to its linear form. Molecular docking results showed that the circular aptamer bound to the target via two hydrogen bonds. This study provides a simple and efficient aptamer circularization modification method for improving aptamer stability and expanding its applications.
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Affiliation(s)
- Zhenxia Ma
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Han Chen
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Yao Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Siyi Gao
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Jiaping Yang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Shihai Cui
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Shiyuan Zhou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Boyang Jiang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Bin Zou
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China
| | - Mingjuan Sun
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China.
| | - Lianghua Wang
- Department of Biochemistry and Molecular Biology, College of Basic Medical Sciences, Naval Medical University, Shanghai, 200433, China.
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Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
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Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
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Li YH, Zhao ML, Zhang P, Yang X, Yuan R, Zhuo Y. Target-Driven Annular DNA Walker Coupled with Electrochemiluminescent Silicon Quantum Dots for APE1 Bioanalysis. Anal Chem 2023; 95:18629-18634. [PMID: 38057277 DOI: 10.1021/acs.analchem.3c04747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
Abstract
Functional DNA walkers with substantial nanostructures have been extensively investigated; however, their stability still faces challenges when exposed to diverse nuclease in clinical biological samples, resulting in the unreliability of actual assessment. This work proposed a target-driven annular DNA walker with enhanced stability enabling the sensitive and reliable response to different concentrations of apurinic/apyrimidinic endonuclease 1 (APE1), by preparing silicon quantum dots (SiQDs) as electrochemiluminescence (ECL) emitters. Specifically, the SiQDs showed significant strong and stable ECL signals by purifying the microenvironment of SiQDs through the dialysis removal of the gel-like layers surrounding the SiQDs. The relative standard deviation (RSD) of their ECL signal had been improved 16.59 times under consecutive scanning compared to that of SiQDs without dialysis, demonstrating a significant improvement in ECL stability. Subsequently, in the presence of APE1, the designed annular DNA walker was activated to move along the numerous quenching probes within the continuous cross-based DNA orbits, which were immobilized to the SiQD-modified electrode, providing ECL readout signals. The linear range of this ECL biosensor was 1.0 × 10-13 U·μL-1 to 1.0 × 10-7 U·μL-1, and the limit of detection (LOD) was as low as 1.766 × 10-14 U·μL-1. This work provides a novel structure of a DNA walker with nuclease resistance for clinical sample detection and designs a new strategy for synthesizing SiQDs with favorable ECL performance, tremendously expanding the ECL application of SiQDs.
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Affiliation(s)
- Ying-Huan Li
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Mei-Ling Zhao
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Pu Zhang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Xia Yang
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ruo Yuan
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
| | - Ying Zhuo
- Key Laboratory of Luminescence Analysis and Molecular Sensing (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P. R. China
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Shang Z, Deng Z, Yi X, Yang M, Nong X, Lin M, Xia F. Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5564-5576. [PMID: 37861233 DOI: 10.1039/d3ay01618h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.
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Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Zixuan Deng
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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Zhou Q, Zhang G, Wu Y, Zhang Q, Liu Y, Chang Y, Liu M. In Vitro Selection of M 2+-Independent, Fast-Responding Acidic Deoxyribozymes for Bacterial Detection. J Am Chem Soc 2023; 145:21370-21377. [PMID: 37683187 DOI: 10.1021/jacs.3c06155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/10/2023]
Abstract
We report on the first efforts to isolate acidic RNA-cleaving DNAzymes (aRCDs) from a random-sequence DNA pool by in vitro selection that are activated by a microbe Escherichia coli (E. coli), at pH 5.3. Importantly, these E. coli-responsive aRCDs only require monovalent metal ions as cofactors for cleaving a fluorogenic chimeric DNA/RNA substrate. Such characteristics can be used to efficiently protect RCDs from both intrinsic chemical instability and external enzymatic degradation. One remarkable DNAzyme, aRCD-EC1, is specific for E. coli, and its target is likely a protein. Furthermore, truncated aRCD-EC1 had significantly improved catalytic activity with an observed rate constant (kobs) of 1.18 min-1, making it the fastest bacteria-responding RCD reported to date. Clinical evaluation of this aRCD-based fluorescent assay using 40 patient urine samples demonstrated a diagnostic sensitivity of 100% and a specificity of 100% at a total analysis time of 50 min without a bacterial culture. This work can expand the repertoire of DNAzymes that are active under nonphysiological conditions, thus facilitating the development of diverse DNAzyme-based biosensors in clinical diagnosis.
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Affiliation(s)
- Qinbin Zhou
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Guangxiao Zhang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Yunping Wu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Qiang Zhang
- School of Bioengineering, Dalian University of Technology, Dalian 116024, China
| | - Yi Liu
- Department of Neurology, Dalian Municipal Central Hospital Affiliated Hospital of Dalian Medical University, Dalian 116033, China
| | - Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian 116024, China
- Dalian POCT Laboratory, Dalian 116024, China
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11
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Chen M, Li M, Ren X, Zhou F, Li Y, Tan L, Luo Z, Cai K, Hu Y. DNAzyme Nanoconstruct-Integrated Autonomously-Adaptive Coatings Enhance Titanium-Implant Osteointegration by Cooperative Angiogenesis and Vessel Remodeling. ACS NANO 2023; 17:15942-15961. [PMID: 37566558 DOI: 10.1021/acsnano.3c04049] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2023]
Abstract
Orthopedic implants have a high failure rate due to insufficient interfacial osseointegration, especially under osteoporotic conditions. Type H vessels are CD31+EMCN+ capillaries with crucial roles in mediating new bone formation, but their abundance in osteoporotic fracture site is highly limited. Herein, we report a nanoengineered composite coating to improve the in situ osseointegration of a Ti implant for osteoporotic fracture repair, which is realized through inhibiting the stimulator of interferon genes (STING) in endothelial cells (ECs) to stimulate type H vessel formation. Autonomously catalytic DNAzyme-ZnO nanoflowers (DNFzns) were prepared through rolling circle amplification (RCA) of STING mRNA-degrading DNAzymes, which were then integrated on the Ti surface and further sequentially complexed with thioketal-bridged polydopamine and naringenin (Ti/DNFzn/PDA-Nar). ECs and mesenchymal stem cells (MSCs) can be recruited to the implant surface by galvanotaxis, accounting for the negative charges of DNFzn/PDA-Nar, subsequently released Nar under reactive oxygen species (ROS) stimulation to upregulate endothelial nitric oxide synthase (eNOS) in recruited ECs, leading to enhanced local angiogenesis. Meanwhile, the coordinately released DNFzns would abolish STING expression in ECs to transform the newly formed vessels into Type H vessels, thus substantially promoting the osseointegration of Ti implants. This study provides application prospects for improving implant osteointegration for osteoporotic fracture treatment.
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Affiliation(s)
- Maohua Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Menghuan Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Xijiao Ren
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Fei Zhou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yanan Li
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Lu Tan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Zhong Luo
- School of Life Science, Chongqing University, Chongqing 400044, China
| | - Kaiyong Cai
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Yan Hu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
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12
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Shi J, Oger PM, Cao P, Zhang L. Thermostable DNA ligases from hyperthermophiles in biotechnology. Front Microbiol 2023; 14:1198784. [PMID: 37293226 PMCID: PMC10244674 DOI: 10.3389/fmicb.2023.1198784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/09/2023] [Indexed: 06/10/2023] Open
Abstract
DNA ligase is an important enzyme ubiquitous in all three kingdoms of life that can ligate DNA strands, thus playing essential roles in DNA replication, repair and recombination in vivo. In vitro, DNA ligase is also used in biotechnological applications requiring in DNA manipulation, including molecular cloning, mutation detection, DNA assembly, DNA sequencing, and other aspects. Thermophilic and thermostable enzymes from hyperthermophiles that thrive in the high-temperature (above 80°C) environments have provided an important pool of useful enzymes as biotechnological reagents. Similar to other organisms, each hyperthermophile harbors at least one DNA ligase. In this review, we summarize recent progress on structural and biochemical properties of thermostable DNA ligases from hyperthermophiles, focusing on similarities and differences between DNA ligases from hyperthermophilic bacteria and archaea, and between these thermostable DNA ligases and non-thermostable homologs. Additionally, altered thermostable DNA ligases are discussed. Possessing improved fidelity or thermostability compared to the wild-type enzymes, they could be potential DNA ligases for biotechnology in the future. Importantly, we also describe current applications of thermostable DNA ligases from hyperthermophiles in biotechnology.
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Affiliation(s)
- Jingru Shi
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
| | - Philippe M. Oger
- University of Lyon, INSA de Lyon, CNRS UMR, Villeurbanne, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, Beijing, China
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou, China
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