1
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Sun J, Ji L, Li Y, Cao X, Shao X, Xia J, Wang Z. Electrochemical aptasensors based on porous carbon derived from graphene oxide/ZIF-8 composites for the detection of Erwinia cypripedii. Talanta 2024; 276:126250. [PMID: 38743969 DOI: 10.1016/j.talanta.2024.126250] [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: 02/26/2024] [Revised: 04/29/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024]
Abstract
In this research, self-screening aptamer and MOFs-derived nanomaterial have been combined to construct electrochemical aptasensor for environmental detection. By utilizing the large specific surface area of reduced graphene oxide (rGO), ZIF-8 was grown in situ on surface of rGO, and the composites was pyrolyzed to obtain MOFs-derived porous carbon materials (rGO-NCZIF). Thanks to the synergistic effect between rGO and NCZIF, the complex exhibits remarkable characteristics, including a high electron transfer rate and electrocatalytic activity. In addition, the orderly arrangement of imidazole ligands within ZIF-8 facilitated the uniform doping of nitrogen elements into the porous carbon, thereby significantly enhancing its electrochemical performance. After carboxylation, rGO-NCZIF was functionalized with self-screening aptamer for fabricating electrochemical aptasensor, which can be used to detect Erwinia cypripedii, a kind of quarantine plant bacteria, with detection limit of 4.92 × 103 cfu/mL. Due to the simplicity and speed, the aptasensor is suitable for rapid customs inspection and quarantine. Additionally, the universality of this sensing strategy was verified through exosomes detection by changing the aptamer. The results indicated that the rGO-NCZIF-based electrochemical aptasensor had practical value in the environmental and medical fields.
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Affiliation(s)
- Jiayue Sun
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao Application Technology Innovation Center of Photoelectric Biosensing for Clinical Diagnosis and Treatment, Qingdao University, Qingdao, 266071, PR China; Technical Center of Qingdao Customs District, Qingdao, 266000, PR China
| | - Lei Ji
- Technical Center of Qingdao Customs District, Qingdao, 266000, PR China
| | - Yan Li
- Technical Center of Qingdao Customs District, Qingdao, 266000, PR China
| | - Xiyue Cao
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao Application Technology Innovation Center of Photoelectric Biosensing for Clinical Diagnosis and Treatment, Qingdao University, Qingdao, 266071, PR China.
| | - Xiuling Shao
- Technical Center of Qingdao Customs District, Qingdao, 266000, PR China.
| | - Jianfei Xia
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao Application Technology Innovation Center of Photoelectric Biosensing for Clinical Diagnosis and Treatment, Qingdao University, Qingdao, 266071, PR China.
| | - Zonghua Wang
- College of Chemistry and Chemical Engineering, Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, Qingdao Application Technology Innovation Center of Photoelectric Biosensing for Clinical Diagnosis and Treatment, Qingdao University, Qingdao, 266071, PR China
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2
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Wang L, Alkhamis O, Canoura J, Yu H, Xiao Y. Rapid Nuclease-Assisted Selection of High-Affinity Small-Molecule Aptamers. J Am Chem Soc 2024; 146:21296-21307. [PMID: 39042584 DOI: 10.1021/jacs.4c00748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Aptamers are nucleic acid bioreceptors that have been widely utilized for a variety of biosensing applications, including in vivo detection methods that would not be possible with antibody-based systems. However, it remains challenging to generate high-quality aptamers for small molecule targets, particularly for use under physiological conditions. We present a highly effective aptamer selection technology for small-molecule targets that utilizes the nuclease EcoRI to remove nonspecific or weakly binding sequences in solution phase, rapidly enriching high-affinity target binders within just a few rounds of selection. As proof-of-concept, we used our nuclease-assisted SELEX (NA-SELEX) method to isolate aptamers for a synthetic cannabinoid, AB-FUBINACA. Within five rounds, we identified two highly specific aptamers that exhibit nanomolar affinity at physiological temperature. We also demonstrate the robustness and reproducibility of NA-SELEX by performing the same selection experiment with fresh reagents and libraries, obtaining the same two aptamers as well as two other high-quality aptamer candidates. Finally, we compare NA-SELEX against a conventional library-immobilized SELEX screen for AB-FUBINACA using the same screening conditions, identifying aptamers with 25-100-fold weaker affinity after 11 rounds of selection. NA-SELEX therefore could be an effective selection method for the isolation of high-quality aptamers for small-molecule targets.
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Affiliation(s)
- Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
| | - Haixiang Yu
- Department of Surgery, Duke University Medical Center, Durham, North Carolina 27710, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Dr., Raleigh, North Carolina 27695, United States
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3
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Liu Y, Wang X, Liu J. Unexpected enrichment of DNA aptamers for Zn 2+ ions from an insulin selection. Chem Commun (Camb) 2024; 60:6280-6283. [PMID: 38809225 DOI: 10.1039/d4cc01546k] [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: 05/30/2024]
Abstract
We serendipitously discovered Zn2+-binding DNA aptamers when selecting insulin aptamers. The Zn-1 aptamer binds to Zn2+ with a dissociation constant (Kd) of ∼1 μM, and has 450-fold higher selectivity for Zn2+ over Cd2+. A strand-displacement based fluorescent sensor achieved a limit of detection of 0.2 μM Zn2+.
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Affiliation(s)
- Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
| | - Xiaoqin Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario, N2L 3G1, Canada.
- Centre for Eye and Vision Research (CEVR), 17W Hong Kong Science Park, Hong Kong, China
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4
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Cao X, Tang L, Song J. Circular Single-Stranded DNA: Discovery, Biological Effects, and Applications. ACS Synth Biol 2024; 13:1038-1058. [PMID: 38501391 DOI: 10.1021/acssynbio.4c00040] [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] [Indexed: 03/20/2024]
Abstract
The field of nucleic acid therapeutics has witnessed a significant surge in recent times, as evidenced by the increasing number of approved genetic drugs. However, current platform technologies containing plasmids, lipid nanoparticle-mRNAs, and adeno-associated virus vectors encounter various limitations and challenges. Thus, we are devoted to finding a novel nucleic acid vector and have directed our efforts toward investigating circular single-stranded DNA (CssDNA), an ancient form of nucleic acid. CssDNAs are ubiquitous, but generally ignored. Accumulating evidence suggests that CssDNAs possess exceptional properties as nucleic acid vectors, exhibiting great potential for clinical applications in genetic disorders, gene editing, and immune cell therapy. Here, we comprehensively review the discovery and biological effects of CssDNAs as well as their applications in the field of biomedical research for the first time. Undoubtedly, as an ancient form of DNA, CssDNA holds immense potential and promises novel insights for biomedical research.
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Affiliation(s)
- Xisen Cao
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Linlin Tang
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jie Song
- Institute of Nano Biomedicine and Engineering, Department of Instrument Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
- Hangzhou Institute of Medicine, Chinese Academy of Sciences, Hangzhou 310022, China
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5
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Yang KZ, Wang M, Gao MY, Wang YT, Zhang ZL. Dynamic selection of high-affinity aptamers using a magnetically activated continuous deflection microfluidic chip. Chem Commun (Camb) 2024; 60:2772-2775. [PMID: 38353965 DOI: 10.1039/d4cc00229f] [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: 03/06/2024]
Abstract
To accelerate the discovery of high-affinity aptamers, a magnetically activated continuous deflection (MACD) chip was designed. The MACD chip could achieve dynamic selection in a continuous flow, which meant that the binding and separation were carried out consecutively. Dynamic selection could make selection efficient. Low-affinity sequences could be eluted in time and high-affinity sequences could be enriched via dynamic selection. The stringency of the conditions could be further increased by lowering the target concentration in the dynamic selection. Finally, a C.al3 aptamer with high-affinity and high-specificity for Candida albicans (C. albicans) was obtained through six rounds of selection. Its dissociation constant (Kd) was 7.9 nM. This demonstrated that dynamic selection using a MACD chip was an effective method for high-affinity aptamer selection.
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Affiliation(s)
- Ke-Zhu Yang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Meng Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Ming-Yue Gao
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Yong-Tao Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
| | - Zhi-Ling Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
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6
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Shi L, Jin Y, Liu J. Intramolecular aptamer switches. Analyst 2024; 149:745-750. [PMID: 38193253 DOI: 10.1039/d3an02022c] [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: 01/10/2024]
Abstract
Aptamer switches as effective biosensing tools have become a focal point of research in engineered aptasensors. Intramolecular aptamer switches are more versatile, affordable, and simpler than classical "open-close" and strand displacement-based aptamer switches. Recently, many new aptamers with an overall hairpin structure have been reported. In this study, intramolecular aptamer switches were developed by adding new base pairs to the end of aptamers. The additional nucleotides can pair with the internal domains of the aptamer, causing a change in its conformation from the original secondary structure without a target. When a target binds to an aptamer, a marked change in the structure of the aptamer is expected. As models for testing this intramolecular aptamer switch idea, aptamers of oxytetracycline (OTC), 17β-estradiol (E2), and adenosine were employed. When the additional base pairs are too long, binding the target to the aptamer becomes more challenging. This research offers valuable insights into the development of intramolecular aptamer switches and their potential applications in biosensor design.
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Affiliation(s)
- Lu Shi
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
| | - Yan Jin
- Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada.
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7
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Ding Y, Gu L, Wang X, Zhang Z, Zhang H, Liu J. Affinity-Guided Coevolution of Aptamers for Guanine, Xanthine, Hypoxanthine, and Adenine. ACS Chem Biol 2024; 19:208-216. [PMID: 38194356 DOI: 10.1021/acschembio.3c00660] [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: 01/10/2024]
Abstract
The simultaneous evolution of multiple aptamers can drastically increase the speed of aptamer discovery. Most previous studies used the same concentration for different targets, leading to the dominance of the libraries by one or a few aptamers and a low success rate. To foster the best aptamers to grow independently in the sequence space, it is important to (1) use low target concentrations close to their dissociation constants and (2) stop at an early round before any sequence starts to dominate. In this study, we demonstrate this affinity-guided selection concept using the capture-SELEX method to isolate aptamers for four important purines: guanine (5 μM), xanthine (50 μM), hypoxanthine (10 μM), and adenine (10 μM). The round 9 library was split, and in round 10, the four targets were individually used to elute the binding sequences. Using thioflavin T fluorescence spectroscopy and isothermal titration calorimetry, we confirmed highly selective aptamers for xanthine, guanine, and adenine. These aptamers have Kd values below 1 μM and around 100-fold selectivity against most competing analytes, and they compare favorably with existing RNA aptamers and riboswitches. A separate selection was performed using hypoxanthine alone, and no selective aptamer was achieved, even with negative selection, explaining the lack of its aptamer in our mixed selection. This affinity-guided multiplex SELEX study offers fundamental insights into aptamer selection and provides high-quality aptamers for three important purines.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Lide Gu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Xiaoqin Wang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Ziyu Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Hanxiao Zhang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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Teodori L, Omer M, Kjems J. RNA nanostructures for targeted drug delivery and imaging. RNA Biol 2024; 21:1-19. [PMID: 38555519 PMCID: PMC10984137 DOI: 10.1080/15476286.2024.2328440] [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] [Accepted: 03/04/2024] [Indexed: 04/02/2024] Open
Abstract
The RNA molecule plays a pivotal role in many biological processes by relaying genetic information, regulating gene expression, and serving as molecular machines and catalyzers. This inherent versatility of RNA has fueled significant advancements in the field of RNA nanotechnology, driving the engineering of complex nanoscale architectures toward biomedical applications, including targeted drug delivery and bioimaging. RNA polymers, serving as building blocks, offer programmability and predictability of Watson-Crick base pairing, as well as non-canonical base pairing, for the construction of nanostructures with high precision and stoichiometry. Leveraging the ease of chemical modifications to protect the RNA from degradation, researchers have developed highly functional and biocompatible RNA architectures and integrated them into preclinical studies for the delivery of payloads and imaging agents. This review offers an educational introduction to the use of RNA as a biopolymer in the design of multifunctional nanostructures applied to targeted delivery in vivo, summarizing physical and biological barriers along with strategies to overcome them. Furthermore, we highlight the most recent progress in the development of both small and larger RNA nanostructures, with a particular focus on imaging reagents and targeted cancer therapeutics in pre-clinical models and provide insights into the prospects of this rapidly evolving field.
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Affiliation(s)
- Laura Teodori
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
| | - Marjan Omer
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
- Center for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus, Denmark
- Center for RNA Therapeutics towards Metabolic Diseases (RNA-META), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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9
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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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10
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Gu L, Zheng J, Zhang Y, Wang D, Liu J. Capture-SELEX of DNA Aptamers for Sulforhodamine B and Fluorescein. Chemistry 2023; 29:e202302616. [PMID: 37793015 DOI: 10.1002/chem.202302616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/17/2023] [Accepted: 10/04/2023] [Indexed: 10/06/2023]
Abstract
While many dye binding aptamers have been reported, most of them were for light-up aptamers that can significantly enhance the quantum yield of fluorophores. Sulforhodamine B (SRhB) was used as a target previously to select both DNA and RNA aptamers, and the DNA aptamer was a G-quadruplex that can bind to a number of rhodamine analogs. In addition, the previous selections were performed by immobilizing the target molecules. In this work, the library immobilization method was used to respectively select aptamers for SRhB and fluorescein. The SRhB aptamer has a non-G-quadruplex structure with a Kd of 1.0 μM measured from isothermal titration calorimetry. Upon titration of the aptamer, the fluorescence of SRhB increased 2.5-fold, and this aptamer does not require Mg2+ for binding. Rhodamine B has even tighter binding suggesting binding through the xanthene moiety of the dyes. No binding was detected for fluorescein. For the fluorescein selection, a dominant aptamer sequence with a Kd of 147 μM was obtained. This study provides two new aptamers for two important fluorophores that can be used to study aptamer-based separation, dye detection and catalysis. Comparison of these aptamers also provides insights into the effect of functional groups on aptamer binding.
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Affiliation(s)
- Lide Gu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2 L 3G1, Canada
| | - Jiajie Zheng
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2 L 3G1, Canada
| | - Yao Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Deli Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2 L 3G1, Canada
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11
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Canoura J, Liu Y, Alkhamis O, Xiao Y. Aptamer-Based Fentanyl Detection in Biological Fluids. Anal Chem 2023; 95:18258-18267. [PMID: 38033203 DOI: 10.1021/acs.analchem.3c04104] [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: 12/02/2023]
Abstract
Fentanyl is a widely abused analgesic and anesthetic drug with a narrow therapeutic window that creates easy opportunities for overdose and death. Rapid, accurate, and sensitive fentanyl detection in biosamples is crucial for therapeutic drug monitoring and overdose diagnosis. Unfortunately, current methods are limited to either sophisticated laboratory-based tests or antibody-based immunoassays, which are prone to false results and are mainly used with urine samples. Here, we have utilized library-immobilized SELEX to isolate new aptamers─nucleic acid-based bioreceptors that are well-suited for biosensing─that can specifically bind fentanyl under physiological conditions. We isolated multiple aptamers with nanomolar affinity and excellent specificity against dozens of interferents and incorporated one of these into an electrochemical aptamer-based sensor that can rapidly detect fentanyl at clinically relevant concentrations in 50% diluted serum, urine, and saliva. Given the excellent performance of these sensors, we believe that they could serve as the basis for point-of-care devices for monitoring fentanyl during medical procedures and determining fentanyl overdose.
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Affiliation(s)
- Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Yingzhu Liu
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina , 27607, United States
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12
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Xu G, Wang C, Yu H, Li Y, Zhao Q, Zhou X, Li C, Liu M. Structural basis for high-affinity recognition of aflatoxin B1 by a DNA aptamer. Nucleic Acids Res 2023; 51:7666-7674. [PMID: 37351632 PMCID: PMC10415127 DOI: 10.1093/nar/gkad541] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/06/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
The 26-mer DNA aptamer (AF26) that specifically binds aflatoxin B1 (AFB1) with nM-level high affinity is rare among hundreds of aptamers for small molecules. Despite its predicted stem-loop structure, the molecular basis of its high-affinity recognition of AFB1 remains unknown. Here, we present the first high-resolution nuclear magnetic resonance structure of AFB1-AF26 aptamer complex in solution. AFB1 binds to the 16-residue loop region of the aptamer, inducing it to fold into a compact structure through the assembly of two bulges and one hairpin structure. AFB1 is tightly enclosed within a cavity formed by the bulges and hairpin, held in a place between the G·C base pair, G·G·C triple and multiple T bases, mainly through strong π-π stacking, hydrophobic and donor atom-π interactions, respectively. We further revealed the mechanism of the aptamer in recognizing AFB1 and its analogue AFG1 with only one-atom difference and introduced a single base mutation at the binding site of the aptamer to increase the discrimination between AFB1 and AFG1 based on the structural insights. This research provides an important structural basis for understanding high-affinity recognition of the aptamer, and for further aptamer engineering, modification and applications.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Chen Wang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Hao Yu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Yapiao Li
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Qiang Zhao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
- School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, P.R. China
- Department of Chemistry, University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xin Zhou
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan 430071, P.R. China
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Ding Y, Xie Y, Li AZ, Huang PJJ, Liu J. Cross-Binding of Four Adenosine/ATP Aptamers to Caffeine, Theophylline, and Other Methylxanthines. Biochemistry 2023; 62:2280-2288. [PMID: 37433121 DOI: 10.1021/acs.biochem.3c00260] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Abstract
The classical DNA aptamer for adenosine and ATP was selected twice using ATP as the target in 1995 and 2005, respectively. In 2022, this motif appeared four more times from selections using adenosine, ATP, theophylline, and caffeine as targets, suggesting that this aptamer can also bind methylxanthines. In this work, using thioflavin T fluorescence spectroscopy, this classical DNA aptamer showed Kd values for adenosine, theophylline, and caffeine of 9.5, 101, and 131 μM, respectively, and similar Kd values were obtained using isothermal titration calorimetry. Binding to the methylxanthines was also observed for the newly selected Ade1301 aptamer but not for the Ade1304 aptamer. The RNA aptamer for ATP also had no binding to the methylxanthines. Molecular dynamics simulations were performed using the classical DNA and RNA aptamers based on their NMR structures, and the simulation results were consistent with the experimental observations, explaining the selectivity profiles. This study suggests that a broader range of target analogues need to be tested for aptamers. For the detection of adenosine and ATP, the Ade1304 aptamer is a better choice due to its better selectivity.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Yachen Xie
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Albert Zehan Li
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Po-Jung Jimmy Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON N2L 3G1, Canada
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Alkhamis O, Canoura J, Willis C, Wang L, Perry J, Xiao Y. Comparison of Aptamer Signaling Mechanisms Reveals Disparities in Sensor Response and Strategies to Eliminate False Signals. J Am Chem Soc 2023. [PMID: 37217444 DOI: 10.1021/jacs.3c03640] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aptamers are nucleic acid-based affinity reagents that have been incorporated into a variety of molecular sensor formats. However, many aptamer sensors exhibit insufficient sensitivity and specificity for real-world applications, and although considerable effort has been dedicated to improving sensitivity, sensor specificity has remained largely neglected and understudied. In this work, we have developed a series of sensors using aptamers for the small-molecule drugs flunixin, fentanyl, and furanyl fentanyl and compare their performance─in particular, focusing on their specificity. Contrary to expectations, we observe that sensors using the same aptamer operating under the same physicochemical conditions produce divergent responses to interferents depending on their signal transduction mechanism. For instance, aptamer beacon sensors are susceptible to false-positives from interferents that weakly associate with DNA, while strand-displacement sensors suffer from false-negatives due to interferent-associated signal suppression when both the target and interferent are present. Biophysical analyses suggest that these effects arise from aptamer-interferent interactions that are either nonspecific or induce aptamer conformational changes that are distinct from those induced by true target-binding events. We also demonstrate strategies for improving the sensitivity and specificity of aptamer sensors with the development of a "hybrid beacon," wherein the incorporation of a complementary DNA competitor into an aptamer beacon selectively hinders interferent─but not target─binding and signaling, while simultaneously overcoming signal suppression by interferents. Our results highlight the need for systematic and thorough testing of aptamer sensor response and new aptamer selection methods that optimize specificity more effectively than traditional counter-SELEX.
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Affiliation(s)
- Obtin Alkhamis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Juan Canoura
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Connor Willis
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Linlin Wang
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Jacob Perry
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
| | - Yi Xiao
- Department of Chemistry, North Carolina State University, 2620 Yarbrough Drive, Raleigh, North Carolina 27695, United States
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Ding Y, Liu J. Pushing Adenosine and ATP SELEX for DNA Aptamers with Nanomolar Affinity. J Am Chem Soc 2023; 145:7540-7547. [PMID: 36947745 DOI: 10.1021/jacs.3c00848] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
The classical DNA aptamer for adenosine and ATP has been the most used small molecule binding aptamer for biosensing, imaging, and DNA nanotechnology. This sequence has recurred multiple times in previous aptamer selections, and all previous selections used a high concentration of ATP as the target. Herein, two separate selections were performed using adenosine and ATP as targets. By pushing the target concentrations down to the low micromolar range, two new aptamers with Kd as low as 230 nM were obtained, showing around 30-fold higher affinity compared to the classical aptamer. The classical aptamer sequence still dominated the library in the early rounds of the selections, but it was suppressed in the later rounds. The new aptamers bind to one target molecule instead of two. Mutation studies confirmed their secondary structures and specific binding. Using the deep sequencing data from the selections, long-standing questions such as the existence of one-site aptamers and mutation distribution in the classical aptamer were addressed. Comparisons were made with previously reported DNA aptamers for ATP. Finally, a strand-displacement biosensor was tested showing selectivity for adenosine and its nucleotides.
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Affiliation(s)
- Yuzhe Ding
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
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