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Liu S, Xu Y, Jiang X, Tan H, Ying B. Translation of aptamers toward clinical diagnosis and commercialization. Biosens Bioelectron 2022; 208:114168. [PMID: 35364525 DOI: 10.1016/j.bios.2022.114168] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/08/2023]
Abstract
The dominance of antibodies in diagnostics has gradually changed following the discovery of aptamers in the early 1990s. Aptamers offer inherent advantages over traditional antibodies, including higher specificity, higher affinity, smaller size, greater stability, ease of manufacture, and low immunogenicity, rendering them the best candidates for point-of-care testing (POCT). In the past 20 years, the research community and pharmaceutical companies have made great efforts to promote the development of aptamer technology. Macugen® (pegaptanib) was the first aptamer drug approved by the US Food and Drug Administration (FDA), and various aptamer-based diagnostics show great promise in preclinical research and clinical trials. In this review, we introduce recent literature, ongoing clinical trials, commercial reagents of aptamer-based diagnostics, discuss the FDA regulatory mechanisms, and highlight the prospects and challenges in translating these studies into viable clinical diagnostic tools.
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Affiliation(s)
- Shan Liu
- Sichuan Provincial Key Laboratory for Human Disease Gene Study, Department of Medical Genetics, Department of Laboratory Medicine, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, University of Electronic Science and Technology, Chengdu, 610072, China
| | - Yixin Xu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China
| | - Xin Jiang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China
| | - Hong Tan
- Department of General Surgery, Chengdu Integrated TCM&Western Medicine Hospital (Chengdu First People's Hospital), Chengdu, 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, 610041, China; Med+ Molecular Diagnostics Institute of West China Hospital/West China School of Medicine, Chengdu, 610041, China.
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Highly efficient porous magnetic polydopamine/copper phosphate with three-dimensional hierarchical nanoflower morphology as a selective platform for recombinant proteins separation. Colloids Surf B Biointerfaces 2021; 209:112149. [PMID: 34653906 DOI: 10.1016/j.colsurfb.2021.112149] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/02/2023]
Abstract
The separation and purification of recombinant pharmaceutical proteins is a fundamental and challenging step in the biotechnology industry. Hierarchical nanostructures with unique features and high stability can be used as efficient adsorbents. In this study, hierarchical magnetic polydopamine-copper phosphate nanoflowers (Cu-PDA MNFs) were synthesized as high-performance magnetic adsorbents in a simple and low-cost method based on green chemistry. The prepared hybrid Cu-PDA MNFs revealed great performance for separating pure recombinant human growth hormone (rhGH) and the rhGH acquired from recombinant Pichia pastoris yeast fermentation. The analysis confirmed that Cu-PDA MNFs exhibited a high adsorption capacity of 257.4 mg rhGH g-1 Cu-PDA MNFs and a fast adsorption rate for approaching the adsorption equilibrium within less than 30 min with a recovery efficiency of 74% of rhGH from the real sample. In addition, recycling tests demonstrated the stability and recyclability of Cu-PDA MNFs for at least six cycles with almost constant adsorption capacity and no toxicity. Based on these results, Cu-PDA MNFs could be considered as a promising candidate for separation and purification of rhGH. This work presents a new approach to using organic-inorganic nanoflowers as the hierarchical nanostructure for purification of pharmaceutical proteins with high performance.
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Le ATH, Krylova SM, Beloborodov SS, Wang TY, Hili R, Johnson PE, Li F, Veedu RN, Belyanskaya S, Krylov SN. How to Develop and Prove High-Efficiency Selection of Ligands from Oligonucleotide Libraries: A Universal Framework for Aptamers and DNA-Encoded Small-Molecule Ligands. Anal Chem 2021; 93:5343-5354. [PMID: 33764056 DOI: 10.1021/acs.analchem.1c00601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Screening molecular libraries for ligands capable of binding proteins is widely used for hit identification in the early drug discovery process. Oligonucleotide libraries provide a very high diversity of compounds, while the combination of the polymerase chain reaction and DNA sequencing allow the identification of ligands in low copy numbers selected from such libraries. Ligand selection from oligonucleotide libraries requires mixing the library with the target followed by the physical separation of the ligand-target complexes from the unbound library. Cumulatively, the low abundance of ligands in the library and the low efficiency of available separation methods necessitate multiple consecutive rounds of partitioning. Multiple rounds of inefficient partitioning make the selection process ineffective and prone to failures. There are continuing efforts to develop a separation method capable of reliably generating a pure pool of ligands in a single round of partitioning; however, none of the proposed methods for single-round selection have been universally adopted. Our analysis revealed that the developers' efforts are disconnected from each other and hindered by the lack of quantitative criteria of selection quality assessment. Here, we present a formalism that describes single-round selection mathematically and provides parameters for quantitative characterization of selection quality. We use this formalism to define a universal strategy for development and validation of single-round selection methods. Finally, we analyze the existing partitioning methods, the published single-round selection reports, and some pertinent practical considerations through the prism of this formalism. This formalism is not an experimental protocol but a framework for correct development of experimental protocols. While single-round selection is not a goal by itself and may not always suffice selection of good-quality ligands, our work will help developers of highly efficient selection approaches to consolidate their efforts under an umbrella of universal quantitative criteria of method development and assessment.
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Affiliation(s)
- An T H Le
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Svetlana M Krylova
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Stanislav S Beloborodov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Tong Y Wang
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Ryan Hili
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Philip E Johnson
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
| | - Feng Li
- Department of Chemistry and Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University and Perron Institute for Neurological and Translational Science, Perth 6150, Australia
| | | | - Sergey N Krylov
- Department of Chemistry and Centre for Research on Biomolecular Interactions, York University, Toronto, Ontario M3J 1P3, Canada
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Mokhtarzadeh A, Ezzati Nazhad Dolatabadi J, Abnous K, de la Guardia M, Ramezani M. Nanomaterial-based cocaine aptasensors. Biosens Bioelectron 2014; 68:95-106. [PMID: 25562736 DOI: 10.1016/j.bios.2014.12.052] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Revised: 12/04/2014] [Accepted: 12/22/2014] [Indexed: 12/17/2022]
Abstract
Up to now, many different methods have been developed for detection of cocaine, but most of these methods are usually time-consuming, tedious and require special or expensive equipment. Therefore, the development of simple, sensitive and rapid detection methods is necessary. In the last decade, aptamers have been used as a new biosensor platform for detection of cocaine in different samples. Aptamers are artificial single-stranded DNA or RNA oligonucleotides capable of binding to specific molecular targets with high affinity and if integrated to nanomaterials, it may lead in precise methods for cocaine detection in the common laboratories. In this review, recent advances and applications of aptamer-based biosensors and nanobiosensors, have been updated, paying attention to the use of fluorescence, colorimetric and electrochemical techniques for the detection and quantitative determination of cocaine.
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Affiliation(s)
- Ahad Mokhtarzadeh
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, P.O. Box 91775-1365, Mashhad, Iran
| | | | - Khalil Abnous
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, P.O. Box 91775-1365, Mashhad, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Mohammad Ramezani
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, P.O. Box 91775-1365, Mashhad, Iran.
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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Hu X, Mu L, Wen J, Zhou Q. Immobilized smart RNA on graphene oxide nanosheets to specifically recognize and adsorb trace peptide toxins in drinking water. JOURNAL OF HAZARDOUS MATERIALS 2012; 213-214:387-392. [PMID: 22366314 DOI: 10.1016/j.jhazmat.2012.02.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 01/14/2012] [Accepted: 02/06/2012] [Indexed: 05/31/2023]
Abstract
The contaminations of peptide toxins in drinking water lead directly to sickness and even death in both humans and animals. A smart RNA as aptamer is covalently immobilized on graphene oxide to form a polydispersed and stable RNA-graphene oxide nanosheet. RNA-graphene oxide nanosheets can resist nuclease and natural organic matter, and specifically adsorb trace peptide toxin (microcystin-LR) in drinking water. The adsorption data fit the pseudo-second-order kinetics and the Langmuir isotherm model. The adsorption capacity of RNA-graphene oxide nanosheets decreases at extreme pH, temperature, ionic strength and natural organic matter, but it is suitable to adsorb trance pollutants in contaminated drinking water. Compared with other chemical and biological sorbents, RNA-graphene oxide nanosheets present specific and competitive adsorption, and are easily synthesized and regenerated. Aptamer (RNA) covalently immobilized on graphene oxide nanosheets is a potentially useful tool in recognizing, enriching and separating small molecules and biomacromolecules in the purification of contaminated water and the preparation of samples.
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Affiliation(s)
- Xiangang Hu
- Key Laboratory of Pollution Processes and Environmental Criteria (Ministry of Education), College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
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Marimuthu C, Tang TH, Tominaga J, Tan SC, Gopinath SCB. Single-stranded DNA (ssDNA) production in DNA aptamer generation. Analyst 2012; 137:1307-15. [PMID: 22314701 DOI: 10.1039/c2an15905h] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However, the success of the DNA selection process through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments is very much dependent on its most critical step, which is the conversion of the dsDNA to ssDNA. There is a plethora of methods available in generating ssDNA from the corresponding dsDNA. These include asymmetric PCR, biotin-streptavidin separation, lambda exonuclease digestion and size separation on denaturing-urea PAGE. Herein, different methods of ssDNA generation following the PCR amplification step in SELEX are reviewed.
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Affiliation(s)
- Citartan Marimuthu
- Infectious Disease Cluster, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200, Kepala Batas, Penang, Malaysia
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Citartan M, Gopinath SCB, Tominaga J, Tan SC, Tang TH. Assays for aptamer-based platforms. Biosens Bioelectron 2012; 34:1-11. [PMID: 22326894 DOI: 10.1016/j.bios.2012.01.002] [Citation(s) in RCA: 132] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Revised: 12/14/2011] [Accepted: 01/06/2012] [Indexed: 11/19/2022]
Abstract
Aptamers are single stranded DNA or RNA oligonucleotides that have high affinity and specificity towards a wide range of target molecules. Aptamers have low molecular weight, amenable to chemical modifications and exhibit stability undeterred by repetitive denaturation and renaturation. Owing to these indispensable advantages, aptamers have been implemented as molecular recognition element as alternative to antibodies in various assays for diagnostics. By amalgamating with a number of methods that can provide information on the aptamer-target complex formation, aptamers have become the elemental tool for numerous biosensor developments. In this review, administration of aptamers in applications involving assays of fluorescence, electrochemistry, nano-label and nano-constructs are discussed. Although detection strategies are different for various aptamer-based assays, the core of the design strategies is similar towards reporting the presence of specific target binding to the corresponding aptamers. It is prognosticated that aptamers will find even broader applications with the development of new methods of transducing aptamer target binding.
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Affiliation(s)
- Marimuthu Citartan
- Infectious Disease Cluster, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200 Kepala Batas, Penang, Malaysia
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Strehlitz B, Reinemann C, Linkorn S, Stoltenburg R. Aptamers for pharmaceuticals and their application in environmental analytics. ACTA ACUST UNITED AC 2011; 4:1-30. [PMID: 22389661 PMCID: PMC3281204 DOI: 10.1007/s12566-011-0026-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 11/10/2011] [Indexed: 01/07/2023]
Abstract
Aptamers are single-stranded DNA or RNA oligonucleotides, which are able to bind with high affinity and specificity to their target. This property is used for a multitude of applications, for instance as molecular recognition elements in biosensors and other assays. Biosensor application of aptamers offers the possibility for fast and easy detection of environmental relevant substances. Pharmaceutical residues, deriving from human or animal medical treatment, are found in surface, ground, and drinking water. At least the whole range of frequently administered drugs can be detected in noticeable concentrations. Biosensors and assays based on aptamers as specific recognition elements are very convenient for this application because aptamer development is possible for toxic targets. Commonly used biological receptors for biosensors like enzymes or antibodies are mostly unavailable for the detection of pharmaceuticals. This review describes the research activities of aptamer and sensor developments for pharmaceutical detection, with focus on environmental applications.
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Affiliation(s)
- Beate Strehlitz
- UFZ-Helmholtz Centre for Environmental Research, Permoserstr. 15, 04318 Leipzig, Germany
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Bane TK, Timmons MS, Kauffman SJ, Catlin DH. Enrichment and immunoprecipitation of 22 kDa human growth hormone spiked into human urine. Drug Test Anal 2009; 1:441-6. [DOI: 10.1002/dta.101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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