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Yu H, Zhu J, Shen G, Deng Y, Geng X, Wang L. Improving aptamer performance: key factors and strategies. Mikrochim Acta 2023; 190:255. [PMID: 37300603 DOI: 10.1007/s00604-023-05836-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 05/16/2023] [Indexed: 06/12/2023]
Abstract
Aptamers are functional single-stranded oligonucleotide fragments isolated from randomized libraries by Systematic Evolution of Ligands by Exponential Enrichment (SELEX), exhibiting excellent affinity and specificity toward targets. Compared with traditional antibody reagents, aptamers display many desirable properties, such as low variation and high flexibility, and they are suitable for artificial and large-scale synthesis. These advantages make aptamers have a broad application potential ranging from biosensors, bioimaging to therapeutics and other areas of application. However, the overall performance of aptamer pre-selected by SELEX screening is far from being satisfactory. To improve aptamer performance and applicability, various post-SELEX optimization methods have been developed in the last decade. In this review, we first discuss the key factors that influence the performance or properties of aptamers, and then we summarize the key strategies of post-SELEX optimization which have been successfully used to improve aptamer performance, such as truncation, extension, mutagenesis and modification, splitting, and multivalent integration. This review shall provide a comprehensive summary and discussion of post-SELEX optimization methods developed in recent years. Moreover, by discussing the mechanism of each approach, we highlight the importance of choosing the proper method to perform post-SELEX optimization.
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Affiliation(s)
- Hong Yu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Jiangxiong Zhu
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Guoqing Shen
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Yun Deng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Xueqing Geng
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China
| | - Lumei Wang
- School of Agriculture and Biology, Key Laboratory of Urban Agriculture, Ministry of Agriculture, Bor S. Luh Food Safety Research Center, Shanghai Jiao Tong University, Shanghai, 200240, People's Republic of China.
- Shanghai Jiao Tong University YunNan (Dali) Research Institute, Dali, 671000, Yunnan, China.
- Shanghai Yangtze River Delta Eco-Environmental Change and Management Observation and Research Station, Ministry of Science and Technology, Ministry of Education, 800 Dongchuan Rd, Shanghai, 200240, China.
- Shanghai Urban Forest Ecosystem Research Station, National Forestry and Grassland Administration, 800 Dongchuan Rd, Shanghai, 200240, China.
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Liu C, Wu K, Li J, Mu X, Gao H, Xu X. Nanoparticle-mediated therapeutic management in cholangiocarcinoma drug targeting: Current progress and future prospects. Biomed Pharmacother 2023; 158:114135. [PMID: 36535198 DOI: 10.1016/j.biopha.2022.114135] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Patients with cholangiocarcinoma (CCA) often have an unfavorable prognosis because of its insidious nature, low resectability rate, and poor response to anticancer drugs and radiotherapy, which makes early detection and treatment difficult. At present, CCA has a five-year overall survival rate (OS) of only 5%, despite advances in therapies. New an increasing number of evidence suggests that nanoplatforms may play a crucial role in enhancing the pharmacological effects and in reducing both short- and long-term side effects of cancer treatment. This document reviews the advantages and shortcomings of nanoparticles such as liposomes, polymeric nanoparticle,inorganic nanoparticle, nano-metals and nano-alloys, carbon dots, nano-micelles, dendrimer, nano-capsule, bio-Nanomaterials in the diagnosis and treatment of CCA and discuss the current challenges in of nanoplatforms for CCA.
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Affiliation(s)
- Chunkang Liu
- Department of Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Kunzhe Wu
- Department of Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Jianyang Li
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xupeng Mu
- Department of Scientific Research Center, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Huan Gao
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xiaohua Xu
- Department of Nephrology, China-Japan Union Hospital of Jilin University, Changchun, China.
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Koowattanasuchat S, Ngernpimai S, Matulakul P, Thonghlueng J, Phanchai W, Chompoosor A, Panitanarak U, Wanna Y, Intharah T, Chootawiriyasakul K, Anata P, Chaimnee P, Thanan R, Sakonsinsiri C, Puangmali T. Rapid detection of cancer DNA in human blood using cysteamine-capped AuNPs and a machine learning-enabled smartphone. RSC Adv 2023; 13:1301-1311. [PMID: 36686949 PMCID: PMC9814906 DOI: 10.1039/d2ra05725e] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023] Open
Abstract
DNA methylation occurs when a methyl group is added to a cytosine (C) residue's fifth carbon atom, forming 5-methylcytosine (5-mC). Cancer genomes have a distinct methylation landscape (Methylscape), which could be used as a universal cancer biomarker. This study developed a simple, low-cost, and straightforward Methylscape sensing platform using cysteamine-decorated gold nanoparticles (Cyst/AuNPs), in which the sensing principle is based on methylation-dependent DNA solvation. Normal and cancer DNAs have distinct methylation profiles; thus, they can be distinguished by observing the dispersion of Cyst/AuNPs adsorbed on these DNA aggregates in MgCl2 solution. After optimising the MgCl2, Cyst/AuNPs, DNA concentration, and incubation time, the optimised conditions were used for leukemia screening, by comparing the relative absorbance (ΔA 650/525). Following the DNA extraction from actual blood samples, this sensor demonstrated effective leukemia screening in 15 minutes with high sensitivity, achieving 95.3% accuracy based on the measurement by an optical spectrophotometer. To further develop for practical realisation, a smartphone assisted by machine learning was used to screen cancer patients, achieving 90.0% accuracy in leukemia screening. This sensing platform can be applied not only for leukemia screening but also for other cancers associated with epigenetic modification.
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Affiliation(s)
| | - Sawinee Ngernpimai
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Piyaporn Matulakul
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Janpen Thonghlueng
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Witthawat Phanchai
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Apiwat Chompoosor
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University Bangkok 10240 Thailand
| | - Uthumporn Panitanarak
- Department of Biostatistics, Faculty of Public Health, Mahidol University Bangkok 10400 Thailand
| | - Yupaporn Wanna
- Department of Statistics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | - Thanapong Intharah
- Department of Statistics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
| | | | - Pimjai Anata
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen University Khon Kaen 40002 Thailand
| | - Prajuab Chaimnee
- Molecular Diagnosis Unit, Central Laboratory, Srinagarind Hospital, Khon Kaen University Khon Kaen 40002 Thailand
| | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University Khon Kaen 40002 Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University Khon Kaen 40002 Thailand
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Margiana R, Hammid AT, Ahmad I, Alsaikhan F, Turki Jalil A, Tursunbaev F, Umar F, Romero Parra RM, Fakri Mustafa Y. Current Progress in Aptasensor for Ultra-Low Level Monitoring of Parkinson's Disease Biomarkers. Crit Rev Anal Chem 2022; 54:617-632. [PMID: 35754381 DOI: 10.1080/10408347.2022.2091920] [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: 10/17/2022]
Abstract
In today's world, Parkinson's disease (PD) has been introduced as a long-term degenerative disorder of the central nervous system which mainly affects approximately more than ten million people worldwide. The vast majority of diagnostic methods for PD have operated based on conventional sensing platforms, while the traditional laboratory tests are not efficient for diagnosis of PD in the early stage due to symptoms of this common neurodegenerative syndrome starting slowly. The advent of the aptasensor has revolutionized the early-stage diagnosis of PD by measuring related biomarkers due to the myriad advantages of originating from aptamers which can be able to sensitive and selective capture various types of related biomarkers. The progress of numerous sensing platforms and methodologies in terms of biosensors based on aptamer application for PD diagnosis has revealed promising results. In this review, we present the latest developments in myriad types of aptasensors for the determination of related PD biomarkers. Working strategies, advantages and limitations of these sensing approaches are also mentioned, followed by prospects and challenges.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia
- Dr. Soetomo General Academic Hospital, Indonesia Surabaya
| | - Ali Thaeer Hammid
- Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - Irfan Ahmad
- Department of Clinical Laboratory Science, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Fahad Alsaikhan
- College of Pharmacy, Prince Sattam Bin Abdulaziz University, Alkharj, Saudi Arabia
| | - Abduladheem Turki Jalil
- Medical Laboratories Techniques Department, Al-Mustaqbal University College, Babylon, Hilla, Iraq
| | - Farkhod Tursunbaev
- Independent Researcher, "Medcloud" Educational Centre, Tashkent, Uzbekistan
- Research Scholar, Department of Science and Innovation, Akfa University, Tashkent, Uzbekistan
| | - Fadilah Umar
- Department of Sports Science, Faculty of Sports, Sebelas Maret University, Surakarta, Indonesia
| | | | - Yasser Fakri Mustafa
- Department of Pharmaceutical Chemistry, College of Pharmacy, University of Mosul, Mosul, Iraq
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Sousa DA, Carneiro M, Ferreira D, Moreira FTC, Sales MGFV, Rodrigues LR. Recent advances in the selection of cancer-specific aptamers for the development of biosensors. Curr Med Chem 2022; 29:5850-5880. [PMID: 35209816 DOI: 10.2174/0929867329666220224155037] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/30/2021] [Accepted: 12/19/2021] [Indexed: 11/22/2022]
Abstract
An early diagnosis has the potential to greatly decrease cancer mortality. For that purpose, specific cancer biomarkers have been molecularly targeted by aptamer sequences to enable an accurate and rapid detection. Aptamer-based biosensors for cancer diagnostics are a promising alternative to those using antibodies, due to their high affinity and specificity to the target molecules and advantageous production. Synthetic nucleic acid aptamers are generated by in vitro Systematic Evolution of Ligands by Exponential enrichment (SELEX) methodologies that have been improved over the years to enhance the efficacy and to shorten the selection process. Aptamers have been successfully applied in electrochemical, optical, photoelectrochemical and piezoelectrical-based detection strategies. These aptasensors comprise a sensitive, accurate and inexpensive option for cancer detection being used as point-of-care devices. This review highlights the recent advances in cancer biomarkers, achievements and optimizations made in aptamer selection, as well as the different aptasensors developed for the detection of several cancer biomarkers.
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Affiliation(s)
- Diana A Sousa
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Mariana Carneiro
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Débora Ferreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
| | - Felismina T C Moreira
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- BioMark@ISEP, School of Engineering, Polytechnic of Porto, Porto, Portugal
| | - Maria Goreti F V Sales
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
- MIT-Portugal Program, Lisbon, Portugal
- BioMark@UC, Faculty of Sciences and Technology, University of Coimbra, Coimbra, Portugal
| | - Lígia R Rodrigues
- CEB- Centre of Biological Engineering, University of Minho, Campus de Gualtar, Braga, Portugal
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Gao J, Liu N, Zhang X, Yang E, Song Y, Zhang J, Han Q. Utilizing the DNA Aptamer to Determine Lethal α-Amanitin in Mushroom Samples and Urine by Magnetic Bead-ELISA (MELISA). Molecules 2022; 27:molecules27020538. [PMID: 35056853 PMCID: PMC8779134 DOI: 10.3390/molecules27020538] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/12/2022] [Accepted: 01/12/2022] [Indexed: 02/01/2023] Open
Abstract
Amanita poisoning is one of the most deadly types of mushroom poisoning. α-Amanitin is the main lethal toxin in amanita, and the human-lethal dose is about 0.1 mg/kg. Most of the commonly used detection techniques for α-amanitin require expensive instruments. In this study, the α-amanitin aptamer was selected as the research object, and the stem-loop structure of the original aptamer was not damaged by truncating the redundant bases, in order to improve the affinity and specificity of the aptamer. The specificity and affinity of the truncated aptamers were determined using isothermal titration calorimetry (ITC) and gold nanoparticles (AuNPs), and the affinity and specificity of the aptamers decreased after truncation. Therefore, the original aptamer was selected to establish a simple and specific magnetic bead-based enzyme linked immunoassay (MELISA) method for α-amanitin. The detection limit was 0.369 μg/mL, while, in mushroom it was 0.372 μg/mL and in urine 0.337 μg/mL. Recovery studies were performed by spiking urine and mushroom samples with α-amanitin, and these confirmed the desirable accuracy and practical applicability of our method. The α-amanitin and aptamer recognition sites and binding pockets were investigated in an in vitro molecular docking environment, and the main binding bases of both were T3, G4, C5, T6, T7, C67, and A68. This study truncated the α-amanitin aptamer and proposes a method of detecting α-amanitin.
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Affiliation(s)
| | | | | | | | | | | | - Qinqin Han
- Correspondence: ; Tel.: +86-(0871)-65939528
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Sakonsinsiri C, Puangmali T, Sreejivungsa K, Koowattanasuchat S, Thanan R, Chompoosor A, Kulchat S, Sithithaworn P. Aptamer-based colorimetric detection of the DNA damage marker 8-oxo-dG using cysteamine-stabilised gold nanoparticles. RSC Adv 2022; 12:25478-25486. [PMID: 36199304 PMCID: PMC9450492 DOI: 10.1039/d2ra01858f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 08/23/2022] [Indexed: 11/22/2022] Open
Abstract
8-Oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG) is a crucial biomarker for oxidative DNA damage and carcinogenesis. Current strategies for 8-oxo-dG detection often require sophisticated instruments and qualified personnel. In this study, cysteamine-stabilised gold nanoparticles (cyst-AuNPs) were synthesised and used for colorimetric detection of 8-oxo-dG in urine. Sensing of 8-oxo-dG is based on the anti-aggregation of cyst-AuNPs, mediated by the specific recognition of 8-oxo-dG and its aptamer. In the absence of 8-oxo-dG, the aptamer was adsorbed onto the surface of cyst-AuNPs, resulting in aggregation and the development of a purple colour solution. Upon addition of the target molecule 8-oxo-dG, the aptamer specifically bound to it and could not induce the aggregation of cyst-AuNPs, leading to the dispersion of cyst-AuNPs in the solution. Simple visual examination could be used to monitor the purple-to-red colour change that started at 12 nM, a threshold concentration for visual analysis. The absorbance at 525 nm increased in direct relation to the number of the target molecule 8-oxo-dG. This aptamer/cyst-AuNPs system showed excellent sensing ability for the 8-oxo-dG concentration in the range of 15–100 nM, with a detection limit as low as 10.3 nM and a detection time of 30 min. Interference experiments showed that the developed colorimetric strategy had a good sensitivity. This simple and rapid colorimetric method has successfully been applied to inspect 8-oxo-dG concentration in real urine samples and provided recoveries between 93.6 and 94.1%, with a limit of quantification (LOQ) of 34.3 nM, which was comparable with an enzyme-linked immunosorbent-based detection of 8-oxo-dG. This new, easy-to-use, and rapid method could be used as an alternative and initiative strategy for the development of an on-site analysis of 8-oxo-dG in urine. A colorimetric assay based on cysteamine-stabilized AuNPs and anti-8-oxo-dG aptamers for the detection of 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxo-dG), which is a critical DNA damage marker, was developed.![]()
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Affiliation(s)
- Chadamas Sakonsinsiri
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Theerapong Puangmali
- Department of Physics, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kaniknun Sreejivungsa
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | - Raynoo Thanan
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Apiwat Chompoosor
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand
| | - Sirinan Kulchat
- Department of Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Paiboon Sithithaworn
- Department of Parasitology, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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