Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment

Qi, Shuo; Duan, Nuo; Khan, Imran Mahmood; Dong, Xiaoze; Zhang, Yin; Wu, Shijia; Wang, Zhouping

doi:10.1016/j.biotechadv.2021.107902

Cited by 90 publications

(37 citation statements)

References 202 publications

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“…The electrostatic complementarity occurs because of an interaction between the positive and negative charges present on the surfaces of the aptamer and the target. Apart from the electrostatic interaction, other intermolecular interactions such as van der Waals forces, hydrogen bonds and π-π stacking make the aptamer–target complex stable [ 25 ]. They feature distinct characteristics such as compact size, low cost, high specificity, facile chemical modification, and most importantly extraordinary flexibility.…”

Section: Label and Label-free Aptasensorsmentioning

confidence: 99%

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

et al. 2022

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Viral infections are becoming the foremost driver of morbidity, mortality and economic loss all around the world. Treatment for diseases associated to some deadly viruses are challenging tasks, due to lack of infrastructure, finance and availability of rapid, accurate and easy-to-use detection methods or devices. The emergence of biosensors has proven to be a success in the field of diagnosis to overcome the challenges associated with traditional methods. Furthermore, the incorporation of aptamers as bio-recognition elements in the design of biosensors has paved a way towards rapid, cost-effective, and specific detection devices which are insensitive to changes in the environment. In the last decade, aptamers have emerged to be suitable and efficient biorecognition elements for the detection of different kinds of analytes, such as metal ions, small and macro molecules, and even cells. The signal generation in the detection process depends on different parameters; one such parameter is whether the labelled molecule is incorporated or not for monitoring the sensing process. Based on the labelling, biosensors are classified as label or label-free; both have their significant advantages and disadvantages. Here, we have primarily reviewed the advantages for using aptamers in the transduction system of sensing devices. Furthermore, the labelled and label-free opto-electrochemical aptasensors for the detection of various kinds of viruses have been discussed. Moreover, numerous globally developed aptasensors for the sensing of different types of viruses have been illustrated and explained in tabulated form.

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Section: Label and Label-free Aptasensorsmentioning

confidence: 99%

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

et al. 2022

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“…MD simulations generate a conformational ensemble of nucleic acid structures at equilibrium and provide detailed atomic motions that aid in understanding structure–function relationships in an aptamer [ 112 , 114 ]. Due to the advantages of incorporating MD simulations into a computational pipeline, an increasing number of published studies report the use of software packages such as NAMD, AMBER, and GROMACS [ 101 , 115 , 116 ]. Ultimately, computational methods could be applied to predict the interactions between an aptamer and its ligand and, hence, refine the nucleic acid sequence to improve the binding affinity and specificity, in addition to being applied for the de novo selection of aptamer in silico [ 114 , 116 ].…”

Section: Nucleic Acid Aptamersmentioning

confidence: 99%

“…Due to the advantages of incorporating MD simulations into a computational pipeline, an increasing number of published studies report the use of software packages such as NAMD, AMBER, and GROMACS [ 101 , 115 , 116 ]. Ultimately, computational methods could be applied to predict the interactions between an aptamer and its ligand and, hence, refine the nucleic acid sequence to improve the binding affinity and specificity, in addition to being applied for the de novo selection of aptamer in silico [ 114 , 116 ]. An overview of the workflow followed for the simulation-based prediction of an aptamer’s interactions with, and affinity for, its ligand is shown in Figure 2 .…”

Section: Nucleic Acid Aptamersmentioning

confidence: 99%

Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety

Evtugyn

Porfireva

Tsekenis

et al. 2022

Sensors

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Antibiotics are often used in human and veterinary medicine for the treatment of bacterial diseases. However, extensive use of antibiotics in agriculture can result in the contamination of common food staples such as milk. Consumption of contaminated products can cause serious illness and a rise in antibiotic resistance. Conventional methods of antibiotics detection such are microbiological assays chromatographic and mass spectroscopy methods are sensitive; however, they require qualified personnel, expensive instruments, and sample pretreatment. Biosensor technology can overcome these drawbacks. This review is focused on the recent achievements in the electrochemical biosensors based on nucleic acid aptamers for antibiotic detection. A brief explanation of conventional methods of antibiotic detection is also provided. The methods of the aptamer selection are explained, together with the approach used for the improvement of aptamer affinity by post-SELEX modification and computer modeling. The substantial focus of this review is on the explanation of the principles of the electrochemical detection of antibiotics by aptasensors and on recent achievements in the development of electrochemical aptasensors. The current trends and problems in practical applications of aptasensors are also discussed.

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“…This interaction between the aptamer recognition element and the reporter is guided by the way they are written into the DNA blueprint of the biosensor (Fowler & Li, 2014). Moreover, benefiting from the target versatility of aptamer, riboswitch, as the gene structure of reporter protein, can achieve the purpose of highly sensitive and specific detection from small organic molecules to heavy metals, proteins, cells, and even complete virus particles (Oueslati et al., 2018; Qi et al., 2022; Stepanova et al., 2017; Sun et al., 2022). Due to the extremely complex environment of living bacterial cells, target diversity represented the detection of each target with its unique challenges (Hoetzel & Suess, 2022).…”

Section: Introductionmentioning

confidence: 99%

Advances in riboswitch‐based biosensor as food samples detection tool

Khan

Sun

et al. 2022

Comp Rev Food Sci Food Safe

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Food safety has always been a hot issue of social concern, and biosensing has been widely used in the field of food safety detection. Compared with traditional aptamer-based biosensors, aptamer-based riboswitch biosensing represents higher precision and programmability. A riboswitch is an elegant example of controlling gene expression, where the target is coupled to the aptamer domain, resulting in a conformational change in the downstream expression domain and determining the signal output. Riboswitch-based biosensing can be extensively applied to the portable real-time detection of food samples. The numerous key features of riboswitch-based biosensing emphasize their sustainability, renewable, and testing, which promises to transform engineering applications in the field of food safety. This review covers recent developments in riboswitch-based biosensors. The brief history, definition, and modular design (regulatory mode, reporter, and expression platform) of riboswitch-based biosensors are explained for better insight into the design and construction. We summarize recent advances in various riboswitch-based biosensors involving theophylline, malachite green, tetracycline, neomycin, fluoride, thrombin, naringenin, ciprofloxacin, and paromomycin, aiming to provide general guidance for the design of riboswitch-based biosensors. Finally, the challenges and prospects are also summarized as a way forward stratagem and signs of progress.

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Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment

Cited by 90 publications

References 202 publications

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

Ultrasensitive Aptasensors for the Detection of Viruses Based on Opto-Electrochemical Readout Systems

Electrochemical Aptasensors for Antibiotics Detection: Recent Achievements and Applications for Monitoring Food Safety

Advances in riboswitch‐based biosensor as food samples detection tool

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