Assays to Estimate the Binding Affinity of Aptamers

Thevendran, Ramesh; Citartan, Marimuthu

doi:10.1016/j.talanta.2021.122971

Cited by 39 publications

(36 citation statements)

References 140 publications

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“…Indeed, in the domain of aptasensors, spacers were usually added to separate the recognition sequence of aptamers from the surface in order to either improve the response of the transducer and/or the affinity. [29][30][31][32][35][36][37] As an example, Martin et al have studied the influence of various spacer lengths and compositions on the recognition capacity of aptamers against immunoglobulin E, thrombin and riboflavin. They demonstrated that poly(dT) linkers are quite efficient spacers for the different aptamer/target pairs in comparison to poly(dA), poly(dC) and poly(dG) linkers.…”

Section: Influence Of the Linker Lengthmentioning

confidence: 99%

Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude

Pons

Perenon

Bonnet

et al. 2022

Analyst

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Section: Influence Of the Linker Lengthmentioning

confidence: 99%

Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude

Pons

Perenon

Bonnet

et al. 2022

Analyst

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“…Capillary electrophoresis (CE) is a separation-based method in which an electrical field is used for the separation of charged components by their molecular size [ 78 ]. For small molecule aptamers, this method is particularly challenging since the target-aptamer complex typically shows a small increase in size when compared to the free aptamer.…”

Section: Aptamer-target Interactions—affinity Thermodynamic Parameter...mentioning

confidence: 99%

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

et al. 2022

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Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

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“…The binding of target molecules released the cDNA, leading to fluorescence recovery. , This is a reliable method, although the cost of synthesis is still very high. Many other fluorescence-based methods were also developed, but they were not widely used. − …”

Section: Introductionmentioning

confidence: 99%

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

Qin

Lopez

et al. 2022

Anal. Chem.

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With more and more new aptamers being reported, a general, cost-effective yet reliable aptamer binding assay is still needed. Herein, we studied cationic conjugated polymer (CCP)-based binding assays taking advantage of the conformational change of aptamer after binding with a target, which is reflected by the fluorescence change of the CCP. Poly(3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene hydrochloride) (PMNT) was used as a model CCP in this study, and the optimal buffer was close to physiological conditions with 100 mM NaCl and 10 mM MgCl2. We characterized four aptamers for K+, adenosine, cortisol, and caffeine. For cortisol and caffeine, the drop in the 580 nm peak intensity was used for quantification, whereas for K+ and adenosine, the fluorescence ratio at 580 over 530 nm was used. The longer stem of the stem-loop structured aptamer facilitated binding of the target and enlarged the detection signal. High specificity was achieved in differentiating targets with analogues. Compared with the SYBR Green I dye-based staining method, our method achieved equal or even higher sensitivity. Therefore, this assay is practicable as a general aptamer binding assay. The simple, label-free, quick response, and cost-effective features will make it a useful method to evaluate aptamer binding. At the same time, this system can also serve as label-free biosensors for target detection.

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Assays to Estimate the Binding Affinity of Aptamers

Cited by 39 publications

References 140 publications

Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude

Conformational transition in SPR experiments: impact of spacer length, immobilization mode and aptamer density on signal sign and amplitude

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

General Label-Free Fluorescent Aptamer Binding Assay Using Cationic Conjugated Polymers

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