Label‐Free Colorimetric Biosensors Based on Aptamers and Gold Nanoparticles: A Critical Review

Zhang, Fang; Liu, Juewen

doi:10.1002/anse.202000023

Cited by 56 publications

(57 citation statements)

References 118 publications

(311 reference statements)

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“…Finally, we revisited the AuNP-based label-free methods, for which artifacts due to dopamine adsorption on AuNPs were previously articulated. [22,37] To have a side-by-side comparison of these two aptamers, we mixed the aptamers and different concentrations of dopamine, and then added AuNPs. [18,34] The bare citrate-capped AuNPs then easily aggregated upon addition of salt and changed color from red to blue.…”

Section: Aunp-based Colorimetric Methodsmentioning

confidence: 99%

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Hou

Liu

2021

ChemBioChem

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Dopamine is an essential neurotransmitter and its detection is important for bioanalytical chemistry. Two very different DNA aptamers have been reported for dopamine, one derived from an RNA aptamer (named Apt1) and other obtained via direct aptamer selection (named Apt2). In this study, we used four homogeneous binding assays to compare these two DNA dopamine aptamers. Thiazole orange (TO) fluorescence assay indicated that the Apt2 specifically bound with dopamine with a Kd of 2.37 μM, which was consistent with that from the isothermal titration calorimetry (ITC) assay. However, Apt1 had much less TO fluorescence change and also no signal from ITC. By labeling the two ends of the two aptamers by a fluorophore and a quencher, the aptamer beacons showed binding of dopamine only for Apt2. Finally, the label‐free AuNP‐based colorimetric assay showed no difference between these two aptamer sequences, and even non‐binding random DNA showed the same response, indicating that AuNPs were not a good probe for detecting dopamine. According to the data, Apt1 does not appear to be able to bind dopamine specifically, while Apt2 showed specific binding and could be used for developing related biosensors.

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Section: Aunp-based Colorimetric Methodsmentioning

confidence: 99%

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Hou

Liu

2021

ChemBioChem

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“…To conclude, the robustness of this sensing scheme can only be validated after undertaking extensive control experiments which include testing the interaction between bare AuNPs and the target of interest. 62 In addition, a control experiment that uses a randomized aptamer sequence is not trustable enough due to the difference in adsorption of each aptamer on AuNPs because of the difference in each nucleotide sequence.…”

Section: Colorimetric Optical Aptasensormentioning

confidence: 99%

Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Sester¹

2021

Preprint

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Aptamers are synthetic nucleic acid single-stranded oligonucleotides that bind to a wide range of ligands, including cells, proteins, DNA strands, metal ions, and small molecules, with high specificity and affinity. Aptamers have also proven to be highly stable, readily adaptable to chemical modifications, and exhibit reversible binding. As a result, aptamer-based biosensors (aptasensors) are promising replacements for antibody-based biosensors in many applications, particularly for small molecule ligands. This thesis explores an aptamer that binds the drug methamphetamine, and its prospects when incorporated in an electrochemical (e-chem) signal transduction platform. Specifically, we examine the range of interactions between the aptamer and ligand, and with electrodes, and identify a number of challenges in generating robust e-chem aptasensors. Due to their size and limited number of functional groups, further understanding of the aptamer-small molecule ligand interactions is required for the design of future aptasensors – particularly the thermodynamics and structural information about the aptamer-ligand interaction. In fact, detecting small molecules with aptasensors can become challenging because target addition may induce little structural change, and therefore numerous nonspecific interactions may emerge as transduced signals from the biosensor. In this thesis, the combination of spectroscopic and calorimetric analytical techniques reveals a conformational selection binding model, in which binding is entropically driven, and the meth binds via hydrophobic and electrostatic interactions and only induces a modest structural change. This first-of-its-kind study is important for the selection and the design of the aptasensor transduction system. Electrochemical (e-chem) aptasensors offer high inherent sensitivity and practicality as a signal transduction platform. Indeed, different e-chem aptasensor formats have been published before, including labelled and label-free sensors. In screening the viability of three commonly used methods – including labelled and label-free, as well voltammetric and impedance-based methods – we find that each of them suffers from instability of the aptamer-functionalised electrode. This instability compromises our ability to resolve real signals and prompted us to develop ways to understand – and suppress – this baseline drift. The functionalization of the electrode is the critical step in terms of self-assembled monolayer (SAM) stability and SAM aptamer density. Consequently, different protocols of SAMformation were explored and evaluated with respect to stability. We find that instability arises from the uncontrolled arrangement of thiolated aptamers on gold electrodes (including aptamers lying down on the electrode), which is in turn affected by the density of aptamers that can be coupled to the surface. As a consequence, a new protocol is developed using disulfide aptamer pairs to increase the density of correctly tethered aptamers, and generate a stable SAM. Because of the high sensitivity of electrochemical platforms, numerous spurious electrochemical signals may be produced, and controlled for in order to confirm a positive ligand-binding signal. The specificity of the aptamer-target interaction can be checked by testing the response with an interferent molecule, or by substituting the aptamer with a non-binding nucleotide sequence. In this work, these control experiments reveal that target and interferent molecules interact directly (and in different ways) with the bare gold surface, as well as perturbing signals from the aptamer in ways that cannot be linked to a specific aptamer-ligand complex formation. Ultimately, these spurious signals compromise our ability to confirm a real binding signal. The results from this work provide the first clear picture of how an aptamer binds to its small molecule target – which we find is entropically driven, and with only minor structural change induced in the aptamer stem. In addition, the label-free EIS measurements on aptamer SAM electrodes reveal the nature of instabilities, and reveal spurious signals that cannot be sufficiently suppressed at this stage. This knowledge highlights the difficulty in fabricating e-chem aptasensors, and will assist in overcoming challenges faced during research and commercialization of aptasensors area, as well as contributing new insights into troubleshooting, data acquisition, and data validation.

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“…The Zhang and Liu [64] mentioned that the success of using DNA in label-free devices based on optical biosensors has inspired the same approach in the aptamer field. However, the authors explain that aptamers can fold DNA and hide its bases, providing slow kinetics of target binding, especially when the target is a small molecule.…”

Section: Label-free Detectionmentioning

confidence: 99%

Mof@Mos2-Based Electrochemical Biosensor for Ca125 Detection

Weifeng¹

2020

BJSTR

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Antibodies and aptamers play a crucial role to improve the analytical performance of biosensors for medical applications. Besides their natural compatibility with many antigens and pathogens, their biochemical structure selectively binds the analyte providing high sensitivity and selectivity. Accordingly, this minireview presents the recent approaches in the field of immunosensors and aptasensors for clinical diagnoses with a focus on the key features of sensors over the conventional diagnostic assays and the trends in this field of knowledge (point-of-care devices for in situ applications, label-free bioreceptors, real-time monitoring of analytes and outstanding transduction techniques).

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Label‐Free Colorimetric Biosensors Based on Aptamers and Gold Nanoparticles: A Critical Review

Cited by 56 publications

References 118 publications

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Comparison of Two DNA Aptamers for Dopamine Using Homogeneous Binding Assays

Electrochemical aptasensors: unravelling the critical interactions between aptamers, ligands, and electrodes

Mof@Mos2-Based Electrochemical Biosensor for Ca125 Detection

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