Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors

Douaki, Ali; Garoli, Denis; Inam, Aqil; Angeli, Martina Aurora Costa; Cantarella, Giuseppe; Rocchia, Walter; Wang, Jiahai; Petti, Luisa; Lugli, Paolo

doi:10.3390/bios12080574

Cited by 20 publications

(14 citation statements)

References 98 publications

(108 reference statements)

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“…The divergent directionality of structure switching for the dopamine vs. serotonin aptamers were corroborated by QCM-D results. Finally, molecular dynamics simulations (MDS), previously shown to predict oligonucleotide tertiary structures accurately, [27][28][29][30][31] were performed to simulate the aptamers in their free vs. target-bound states. Correlations between experimental and theoretical findings demonstrate the potential of MDS as a tool to predict aptamer structure-switching mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Stuber

Douaki

Hengsteler

et al. 2023

Preprint

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Aptamers that undergo conformational changes upon small molecule recognition have been shown to gate the ionic flux through nanopores by rearranging charge density within the aptamer-occluded orifice. However, mechanistic insight into such systems where biomolecular interactions are confined in nanoscale spaces, is limited. To shed light on the fundamental mechanisms that facilitate the detection of small-molecule analytes inside structure-switching aptamer-modified nanopores, we correlated experimental observations to theoretical models. We developed a novel dopamine aptamerfunctionalized nanopore sensor with femtomolar detection limits and compared the sensing behavior with a serotonin sensor fabricated with the same methodology. When sensing these two neurotransmitters with comparable mass and equal charge, the sensors showed an opposite electronic behavior. This distinctive phenomenon was extensively studied using complementary experimental techniques such as quartz crystal microbalance with dissipation monitoring, in combination with theoretical assessment by the finite element method and molecular dynamic simulations. Taken together, our studies demonstrate that the sensing behavior of highly sensitive aptamer-modified nanopores correlates with the structure-switching mechanisms unique to the selected aptamers targeting specific small-molecule analytes. We believe that such investigations not only improve our understanding of the complex interactions occurring in confined nanoscale environments, but will also drive further innovations in biomimetic nanopore technologies.

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Section: Introductionmentioning

confidence: 99%

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Stuber

Douaki

Hengsteler

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…Wearable electrochemical sensors for

-THC and CBD require further research and development to create POC devices. These devices typically require sensing electrodes, microfluidic and filtering systems, electronics, and wireless communication for data transmission [ 62 , 63 , 64 , 65 , 66 ]. However, integrating all of these components to create small, non-invasive platforms is not easy [ 62 , 65 , 66 , 67 , 68 ].…”

Section: Research Challenges and Future Perspectivesmentioning

confidence: 99%

“…These devices typically require sensing electrodes, microfluidic and filtering systems, electronics, and wireless communication for data transmission [ 62 , 63 , 64 , 65 , 66 ]. However, integrating all of these components to create small, non-invasive platforms is not easy [ 62 , 65 , 66 , 67 , 68 ]. Detecting cannabinoids in biofluids, such as saliva, tears, and subcutaneous interstitial fluid non-invasively is a challenge [ 47 , 69 ].…”

Section: Research Challenges and Future Perspectivesmentioning

confidence: 99%

Nanomaterials-Based Electrochemical Δ9-THC and CBD Sensors for Chronic Pain

2023

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Chronic pain is now included in the designation of chronic diseases, such as cancer, diabetes, and cardiovascular disease, which can impair quality of life and are major causes of death and disability worldwide. Pain can be treated using cannabinoids such as Δ9-tetrahydrocannabinol (Δ9-THC) and cannabidiol (CBD) due to their wide range of therapeutic benefits, particularly as sedatives, analgesics, neuroprotective agents, or anti-cancer medicines. While little is known about the pharmacokinetics of these compounds, there is increasing interest in the scientific understanding of the benefits and clinical applications of cannabinoids. In this review, we study the use of nanomaterial-based electrochemical sensing for detecting Δ9-THC and CBD. We investigate how nanomaterials can be functionalized to obtain highly sensitive and selective electrochemical sensors for detecting Δ9-THC and CBD. Additionally, we discuss the impacts of sensor pretreatment at fixed potentials and physiochemical parameters of the sensing medium, such as pH, on the electrochemical performance of Δ9-THC and CBD sensors. We believe this review will serve as a guideline for developing Δ9-THC and CBD electrochemical sensors for point-of-care applications.

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“…These include fragment-based methods: RNAComposer ( (accessed on 12 October 2022)), 3dRNA ( (accessed on 12 October 2022)), and Vfold 3D ( (accessed on 12 October 2022)); and energy-based method: simRNA ( (accessed on 12 October 2022)) [ 62 ]. Molecular docking tools include AutoDock, AutoDock Vina, and DOCK, which were used to predict the predominant binding modes and regions of the target molecule based on the generated binding scores for specific sequences [ 63 , 64 , 65 ]. After a few prediction steps, the aptamer candidates are shortlisted and subjected to binding tests and characterization.…”

Section: Principle and General Procedures Of Capture-selex For Aptame...mentioning

confidence: 99%

Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application

2022

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Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule–aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.

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Smart Approach for the Design of Highly Selective Aptamer-Based Biosensors

Cited by 20 publications

References 98 publications

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

Nanomaterials-Based Electrochemical Δ9-THC and CBD Sensors for Chronic Pain

Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application

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