Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit

Munzar, Jeffrey D.; Ng, Andy; Juncker, David

doi:10.1038/s41467-017-02556-3

Cited by 46 publications

(77 citation statements)

References 57 publications

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“…According to our results ( Figure 8 ), after 2 days in air, hybridization is no longer favored over G-quadruplex structure or multimer formation. Such concurrent behavior between hybridization and multimer formation has already been demonstrated for TBA–15 [ 39 ]. However, as suggested in this reference, when subjected to sodium-only buffer incubation, the TBA–15 hybridization is favored over G-quadruplex formation.…”

Section: Resultssupporting

confidence: 53%

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

et al. 2020

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Field effect transistors (FETs) based on networks of randomly oriented Si nanowires (Si nanonets or Si NNs) were biomodified using Thrombin Binding Aptamer (TBA–15) probe with the final objective to sense thrombin by electrical detection. In this work, the impact of the biomodification on the electrical properties of the Si NN–FETs was studied. First, the results that were obtained for the optimization of the (3-Glycidyloxypropyl)trimethoxysilane (GOPS)-based biofunctionalization process by using UV radiation are reported. The biofunctionalized devices were analyzed by atomic force microscopy (AFM) and scanning transmission electron microscopy (STEM), proving that TBA–15 probes were properly grafted on the surface of the devices, and by means of epifluorescence microscopy it was possible to demonstrate that the UV-assisted GOPS-based functionalization notably improves the homogeneity of the surface DNA distribution. Later, the electrical characteristics of 80 devices were analyzed before and after the biofunctionalization process, indicating that the results are highly dependent on the experimental protocol. We found that the TBA–15 hybridization capacity with its complementary strand is time dependent and that the transfer characteristics of the Si NN–FETs obtained after the TBA–15 probe grafting are also time dependent. These results help to elucidate and define the experimental precautions that must be taken into account to fabricate reproducible devices.

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Section: Resultssupporting

confidence: 53%

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

et al. 2020

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“…This aptasensor showed a LDR between 0.2 and 15000 µM. Recently, Munzar and coworkers described a method for screening optimal aptamer-complementary strands based on the DNA microarray technology in order to improve strand displacement assays [63]. Interestingly, this work shows that complementary strands can enhance the binding activity of single stranded aptamers that were previously discovered in solution.…”

Section: Aptasensor Electrochemistry Architecturesmentioning

confidence: 95%

Challenges in Electrochemical Aptasensors and Current Sensing Architectures Using Flat Gold Surfaces

Rozenblum

Pollitzer²,

Radrizzani

2019

Chemosensors

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In recent years, reagentless aptamer biosensors, named aptasensors, have shown significant advancements. Particularly, electrochemical aptasensors could change the field of biosensors in this era, where digitalization seems to be a common goal of many fields. Biomedical devices are integrating electronic technologies for detecting pathogens, biomolecules, small molecules, and ions, and the physical-chemical properties of nucleic acid aptamers makes them very interesting for these devices. Aptamers can be easily synthesized and functionalized with functional groups for immobilization and with redox chemical groups that allow for the conversion of molecular interactions into electrical signals. Furthermore, non-labeled aptamers have also been utilized. This review presents the current challenges involved in aptasensor architectures based on gold electrodes as transducers.

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“…[92] Recently,M unzar et al designed an array-based method to optimize cDNAl ength for aptamer-based stranddisplacement sensors. [220] Their array contained thousands of spots,each containing acluster of unique covalently attached DNAofdiffering lengths and sequence that are complementary to various regions of an aptamer.T he aptamer,l abeled with af luorophore,w as attached to the array surface via hybridization with the immobilized cDNAs trands.T arget binding caused the aptamer to dissociate,w hich resulted in areduction of fluorescence.Based on fluorescence changes at specific locations on the array,t he regions of the aptamer responsible for target binding could be identified. This assay could also provide information about the binding mechanism of aptamers (i.e.induced fit or conformational selection) and the cDNAs equences that were most suitable for sensor development.…”

Section: Sensors Based On Target-induced Strand Displacementmentioning

confidence: 99%

Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development

Alkhamis

Canoura

et al. 2021

Angewandte Chemie

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Aptamers are short oligonucleotides isolated in vitro from randomizedlibraries that can bind to specific molecules with high affinity,and offer an umber of advantages relative to antibodies as biorecognition elements in biosensors.H owever,i tremains difficult and labor-intensive to develop aptamer-based sensors for small-molecule detection. Here,w er eview the challenges and advances in the isolation and characterization of small-molecule-binding DNAa ptamers and their use in sensors.First, we discuss in vitro methodologies for the isolation of aptamers,and provide guidance on selecting the appropriate strategy for generating aptamers with optimal binding properties for agiven application. We next examine techniques for characterizing aptamer-target binding and structure.A fterwards,w ediscuss various small-molecule sensing platforms based on original or engineered aptamers,and their detection applications.F inally,w econclude with ageneral workflow to develop aptamer-based small-molecule sensors for real-world applications. Aus dem Inhalt 1. Introduction 16939 2. Challenges and Advances in Aptamer Isolation 16942 3. Challenges and Advances in Aptamer Characterization 16949 4. Challenges and Advances in Developing Aptamer-Based Small-Molecule Sensors 16953

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Comprehensive profiling of the ligand binding landscapes of duplexed aptamer families reveals widespread induced fit

Cited by 46 publications

References 57 publications

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

Challenges in Electrochemical Aptasensors and Current Sensing Architectures Using Flat Gold Surfaces

Advances and Challenges in Small‐Molecule DNA Aptamer Isolation, Characterization, and Sensor Development

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