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

Abstract

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

Aptamer Conformational Dynamics Modulate Neurotransmitter Sensing in Nanopores

“…Aptamer-integrated solid-state nanopores can serve as biomimetic systems that simulate how protein channels control ionic transport selectively in response to small-molecule binding. Aptamers are artificial, single-stranded oligonucleotides isolated through an iterative evolutionary method to interact specifically with analytes of interest. , Advances in selection methodologies have enabled the discovery of aptamers targeting small molecules, , which are conventionally difficult targets with minimal available functional groups for recognition. − Coupling such selective bioreceptors inside nanoscale pores with geometries that complement and confine the aptamer–target interactions enables measurements that approach single-molecule sensitivities. − Nanoscale pores can be prepared using different strategies. − In particular, glass nanopipettes are one of the most convenient nanopore platforms due to the ease of fabrication via laser pulling, which can yield pore sizes ranging from a few to tens of nanometers with high reproducibility. , …”

“…Aptamers are artificial, single-stranded oligonucleotides isolated through an iterative evolutionary method to interact specifically with analytes of interest. 1 , 2 Advances in selection methodologies have enabled the discovery of aptamers targeting small molecules, 2 , 3 which are conventionally difficult targets with minimal available functional groups for recognition. 4 − 6 Coupling such selective bioreceptors inside nanoscale pores with geometries that complement and confine the aptamer–target interactions enables measurements that approach single-molecule sensitivities.…”

Real-Time Monitoring of Neurotransmitters in the Brain of Living Animals

“…They can selectively bind to a variety of target analytes, including ions, small molecules, proteins, and peptides up to whole cells . Aptamers are produced through Systematic Evolution of Ligands by Exponential Enrichment (SELEX), which exposes a large library of random RNA or DNA sequences to the analyte of interest . In this way, the bound sequences are separated and amplified.…”

Effects of Nucleic Acid Structural Heterogeneity on the Electrochemistry of Tethered Redox Molecules

“…Structure switching sensors such as electrochemical aptamer-based (E-AB) sensors rely on a measurable conformational change of the electrode-bound nucleic acid aptamer in the presence of a target. − Aptamers are single-stranded DNA or RNA oligonucleotides selected to bind to a specific target analyte through a process termed SELEX. − The interest in the development of aptamer-based sensors is growing because of the ability to detect virtually any analyte of interest through the selection of the nucleic acid sequence specific to the target analyte. However, the functionality of this class of sensing strategies, including electrochemical, aptamer-based sensors, is dependent on the target-induced conformational change of the nucleic acid measured by changes in the faradic current associated with the oxidation/reduction of a redox moiety at the 3′ position of the aptamer.…”