Rapid and Label-Free Strategy to Isolate Aptamers for Metal Ions

Abstract

Generating aptamers that bind to specific metal ions is challenging because existing aptamer discovery methods typically require chemical labels or modifications that can alter the structure and properties of the ions. In this work, we report an aptamer discovery method that enables us to generate high-quality structure-switching aptamers (SSAs) that undergo a conformational change upon binding a metal ion target, without the requirement of labels or chemical modifications. Our method is more efficient than conventional selection methods because it enables direct measurement of target binding via fluorescence-activated cell sorting (FACS), isolating only the desired aptamers with the highest affinity. Using this strategy, we obtained a highly specific DNA SSA with ~30-fold higher affinity than the best aptamer for Hg2+ in the literature. We also discovered DNA aptamers that bind to Cu2+ with excellent affinity and specificity. Both aptamers were obtained within four rounds of screening, demonstrating the efficiency of our aptamer discovery method. Given the growing availability of FACS, we believe our method offers a general strategy for discovering high-quality aptamers for other ions and small-molecule targets in an efficient and reproducible manner.

Label-free sensing of the binding state of MUC1 peptide and anti-MUC1 aptamer solution in fluidic chip by terahertz spectroscopy

“…Aptamers, single-stranded RNA or DNA oligonucleotide selected by the systematic evolution of ligands by exponential enrichment (SELEX) methodology, interact with targets by forming special three-dimensional conformations. Since the concept of aptamer was first proposed by Ellington in 1990 [7], it has been presented as a regnant bioreceptor for the construction of various aptasensors to detect ions [8,9], proteins [1,10], and cells [11,12], as aptamers possess high affinity, exquisite specificity, reduced immunogenicity, increased stability, and good reproducibility. Moreover, aptamers could be massively synthesized and easily modified via chemical processes, which is more costeffective [13].…”

A highly specific sodium aptamer probed by 2-aminopurine for robust Na+sensing

“…So far, few high-performance metal aptamers were isolated using selection methods. While it is possible to immobilize the DNA library (55) or using emulsion droplets to bypass metal immobilization (56), this work suggests an alternative method to obtain aptamers via DNAzyme selection. In this method, no immobilization of metal ions or the library, or the use of emulsion is needed.…”

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

“…[68] Other screening methods such as those based on microdroplets are also highlyd esirable. They have now been used for aptamer screening form olecular targets, [69][70][71][72] and their application for surfaces has yet to be demonstrated. Most previous work focusedo ng old and carbon nanotubes for screening, and even for these two, the number of tested DNA sequences is still very limited.…”