Modulating the Substrate Selectivity of DNA Aptamers Using Surfactants

Abstract

Nucleic acid aptamers have a number of advantages compared to antibodies, including greater ease of production and increased thermal stability. We hypothesized that aptamers may also be capable of functioning in the presence of high concentrations of surfactants, which readily denature antibodies and other protein-based affinity reagents. Here we report the first systematic investigation into the compatibility of DNA aptamers with surfactants. We find that neutral and anionic surfactants have only a minor impact on the ability of aptamers to fold and bind hydrophilic target molecules. Additionally, we demonstrate that surfactants can be utilized to modulate the substrate binding preferences of aptamers, likely due to the sequestration of hydrophobic target molecules within micelles. The compatibility of aptamers with commonly used surfactants is anticipated to expand their scope of potential applications, and the ability to modulate the substrate binding preferences of aptamers using a simple additive provides a novel route to increasing their selectivity in analytical applications.

Oligonucleotide Detection and Optical Measurement with Graphene Oxide in the Presence of Bovine Serum Albumin Enabled by Use of Surfactants and Salts

“…Triton X-100 clearly modulated the strong MgCl 2 effect on oligonucleotide-GO binding, extending prior observations that it modulated DNA target-probe interactions [54] to oligonucleotide-nanomaterial interactions as well. In complex solutions, the enhanced variable partitioning of target-probe binding could increase the ssDNA probe selectivity toward hydrophilic steroid analytes.…”

“…Such a reduction in non-specific interactions could increase the binding affinity between the probe and the target. Among a range of common surfactants spanning cationic, anionic, non-ionic and zwitterionic states, Triton X-100, Tween-20 (both neutral and non-ionic) and SDS (anionic), unlike zwitterionic or positively charged alternatives, maintained a good oligonucleotide biosensor response [54]. Hydrophobic interactions played an important role in the binding of either SDS or Triton X-100 to GO [55].…”

Collaboration between primitive cell membranes and soluble catalysts

“…Recently, several other groups have observed that lipid assemblies can bind biopolymer building blocks 30 and modulate DNA aptamer specificity 31 . Our results here demonstrate that the functional repertoire of lipids extends yet further, into the realm of enabling soluble catalysts to promote reactions that are otherwise disfavoured or impossible in aqueous solution.…”

In vitro selection of an XNA aptamer capable of small-molecule recognition

“…Aptamers provide numerous advantages over antibodies including increased thermal stability and tolerance to surfactants. Additionally, aptamers can be chemically synthesized, enabling more cost-effective production and allowing for the incorporation of a wide range of labels and non-natural functional groups ( 4 ). However, aptamers comprised of native DNA and RNA retain some limitations due to their instability in biological fluids and cellular environments ( 5 ).…”