In Vitro Selection of an ATP-Binding TNA Aptamer.

Li Zhang,John C Chaput

doi:10.3390/molecules25184194

Li Zhang, John C Chaput

Open Access

https://doi.org/10.3390/molecules25184194

Copy DOI

Abstract

Recent advances in polymerase engineering have made it possible to isolate aptamers from libraries of synthetic genetic polymers (XNAs) with backbone structures that are distinct from those found in nature. However, nearly all of the XNA aptamers produced thus far have been generated against protein targets, raising significant questions about the ability of XNA aptamers to recognize small molecule targets. Here, we report the evolution of an ATP-binding aptamer composed entirely of α-L-threose nucleic acid (TNA). A chemically synthesized version of the best aptamer sequence shows high affinity to ATP and strong specificity against other naturally occurring ribonucleotide triphosphates. Unlike its DNA and RNA counterparts that are susceptible to nuclease digestion, the ATP-binding TNA aptamer exhibits high biological stability against hydrolytic enzymes that rapidly degrade DNA and RNA. Based on these findings, we suggest that TNA aptamers could find widespread use as molecular recognition elements in diagnostic and therapeutic applications that require high biological stability.

Highlights

Aptamers are functional nucleic acid molecules that fold into 3D structures with specific ligand-binding activity [1]
adenosine triphosphate (ATP)-agarose beads, demonstrating that the selection had successfully enriched for a population of threose nucleic acid (TNA) aptamers with affinity to ATP
An additional three rounds of selective amplification were performed to favor the enrichment of aptamers from the random region by including short DNA oligonucleotides that were complementary to both primer-binding sites

Summary

Introduction

Aptamers are functional nucleic acid molecules that fold into 3D structures with specific ligand-binding activity [1]. Aptamers have been generated by in vitro selection to bind a wide range of targets from small molecules to whole cells and viruses [2]. The in vitro selection process used to generate aptamers allows for greater control over the binding conditions, which enables aptamers to be tailored for specific applications [4]. Small molecules play key roles in many biological processes, functioning as toxins, nutrients, enzyme cofactors, sources of energy, and as cell signaling molecules. Small molecule targets account for only ~23% of aptamers produced by in vitro selection, making them significantly less abundant than protein aptamers [4].

Methods

Results

Conclusion