Incorporation of a metal-mediated base pair into an ATP aptamer - using silver(I) ions to modulate aptamer function.

Marius H Heddinga,Jens Müller

doi:10.3762/bjoc.16.236

Abstract

For the first time, a metal-mediated base pair has been used to modulate the affinity of an aptamer towards its target. In particular, two artificial imidazole 2’-deoxyribonucleosides (Im) were incorporated into various positions of an established ATP-binding aptamer (ATP, adenosine triphosphate), resulting in the formation of three aptamer derivatives bearing Im:Im mispairs with a reduced ATP affinity. A fluorescence spectroscopy assay and a binding assay with immobilized ATP were used to evaluate the aptamer derivatives. Upon the addition of one Ag(I) ion per mispair, stabilizing Im–Ag(I)–Im base pairs were formed. As a result, the affinity of the aptamer derivative towards ATP is restored again. The silver(I)-mediated base-pair formation was particularly suitable to modulate the aptamer function when the Im:Im mispairs (and hence the resulting metal-mediated base pairs) were located close to the ATP-binding pocket of the aptamer. Being able to trigger the aptamer function opens new possibilities for applications of oligonucleotides.

Highlights

Aptamers are oligonucleotides capable of recognizing and binding to specific molecules up to the size of proteins [1]
For 1cf, the imidazole 2’-deoxyribonucleosides (Im):Im pair is located towards the termini, whereas in derivative 1df it is close to the loop region
The metal-mediated Im–Ag(I)–Im base pair can be used to modulate the affinity of the ATP-binding aptamer to its target

Summary

Introduction

Aptamers are oligonucleotides capable of recognizing and binding to specific molecules up to the size of proteins [1]. A slight disadvantage of using this metal-mediated base pair could be the fact that Ag(I) is known to have an affinity to adenine derivatives (such as ATP, i.e., the target molecule of the aptamer) [37,38]. To evaluate whether the Ag(I)-mediated base pairs are formed in the aptamer derivatives, melting curves and circular dichroism (CD) spectra were recorded in the presence of increasing amounts of Ag(I).

Results

Conclusion