Structure and target interaction of a G-quadruplex RNA-aptamer

Abstract

G-quadruplexes have recently moved into focus of research in nucleic acids, thereby evolving in scientific significance from exceptional secondary structure motifs to complex modulators of gene regulation. Aptamers (nucleic acid based ligands with recognition properties for a specific target) that form Gquadruplexes may have particular potential for therapeutic applications as they combine the characteristics of specific targeting and Gquadruplex mediated stability and regulation. We have investigated the structure and target interaction properties of one such aptamer: AIR-3 and its truncated form AIR-3A. These RNA aptamers are specific for human interleukin-6 receptor (hIL-6R), a key player in inflammatory diseases and cancer, and have recently been exploited for in vitro drug delivery studies. With the aim to resolve the RNA structure, global shape, RNA: protein interaction site and binding stoichiometry, we now investigated AIR-3 and AIR-3A by different methods including RNA structure probing, Small Angle X-ray scattering and microscale thermophoresis. Our findings suggest a broader spectrum of folding species than assumed so far and remarkable tolerance toward different modifications. Mass spectrometry based binding site analysis, supported by molecular modeling and docking studies propose a general Gquadruplex affinity for the target molecule hIL-6R.

Development and characterization of novel 2′-F-RNA aptamers specific to human total and glycated hemoglobins

“…Analysis of predicted secondary structures using VIENNA RNAfold algorithm (see Materials and methods) revealed G-quadruplex (GQ) forming motifs for sequences H5, H7, H5136, and H9. While GQ motifs are quite uncommon for RNA aptamers, several GQ forming RNA aptamers have been previously reported, including those for prion proteins [15,16], human interleukin-6 receptor [17],…”

Octa-repeat domain of the mammalian prion protein mRNA forms stable A-helical hairpin structure rather than G-quadruplexes

“…To gain insights into the size and shape of folded wt and ΔG4 PrP octa-repeat mRNA, we next performed SAXS measurements at different RNA concentrations and in the presence of 100 mM LiCl or KCl and 1 mM PDS. RNA preparation, SAXS measurements and data analysis were done using a procedure described previously for G-quadruplex dimers of an RNA aptamer 38 . The processed scattering data and the computed distance distribution functions are summarized in Supplementary Table S1 and Supplementary Fig.…”

G-quadruplex-based aptamers against protein targets in therapy and diagnostics

“…Another G4-forming aptamer potentially useful in drug delivery, named AIR-3A, has been discovered by Meyer et al AIR-3A is an RNA aptamer of sequence r(GGGGAGGCUGUGGUGAGGG) that specifically recognizes the receptor of interleukin-6 (IL-6), a cytokine that plays a key role in inflammatory diseases and cancer. AIR-3A was proved to specifically deliver proteins towards cells expressing IL-6R (Interleukin-6 Receptor) on their surface, such as hepatocytes, monocytes, macrophages, lymphocytes and HIV-infected cells [141,142], further stimulating the research on novel drug delivery systems useful not only in anticancer, but also in anti-HIV treatments.…”