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RAID3 - An interleukin-6 receptor-binding aptamer with post-selective modification-resistant affinity

DOI: 10.1080/15476286.2015.1079681 DOI Help

Authors: Florian Mittelberger (University of Hamburg) , Cindy Meyer (Rockefeller University) , Georg H. Waetzig (CONARIS Research Institute AG) , Martin Zacharias (Technical University Munich) , Erica Valentini (University of Hamburg) , Dmitri I. Svergun (European Molecular Biology Laboratory, Hamburg) , Katharina Berg (University of Hamburg) , Inken Lorenzen (University of Kiel) , Joachim Grötzinger (University of Kiel) , Stefan Rose-John (University of Kiel) , Ulrich Hahn (University of Hamburg)
Co-authored by industrial partner: No

Type: Journal Paper
Journal: Rna Biology , VOL 12 , PAGES 1043 - 1053

State: Published (Approved)
Published: July 2015

Abstract: Aptamers are an emerging class of highly specific targeting ligands. They can be selected in vitro for a large variety of targets, ranging from small molecules to whole cells. Most aptamers selected are nucleic acid-based, allowing chemical synthesis and easy modification. Although their properties make them interesting drug candidates for a broad spectrum of applications and an interesting alternative to antibodies or fusion proteins, they are not yet broadly used. One major drawback of aptamers is their susceptibility to abundant serum nucleases, resulting in their fast degradation in biological fluids. Using modified nucleic acids has become a common strategy to overcome these disadvantages, greatly increasing their half-life under cell culture conditions or even in vivo. Whereas pre-selective modifications of the initial library for aptamer selection are relatively easy to obtain, post-selective modifications of already selected aptamers are still generally very labor-intensive and often compromise the aptamers ability to bind its target molecule. Here we report the selection, characterization and post-selective modification of a 34 nucleotide (nt) RNA aptamer for a non-dominant, novel target site (domain 3) of the interleukin-6 receptor (IL-6R). We performed structural analyses and investigated the affinity of the aptamer to the membrane-bound and soluble forms (sIL-6R) of the IL-6R. Further, we performed structural analyses of the aptamer in solution using small-angle X-ray scattering and determined its overall shape and oligomeric state. Post-selective exchange of all pyrimidines against their 2′-fluoro analogs increased the aptamers stability significantly without compromising its affinity for the target protein. The resulting modified aptamer could be shortened to its minimal binding motif without loss of affinity.

Journal Keywords: Aptamers; cell biology; cytokine signaling; Interleukin-6 receptor; internalization; molecular modelling; post-selective modification; protein-RNA interactions; SAXS

Subject Areas: Biology and Bio-materials, Chemistry

Instruments: B21-High Throughput SAXS

Added On: 09/05/2016 09:32

Discipline Tags:

Health & Wellbeing Biochemistry Chemistry Structural biology Life Sciences & Biotech

Technical Tags:

Scattering Small Angle X-ray Scattering (SAXS)