Aptamer-ligand recognition studied by native ion mobility-mass spectrometry

TALANTA

卷:224

Article

Daems, Elise^1,2  Dewaele, Debbie¹  Barylyuk, Konstantin^1,5  De Wael, Karolien²  Sobott, Frank^1,3,4 

[1] Univ Antwerp, BAMS Res Grp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium

[2] Univ Antwerp, AXES Res Grp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium

[3] Univ Leeds, Astbury Ctr Struct Mol Biol, Leeds LS2 9JT, W Yorkshire, England

[4] Univ Leeds, Sch Mol & Cellular Biol, Leeds LS2 9JT, W Yorkshire, England

[5] Univ Cambridge, Hopkins Bldg,Tennis Court Rd, Cambridge CB2 1QW, England

关键词: Oligonucleotide structure;    Aptamers;    Ligand affinity;    Native mass spectrometry;    Ion mobility;   

DOI  :  10.1016/j.talanta.2020.121917

来源: Elsevier

【 摘 要 】

The range of applications for aptamers, small oligonucleotide-based receptors binding to their targets with high specificity and affinity, has been steadily expanding. Our understanding of the mechanisms governing aptamerligand recognition and binding is however lagging, stymieing the progress in the rational design of new aptamers and optimization of the known ones. Here we demonstrate the capabilities and limitations of native ion mobilitymass spectrometry for the analysis of their higher-order structure and non-covalent interactions. A set of related cocaine-binding aptamers, displaying a range of folding properties and ligand binding affinities, was used as a case study in both positive and negative electrospray ionization modes. Using carefully controlled experimental conditions, we probed their conformational behavior and interactions with the high-affinity ligand quinine as a surrogate for cocaine. The ratios of bound and unbound aptamers in the mass spectra were used to rank them according to their apparent quinine-binding affinity, qualitatively matching the published ranking order. The arrival time differences between the free aptamer and aptamer-quinine complexes were consistent with a small ligand-induced conformational change, and found to inversely correlate with the affinity of binding. This mass spectrometry-based approach provides a fast and convenient way to study the molecular basis of aptamer-ligand recognition.

【 授权许可】

Free