Investigating the malleability of RNA aptamers

TitleInvestigating the malleability of RNA aptamers
Publication TypeJournal Article
Year of Publication2013
AuthorsIlgu M, Wang TJ, Lamm MH, Nilsen-Hamilton M
Journal TitleMethods
Volume63
Pages178-187
Date Published09
Type of ArticleArticle
ISBN Number1046-2023
Accession NumberWOS:000326005600011
Keywords2-aminopurine, Affinity measurement, algorithms, Aptamer, binding-affinity, cocaine, dependence, environment effects, Ionic, molecular dynamics simulation, molecular-dynamics, neomycin-b, recognition, resolution, simulation
Abstract

Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemical analysis with NMR spectroscopy and computational modeling to explore the relation between ligand binding and structural malleability of some well-studied aptamers. Several methods for determining aptamer binding affinity and specificity are discussed, including isothermal titration calorimetry, steady state fluorescence of 2-aminopurine substituted aptamers, and dye displacement assays. Also considered are aspects of molecular dynamics simulations specific to aptamers including adding ions and simulating aptamer structure in the absence of ligand when NMR spectroscopy or X-ray crystallography structures of the unoccupied aptamer are not available. We focus specifically on RNA aptamers that bind small molecule ligands as would be applied in sensors or integrated into riboswitches such as to measure the products of metabolic activity. (C) 2013 Elsevier Inc. All rights reserved.

URL<Go to ISI>://WOS:000326005600011
DOI10.1016/j.ymeth.2013.03.016