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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
JournalMethods
Volume63
Pagination178-187
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

inity 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.

DOI10.1016/j.ymeth.2013.03.016
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