Investigating the malleability of RNA aptamers

Journal Article · Mon Mar 25 04:00:00 EDT 2013 · Methods

DOI:https://doi.org/10.1016/j.ymeth.2013.03.016· OSTI ID:1127459

Ilgu, Muslum; Wang, Tianjiao; Lamm, Monica H.; Nilsen-Hamilton, Marit

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.The paper discusses 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.

• Research Organization: Ames Laboratory (AMES), Ames, IA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: AC02-07CH11358
• OSTI ID: 1127459
• Report Number(s): IS-T--8159
• Journal Information: Methods, Journal Name: Methods Journal Issue: 2 Vol. 63; ISSN 1046-2023
• Publisher: Elsevier
• Country of Publication: United States
• Language: English

Related Subjects

Affinity measurement
Ionic environment effects
Molecular dynamics simulation
59 BASIC BIOLOGICAL SCIENCES
Aptamer