Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers.

ABSTRACT: Interferometric measurements of free solution assays (FSAs) quantify changes in molecular conformation and hydration upon binding. Here, we demonstrate that aptamer probes designed to undergo varying levels of conformational change upon binding produce corresponding variations in FSA signals. A series of hairpin aptamers were synthesized for the small molecule (tenofovir) with identical loop regions that contain the binding pocket, with between 2 and 10 self-associating base pairings in the stem region. Aptamers selected for tenofovir showed a decrease in the FSA signal and binding affinity (increase in K D) with increasing stem length. Thermodynamic calculations of the Gibbs free energy (ΔG) reported a decrease in ΔG with respect to a corresponding increase in the aptamer stem length. Col

SUBMITTER: Kammer MN 

PROVIDER: S-EPMC7254501 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature