Experimental and mathematical evidence that thrombin-binding aptamers form a 1 aptamer:2 protein complex.

ABSTRACT: The thrombin-binding 15mer and 29mer ssDNA aptamers are a widely used model system. Despite their ubiquity, controversies persist regarding the nature of the aptamer-protein interactions. Reported affinities vary widely; the role of metal ions in binding is unclear; the structure of the complex is contested. We interrogated the effects of instrument, buffer, and mathematical model on apparent affinities of thrombin aptamers for their target. Instrumental method had a pronounced effect on affinity constants for the 15mer and marginal effect the apparent affinity of the 29mer. Buffer composition and ionic environment did not have significant effects. Affinity probe capillary electrophoresis experiments revealed distinct peaks from samples of 29mer aptamer and thrombin, supporting the model o

SUBMITTER: Mears KS 

PROVIDER: S-EPMC8372783 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature