An Analysis of the Affinity and Stability of Base Pair Modifications of the Glucose-Binding and Cocaine-Binding Aptamers

Aptamers are selected to bind to their ligands, usually with high affinity and selectivity for targets. An aptamer was previously selected to bind glucose with a Kd of 10mM which is physiologically relevant as the blood glucose concentration typically falls between 4-11 mM. NMR spectroscopy is suited to study weak aptamer-ligand interactions and was used to investigate the affinity of sequence modified glucose-binding aptamers to try and determine a sequence with a greater binding affinity. Three of thirteen modifications bound to glucose, the change of a G-T base pair to a G-C base pair (Glumod-7) with a Kd of 2.9mM±0.3mM, the alteration of the terminal triloop from a C-T-C to a G-A-A (Gumod-8) with a Kd of 12mM±3mM, and the truncation by 3 base pairs (Glumod-12) which was too weak to determine a Kd. Glumod-7 was the only sequence which had a comparable Kd and would require further investigation in terms of stability using NMR thermomelts. Cocaine-binding aptamers are intriguing as they are composed of three stems centered around two mismatch A-G base pairs and are very well studied in terms of secondary structure and affinity. The thermostability of cocaine-binding aptamers as a function of number of base pairs in stem one was investigated by DSC. There was a trend observed of increasing in stability from 1 base pair to 6 base pairs with a decrease seen at 7 base pairs. The most thermodynamically stable aptamer was determined to be MN4, a preformed structure.