Temperature and molecular crowding effects on the sensitivity of T30695 aptamer toward Pb2+ion: a joint molecular dynamics simulation and experimental study

The aptamer-target binding affinity can be influenced by some environmental parameters, e.g. temperature and molecular crowding agents. Molecular dynamics (MD) simulation is a potent approach to highlight the effect of such parameters. In this study, we represent an MD simulation investigation to clarify the influence of temperature and molecular crowding on the sensitivity of T30695 aptamer toward Pb2+. The binding Gibbs energies (ΔGbind) are calculated for the aptamer-Pb2+ complex at the different temperatures, clarifying that its greatest value is at 37°C. Hence, the aptamer possesses the highest specificity toward Pb2+ at this temperature. The MD simulation results of the crowding effect, imitated by ethanol, proves that the most aptamer sensitivity toward Pb2+ is in the solution with 5% v/v concentration of ethanol. The aptamer specificity is studied under the MD-introduced optimal conditions by a colorimetric approach. The detection limits of 192 and 83.61 pM are obtained at 27°C and 37°C, respectively. They are computed 192 and 148 pM in the aqueous and ethanol solutions, respectively. The experimental results are in agreement with the MD ones, proving success of MD simulation to specify the environmental conditions in which the sensitivity of the aptamer is the greatest toward its target.