Effects of temperature and molecular crowding on the sensitivity of the 8GZL DNA aptamer toward Cd ²⁺ : a molecular dynamics study

Aptamers show great promise for the specific detection of heavy metal ions, yet their binding affinity can be significantly influenced by environmental conditions. We investigated how temperature and molecular crowding modulate the sensitivity of the 8GZL DNA aptamer towards Cd2+ using molecular dynamics simulations. Calculated results demonstrate that the aptamer exhibits optimal Cd2+ binding affinity at 303 K among commonly encountered temperatures. Furthermore, simulations employing ethanol as a crowding agent reveal that a 5% crowding concentration yields the highest sensitivity. This study reveals that different temperatures and molecular crowding in aqueous solutions can affect the binding of aptamer to Cd2+, providing a theoretical framework for optimizing heavy metal detection in complex environments.