Theoretical analysis of divalent cation effects on aptamer recognition of neurotransmitter targets
Ali Douaki, Annina Stuber, Julian Hengsteler, Dmitry Momotenko, David M. Rogers, Walter Rocchia, Jonathan D. Hirst, Nako Nakatsuka, Denis Garoli
Abstract
) present in brain fluid, have been shown to affect the conformational dynamics of aptamers upon target recognition. Thus, for biosensors that transduce aptamer structure switching as the signal response, it is critical to interrogate the influence of divalent cations on each unique aptamer sequence. Herein, we demonstrate the potential of molecular dynamics (MD) simulations to predict the behaviour of dopamine and serotonin aptamers on sensor surfaces. The simulations enable molecular-level visualization of aptamer conformational changes that, in some cases, are significantly influenced by divalent cations. The correlations of theoretical simulations with experimental findings validate the potential for MD simulations to predict aptamer-specific behaviors on biosensors.