One method for detecting dopamine involves the use of RNA and DNA aptamers. Aptamers are single-stranded sequences of DNA or RNA that bind with high affinity to specific target molecules. Various aptamers have been developed to measure dopamine, making it crucial to identify which one exhibits the strongest interaction with it. This study, for the first time, examines the interaction between dopamine and aptamers using molecular dynamics simulations. The findings reveal that all three aptamers can interact with and detect dopamine. By calculating the binding Gibbs energy (ΔGbind) between the aptamers and dopamine, it was determined that the DNA aptamer with 44 nucleotide residues is the most selective for dopamine. Additional analyses of the root-meansquare deviation (RMSD), root-mean-square fluctuation (RMSF), radial distribution function (RDF), and radius of gyration (Rg) which assess structural stability and fluctuations further support that this aptamer has the most effective interaction with dopamine.

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