In this article, a neoacetalization-based method for post-SELEX modification of aptamers is introduced. Three modified quinine binding aptamer scaffolds were synthesized by replacing three different nucleosides of the binding site with a (2R,3S)-4-(methoxyamino)butane-1,2,3-triol residue. These aptamer scaffolds were incubated in different aldehyde mixtures with and without quinine, allowing the reversible formation of N-methoxy-1,3-oxazinane (MOANA) nucleoside analogues through dynamic combinatorial chemistry. UHPLC-MS analysis identified two aldehydes, namely methyl 4-formylbenzoate and 3-nitrobenzaldehyde, with significantly different tendency to react with one of the aptamer scaffolds in the presence and absence of quinine. The quinine binding affinity of these two modified aptamers was determined by isothermal titration calorimetry (ITC). Unexpectedly, the 3-nitrobenzaldehyde derivatized aptamer dimerized on binding quinine at the relatively high concentration of the ITC. In addition, we discovered that with another modified aptamer, quinine binding caused cleavage of the N–O bond of the (2R,3S)-4-(methoxyamino)butane-1,2,3-triol residue.