In the case of the opposite system, containing the imidazolium bridged di-adenosine intermediate (ApAIpA) with two complementary uridine nucleotides within the templating strand, we did not observe any clusters that could enable accurate recognition for both WC contacts at the same time. For all the identified clusters with the DBSCAN and Kmeans procedures the 5 ′ -end of the templating strand was largely disordered, often sampling random coil arrangements. The K-means clustering algorithm returned one cluster char-acterized by a Hoogsteen base pairing interaction of the adjacent adenine nucleobase and a WC base pair formed by the terminal nucleobase of ApAIpA with the template. However, this cluster represents only 8.0% of the analyzed trajectory (Supporting Information Fig. ). Formation of only one WC interaction between ApAIpA and the template can be assigned to merely 31.2% of the analyzed trajectory frames, which demonstrates lower binding specificity of this activated dinucleotide when compared to the GpAIpG parent system. Instead, 67,5% of the frames from K-means analysis displayed G-stacked structure, similar to what was observed for GpAIpC (Fig4 e)) and 19.5% adopted the O-stacked geometry (Fig4 f)). In the average structures representing these motifs, the C3 ′ -endo conformation was predominantly observed, accompanied by the anti orientation of the nucleobases.