A3A affinity to a target cytidine in the loop region of an RNA hairpin was also tested. The exact SDHB hairpin RNA sequence including UC in the loop of this hairpin versus a modified SDHB hairpin RNA replacing the AUC with AAA was compared. A3A had specific affinity for the hairpin RNA containing UC compared to AA (37 nM vs 202 nM respectively) (Fig. 6b). In contrast to what has been previously proposed19, we found that A3A has high affinity and specificity for RNA. Furthermore, A3A has a higher affinity for AUC in the loop region of a hairpin compared to UUC in a linear sequence (Supplementary Fig. 4). The potential UUC substrate sequence in linear RNA has no measurable affinity, comparable to linear RNA without a potential substrate sequence. Overall, A3A has higher affinity for target sequence in the context of a pre-ordered loop region rather than linear DNA, and specific affinity for RNA hairpins with a substrate site.