Slow molecular recognition by RNA

Rate constants for association involving RNA, separated into RNA/RNA associations (left), RNA/small molecule associations (middle), and RNA duplex formation (right). Rate constants between structured RNAs and RNA ligands are shown in the first three columns, and are further subdivided into interactions that involve formation of base pairs only (BP), formation of base pairs and additional tertiary interactions (BP + 3°), and formation of non-Watson–Crick, tertiary interactions only (3°). For the binding of non-RNA ligands to structured RNAs, association rate constants are broken down into naturally occurring and in vitro–selected RNAs. Values are presented in Supplemental Tables S1–S3 and S5, and “N” is the number of examples in each column. The median values are as follows: RNA-ligand: BP: 3.3 × 10⁵ M⁻¹ sec⁻¹; (BP + 3°): 5.7 × 10⁶ M⁻¹ sec⁻¹; 3°: 2.0 × 10³ M⁻¹ sec⁻¹. The median values for RNA-small molecule ligands are 5.5 × 10⁴ and 8.1 × 10⁴ M⁻¹ sec⁻¹ for natural and in vitro RNAs, respectively. The median value for RNA duplex is 1.3 × 10⁶ M⁻¹ sec⁻¹.