Table 1.

Summary of exemplary primary, secondary and tertiary catalytic effects.

Sysa	Variantb	Effectsc	k/k′d	Changee
VSr	A621 :S(SP)	1° β		NPO thio substitution disrupts Mg2+ binding
		2° γ	>103	pKa up-shift of G638:N1 (due to loss of Mg2+)
		3° γ		Disrupt anchoring of G638 (due to loss of Mg2+)
	G638I/A756(3cP)	2° β		NPO charge destabilization (loss of H-bonds)
		3° γ	140	Disruption of G638:N1 (general base) positioning
		3° δ		Disruption of A756:N1 (general acid) positioning
	G623(7cG)	3° β		Disruption of Mg2+ binding pocket (G623:N7)
		2° γ	>103	pKa up-shift of G638:N1 (due to loss of Mg2+)
		3° γ		Disrupt anchoring of G638 (due to loss of Mg2+)
	C17(dC)	1° γ	>103	Nucleophile knockout (C17:O2’ removal)
HHr	G12(3cG)	2° γ	>200	pKa up-shift of G12:N1 (general base)
	A9G	3° γ	>300	Disrupt anchoring of G12 (due to loss of H-bonds)
	A1 (3cA)	1° δ	>>105	General acid (A1 :N3) knockout
Twr	A1 (1 cA)	2° γ	0.05f	pKa up-shift of A1:N3 (general acid)
	A1 (2AP)	3° δ	>105	Disruption of A1 position (due to loss of H-bonds)
		2° δ		pKa down-shift of A1:N3 (due to loss of NPO interactions)

^aRibozyme systems: Varkud satellite (VSr), hammerhead (HHr) and twister (Twr) ribozymes.

^bIdentity of the all chemical modifications to the wild type (WT) ribozyme/substrate.

^cExemplary effects (discussed as “specific examples” in the text) are shown in bold and left-aligned and additional effects (indicated by “Note” in text) are right-aligned.

^dRelative rates of the mutations to the native system for VSr³⁴, HHr^35–37 , and Twr^38–39. The k/k′ value for A621:S(SP) thio substitution for VSr is equivalent to k_O/k_S.

^eSummary of the change in the system caused by the mutation.

^fBased on A19U variant.