Table 1.

Energy values for terminator hairpin formation and folding traps. Functional riboswitches require that the values of both parameters lie within a relatively narrow range. For the theophylline-binding aptamer, the terminator stability should be higher than −18.1 kcal/mol and lower than −29.0 kcal/mol. Furthermore, the formation barrier of the functional terminator hairpin should not exceed 6.7 kcal/mol to prevent potential kinetic folding traps. The functional constructs are marked with “+”.

Riboswitch	Terminator free energy (kcal/mol)	Terminator formation barrier (kcal/mol)	Riboswitch functionality
RS10	−21.9	2.4	+
RS10loop	−24.8	1.6	+
RS10loopA	−24.3	10.0	−
RS8	−29.0	12.2	−
RS8ΔCC	−22.1	2.9	+
RS8ΔCU	−24.5	6.7	+
RS8Δ4bp	−18.1	2.9	−
RS10loop8	−22.6	2.4	+
RS8ΔCUloop10	−23.9	2.9	+