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To function as gene regulatory elements in response to environmental signals,riboswitches must adopt specific secondary structures on appropriate timescales. We employ kinetic Monte Carlo simulation to model the time-dependentfolding during transcription of TPP riboswitch expression platforms. Accordingto our simulations, riboswitch transcriptional terminators, which must adopt aspecific hairpin configuration by the time they have been transcribed, foldwith higher efficiency than Shine-Dalgarno sequesterers, whose proper structureis required only at the time of ribosomal binding. Our findings suggest boththat riboswitch transcriptional terminator sequences have been naturallyselected for high folding efficiency, and that sequesterers can maintain theirfunction even in the presence of significant misfolding.

Folding Kinetics of Riboswitch Transcriptional Terminators and Sequesterers