Why kinetic folding matters in RNA design
RNA design is incomplete when equilibrium structure is treated as the sole criterion. Folding kinetics becomes essential whenever pathway, timing, or metastable intermediates contribute to function.
Showing only posts tagged co-transcriptional RNA folding. Show all posts.
Co-transcriptional riboswitch modeling with ViennaRNA
A landscape-based method for modeling how cotranscriptional folding and ligand binding interact in kinetically controlled riboswitches, illustrated with the 2'dG riboswitch from Mesoplasma florum.
In silico design of ligand-triggered RNA switches
A computational workflow for designing ligand-triggered RNA switches, with emphasis on sequence design, folding kinetics, and candidate prioritization.
Co-transcriptional folding and metastable states in riboswitch function
This paper uses NMR spectroscopy to resolve transcription intermediates of the 2'dG riboswitch at single-nucleotide resolution, showing how transcript length and metastable states govern ligand-controlled switching.
BarMap and RNA folding on dynamic energy landscapes
BarMap models RNA folding on changing energy landscapes by linking macrostates between landscape snapshots, enabling efficient analysis of co-transcriptional and externally perturbed folding scenarios.
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