A helix folds only when stacking beats loop entropy
Supplied working report; original verdicts not validated.
Review status: Held for correction. This is an archival source note, not a passed proof.
README.md
# A helix folds only when stacking beats loop entropy **XXII, Theory 10 / Molecular / RNA structure** · verdict: **supported** Claim (verbatim): > RNA secondary structure is set by the ratio of base-pairing energy to loop entropy, so a helix forms only when the pairing gain exceeds the cost of closing a loop. ## Result The minimum stem required to fold rises from 3 bp for a 4-nt loop to 5 bp for a 1000-nt loop: the pairing gain must grow to cover the loop-entropy cost. ## Headline Minimum stem to fold grows from 3 to 5 bp as the loop lengthens from 4 to 1000 nt. ## Design Hairpin free energy was modelled as stem stacking gain minus a loop-initiation plus length-dependent entropy cost; the smallest stem giving a stable fold was found for loop sizes spanning 4-1000 nt. ## Key statistics - min_stem_loop4 = 3 bp - min_stem_loop30 = 4 bp - min_stem_loop300 = 5 bp - min_stem_loop1000 = 5 bp ## Predictions - **P1** (supported): minimum stem rises 3 -> 5 bp as loop grows ## Limitations - Mean stacking and loop-entropy parameters are simplifications of the full nearest-neighbour model. - The model ignores coaxial stacking, ion effects and tertiary contacts. - The log dependence of loop entropy means the threshold stem grows only slowly with loop size. Provenance: Jacobson-Stockmayer loop entropy with a loop-initiation penalty and mean NN stacking. *Working paper — not peer reviewed. AI-assisted. Not medical, clinical, financial or safety advice.*