title: Loop Entropy Assists Tertiary Order: Loopy Stabilization of Stacking Motifs.
abstract: The free energy of an RNA fold is a combination of favorable base pairing and stacking interactions competing with entropic costs of forming loops. Here we show how loop entropy, surprisingly, can promote tertiary order. A general formula for the free energy of forming multibranch and other RNA loops is derived with a polymer-physics based theory. We also derive a formula for the free energy of coaxial stacking in the context of a loop. Simulations support the analytic formulas. The effects of stacking of unpaired bases are also studied with simulations.
authors.affiliation: Physics Department, Williams College, Williamstown, MA 01267, USA; Tel.: +1-413-597-3520;
authors.forename: Daniel P
authors.initials: DP
authors.lastname: Aalberts
keywords: Hairpin loops; RNA; coaxial stacking; multibranch loops; polymer simulations; secondary structure; tertiary structure