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.

Keywords

• RNA
• coaxial stacking
• tertiary structure
• secondary structure
• multibranch loops
• Hairpin loops
• polymer simulations