Excluded-volume effects on the stacking of RNA base pairs

We validate the implementation of a path-integral formalism to compute the thermodynamics of stacking of RNA base pairs, restricting the analysis to intramolecular interactions. We estimate the effective contact volume, an empirical parameter that determines the excluded-volume effects. This is done by comparing the analytical result with the energetics of duplex growth that takes place after a loop closure or nucleation event. As an illustrative example, the derivation is specialized to the polymer (CG${)}_{\mathit{n}}$, n→∞ (C denotes cytosine, G denotes guanosine) in the limit of infinitely long tails.