(A, filled triangle) The number of single-stranded RNA chain conformations grows much faster than (unfilled triangle) the number of the end–end configurations (relative coordinates) of the chain. (B) We study the excluded volume effects on the loop entropy for a given pseudoknot with S1 = 4 bp, S2 = 4 bp, L1 = 4 nt, and L3 = 2 nt. We vary the loop length for L2 from 1 nt to 7 nt and find that we can neglect the loop–loop excluded volume interactions. (Open square) Results without excluded volume interactions; (filled triangle) results without considering the loop–loop excluded volume interactions; (open triangle) results with all the excluded volume interactions fully considered. (C) Comparison between the conformational entropy from the exact computer enumeration and the entropy from our theory. The deviation is small (<1 k B T in free energy).
