Conformational entropy of a pseudoknot polymer

Yu Jane Sheng, You Chin Mou, Heng Kwong Tsao

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The thermodynamics and kinetics of ABAB pseudoknot formation owing to reversible intrachain reactions are investigated for a flexible polymer based on the off-lattice Monte Carlo simulations. The polymer is made of N hard spheres tethered by inextensible bonds and consists of two reactive pairs AA and BB with binding energies - ε1 and - ε2, respectively, and three loop lengths (ℓ1, ℓ2, and ℓ3). Although two intermediate states, loops A and B, may be formed, the folding path goes mainly through the intermediate loop whose free energy reduction associated with coil-to-loop crossover is greater. The conformational entropy loss is found to follow ΔS=α ln N+G, where α≃2.48 for coil-loop crossover and α≃2.43 for loop-pseudoknot crossover. The constant G depends on the three loop lengths and the two end-to-reactive site lengths (L1 and L2). For a given total loop length, G is maximum when the three loop lengths are equal (ℓ1 = ℓ2 = ℓ3). When ℓ1 = ℓ3, the entropy loss is minimum if ℓ2 =0. However, the condition ℓ1 ≠ ℓ3 makes G even smaller. This consequence indicates that asymmetry in loop lengths is thermodynamically favorable and this fact is consistent with observations of pseudoknotted RNA structures.

Original languageEnglish
Article number124904
JournalJournal of Chemical Physics
Issue number12
StatePublished - 2006


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