title: Conformational entropy of a pseudoknot polymer.
abstract: 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 -epsilon1 and -epsilon2, 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 DeltaS=alpha ln N+G, where alpha approximately 2.48 for coil-loop crossover and alpha approximately 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 not equal 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.
authors.affiliation: Department of Chemical Engineering, National Taiwan University, Taipei, Taiwan 106, Republic of China. yjshen@ntu.edu.tw
authors.forename: Yu-Jane
authors.initials: YJ
authors.lastname: Sheng
authors.forename: You-Chin
authors.initials: YC
authors.lastname: Mou
authors.forename: Heng-Kwong
authors.initials: HK
authors.lastname: Tsao
mesh_terms: D000465:Algorithms; D004247:DNA / Q000737:chemistry; D019277:Entropy; D007700:Kinetics; D015233:Models, Statistical; D008962:Models, Theoretical; D008968:Molecular Conformation; D009010:Monte Carlo Method; D009690:Nucleic Acid Conformation; D011108:Polymers / Q000737:chemistry*; D011336:Probability; D012313:RNA / Q000737:chemistry; D012333:RNA, Messenger / Q000737:chemistry; D013696:Temperature; D013816:Thermodynamics
chemical_list: D011108:Polymers; D012333:RNA, Messenger; D012313:RNA; D004247:DNA