title: Atomistic analysis of pseudoknotted RNA unfolding.
abstract: As important functional structures, RNA pseudoknots provide excellent models for studying the interplay between secondary and tertiary structures and the roles of triplexes, noncanonical interactions, and coaxial stacking in the folding/unfolding process. Here we report a first atomistic and statistical analysis of the unfolding of the pseudoknot within gene 32 mRNA of bacteriophage T2. Multiple unfolding pathways, diverse transition states, and various intermediate structures were observed. Water molecules were found to be coupled with the unfolding process via the expulsion or concurrent mechanism.
authors.affiliation: National Laboratory of Solid State Microstructure and Department of Physics, Nanjing University, Nanjing 210093, China.
authors.forename: Yujie
authors.initials: Y
authors.lastname: Zhang
authors.forename: Jian
authors.initials: J
authors.lastname: Zhang
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
mesh_terms: D017122:Bacteriophage T4 / Q000737:chemistry* / Q000235:genetics; D003627:Data Interpretation, Statistical; D019277:Entropy; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry*
chemical_list: D012333:RNA, Messenger; D012367:RNA, Viral