title: An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.
abstract: A previous NMR structure of the duplex 5'GGU GGA GGCU/PCCG AAG CCG5' revealed an unusually stable RNA internal loop with three consecutive sheared GA pairs. Here, we report NMR studies of two duplexes, 5'GGU GGA GGCU/PCCA AAG CCG5' (replacing the UG pair with a UA closing pair) and 5'GGU GAA GGCU/PCCG AAG CCG5' (replacing the middle GA pair with an AA pair). An unusually stable loop with three consecutive sheared GA pairs forms in the duplex 5'GGU GGA GGCU/PCCA AAG CCG5'. The structure contrasts with that reported for this loop in the crystal structure of the large ribosomal subunit of Deinococcus radiodurans [Harms, J., Schluenzen, F., Zarivach, R., Bashan, A., Gat, S., Agmon, I., Bartels, H., Franceschi, F., and Yonath, A. (2001) Cell 107, 679-688]. The middle AA pair in the duplex 5'GGU GAA GGCU/PCCG AAG CCG5' rapidly exchanges orientations, resulting in alternative base stacking and pseudosymmetry with exclusively sheared pairs. The U GAA G/G AAG C internal loop is 2.1 kcal/mol less stable than the U GGA G/G AAG C internal loop at 37 degrees C. Structural, energetic, and dynamic consequences upon functional group substitutions within related 3 x 3 and 3 x 6 internal loops are also reported.
authors.affiliation: Department of Chemistry, University of Rochester, RC Box 270216, Rochester, New York 14627, USA.
authors.forename: Gang
authors.initials: G
authors.lastname: Chen
authors.forename: Scott D
authors.initials: SD
authors.lastname: Kennedy
authors.forename: Jing
authors.initials: J
authors.lastname: Qiao
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Krugh
authors.forename: Douglas H
authors.initials: DH
authors.lastname: Turner
mesh_terms: D000225:Adenine / Q000737:chemistry*; D020029:Base Pairing; D034301:Deinococcus / Q000235:genetics; D006147:Guanine / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry; D012335:RNA, Ribosomal / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D009692:Nucleic Acid Heteroduplexes; D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D006147:Guanine; D000225:Adenine