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Publication Abstract from PubMed

ABSTRACT: Thermodynamic stabilities of 2 x 2 nucleotide tandem AG internal loops in RNA range from -1.3 to +3.4 kcal/mol at 37 degrees C and are not predicted well with a hydrogen bonding model. To provide structural information to facilitate development of more sophisticated models for the sequence dependence of stability, we report the NMR solution structures of five RNA duplexes: (rGACGAGCGUCA)2, (rGACUAGAGUCA)2, (rGACAAGUGUCA)2, (rGGUAGGCCA)2 and (rGACGAGUGUCA)2. The structures of these duplexes are compared to that of the previously solved (rGGCAGGCC)2 (Wu, M., SantaLucia, Jr., J. and Turner, D. H. (1997) Biochemistry 36: 4449-4460). For loops bounded by Watson-Crick pairs, the AG and Watson-Crick pairs are all head-to-head imino-paired (cis Watson-Crick/Watson-Crick). The structures suggest that the sequence-dependent stability may reflect non-hydrogen bonding interactions. Of the two loops bounded by G-U pairs, only the 5 UAGG/3 GGAU loop adopts canonical UG wobble pairing (cis Watson-Crick/Watson-Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5 GAGU/3 UGAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGAGUGUCA)2) in a syn glycosidic bond conformation and forming a sheared GG pair (G4-G6*, GG trans Watson-Crick/Hoogsteen), both uracils (U7 and U7*) flipped out of the helix, and an AA pair (A5-A5*) in an undetermined conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.

RNA Internal Loops with Tandem AG Pairs: The Structure of the 5 GAGU/3 UGAG Loop can be Dramatically Different from Others, Including 5 AAGU/3 UGAA.,Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD Biochemistry. 2010 May 20. PMID:20481618^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.