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• 作者：Nicholas B. Hammond ; Blanton S. Tolbert ; Ryszard Kierzek ; Douglas H. Turner ; Scott D. Kennedy
• 刊名：Biochemistry
• 出版年：2010
• 出版时间：July 13, 2010
• 年：2010
• 卷：49
• 期：27
• 页码：5817-5827
• 全文大小：1041K
• 年卷期：v.49,no.27(July 13, 2010)
• ISSN：1520-4995

文摘

Thermodynamic stabilities of 2 × 2 nucleotide tandem AG internal loops in RNA range from −1.3 to +3.4 kcal/mol at 37 °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: (rGACGss="uu">AGCGUCA)<sub>2sub>, (rGACUss="uu">AGAGUCA)<sub>2sub>, (rGACAss="uu">AGUGUCA)<sub>2sub>, (rGGUss="uu">AGGCCA)<sub>2sub>, and (rGACGss="uu">AGUGUCA)<sub>2sub>. The structures of these duplexes are compared to that of the previously solved (rGGCss="uu">AGGCC)<sub>2sub> (Wu, M., SantaLucia, J., Jr., 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′Uss="uu">AGG/3′Gss="uu">GAU loop adopts canonical UG wobble pairing (cis Watson−Crick/Watson−Crick), with AG pairs that are only weakly imino-paired. Strikingly, the 5′Gss="uu">AGU/3′Uss="uu">GAG loop has two distinct duplex conformations, the major of which has both guanosine residues (G4 and G6 in (rGACGss="uu">AGUGUCA)<sub>2sub>) 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 a dynamic or stacked conformation. These structures provide benchmarks for computational investigations into interactions responsible for the unexpected differences in loop free energies and structure.