ArticleBiochemistry2010
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.
Article in Biochemistry, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Longer Is Not Always Better: Effects of Equilibration Length on Umbrella Sampling Estimations for RNA Hairpin Folding Stabilities.bioRxiv : the preprint server for biology · 2026Article
- Characterizing RNA 3D structural features from DMS reactivity.Nucleic acids research · 2026Article
- NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.Biophysical journal · 2026Article
- An RNA excited conformational state at atomic resolution.Nature communications · 2023Article
- Nuclear Magnetic Resonance Reveals That GU Base Pairs Flanking Internal Loops Can Adopt Diverse Structures.Biochemistry · 2019Article
- Molecular dynamics correctly models the unusual major conformation of the GAGU RNA internal loop and with NMR reveals an unusual minor conformation.RNA (New York, N.Y.) · 2018Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Surprising Sequence Effects on GU Closure of Symmetric 2 × 2 Nucleotide RNA Internal Loops.Biochemistry · 2018Article
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- Resolving sugar puckers in RNA excited states exposes slow modes of repuckering dynamics.Nucleic acids research · 2017Article
- Article
- Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.Biochemistry · 2015Article
- De novo tertiary structure prediction using RNA123--benchmarking and application to Macugen.Journal of molecular modeling · 2014Article
- Thermodynamic and phylogenetic insights into hnRNP A1 recognition of the HIV-1 exon splicing silencer 3 element.Biochemistry · 2014Article
- Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site.Biochemistry · 2013Article
- Atomic-accuracy prediction of protein loop structures through an RNA-inspired Ansatz.PloS one · 2013Article
- Novel conformation of an RNA structural switch.Biochemistry · 2012Article
- Prevalence of syn nucleobases in the active sites of functional RNAs.RNA (New York, N.Y.) · 2011Article
- NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions.RNA (New York, N.Y.) · 2011Article
- Synthesis and properties of triazole-linked RNA.Bioorganic & medicinal chemistry letters · 2011Article
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5 authors.
Funding
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, 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'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 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.
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