ArticleBiochemistry2006
An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 28 citations in OpenAlex.
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- Solution Structure of NPSL2, A Regulatory Element in the oncomiR-1 RNA.Journal of molecular biology · 2022Article
- Dynamical Signatures of Multifunnel Energy Landscapes.The journal of physical chemistry letters · 2022Review
- Fidelity of base-pair recognition by a 3'-5' polymerase: mechanism of theRNA (New York, N.Y.) · 2021Article
- Why Nature Chose Potassium.Journal of molecular evolution · 2019Review
- How to benchmark RNA secondary structure prediction accuracy.Methods (San Diego, Calif.) · 2019Review
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- Modeling RNA secondary structure folding ensembles using SHAPE mapping data.Nucleic acids research · 2018Article
- Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.RNA (New York, N.Y.) · 2017Article
- The loss of a hydrogen bond: Thermodynamic contributions of a non-standard nucleotide.Nucleic acids research · 2017Article
- Revised RNA Dihedral Parameters for the Amber Force Field Improve RNA Molecular Dynamics.Journal of chemical theory and computation · 2017Article
- Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- Ensemble analysis of primary microRNA structure reveals an extensive capacity to deform near the Drosha cleavage site.Biochemistry · 2013Article
- Molecular Mechanics Investigation of an Adenine-Adenine Non-Canonical Pair Conformational Change.Journal of chemical theory and computation · 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
- A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.Biochemistry · 2009Article
- Stacking effects on local structure in RNA: changes in the structure of tandem GA pairs when flanking GC pairs are replaced by isoG-isoC pairs.The journal of physical chemistry. B · 2007Article
- NMR structures of (rGCUGAGGCU)2 and (rGCGGAUGCU)2: probing the structural features that shape the thermodynamic stability of GA pairs.Biochemistry · 2007Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.