ArticleThe journal of physical chemistry. B2007
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.
Article in The journal of physical chemistry. B, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Structure of an internal loop motif with three consecutive U•U mismatches from stem-loop 1 in the 3'-UTR of the SARS-CoV-2 genomic RNA.Nucleic acids research · 2024Article
- Accurate geometrical restraints for Watson-Crick base pairs.Acta crystallographica Section B, Structural science, crystal engineering and materials · 2019Article
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Physics-based all-atom modeling of RNA energetics and structure.Wiley interdisciplinary reviews. RNA · 2017Review
- Article
- Modified Amber Force Field Correctly Models the Conformational Preference for Tandem GA pairs in RNA.Journal of chemical theory and computation · 2014Article
- Recognition of RNA duplexes by chemically modified triplex-forming oligonucleotides.Nucleic acids research · 2013Article
- Revision of AMBER Torsional Parameters for RNA Improves Free Energy Predictions for Tetramer Duplexes with GC and iGiC Base Pairs.Journal of chemical theory and computation · 2012Article
- 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
- Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides.Nucleic acids research · 2010Article
- 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.Biochemistry · 2010Article
- Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base Pairs.Journal of chemical theory and computation · 2009Article
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6 authors.
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Abstract
The Watson-Crick-like isoG-isoC (iGiC) pair, with the amino and carbonyl groups transposed relative to the Watson-Crick GC pair, provides an expanded alphabet for understanding interactions that shape nucleic acid structure. Here, thermodynamic stabilities of tandem GA pairs flanked by iGiC pairs are reported along with the NMR structures of the RNA self-complementary duplexes (GCiGGAiCGCA)2 and (GGiCGAiGCCA)2. A sheared GA pairing forms in (GCiGGAiCGCA)2, and an imino GA pairing forms in (GGiCGAiGCCA)2. The structures contrast with the formation of tandem imino and sheared GA pairs flanked by GC pairs in the RNA self-complementary duplexes (GCGGACGC)2 and (GGCGAGCC)2, respectively. In both iGiC duplexes, Watson-Crick-like hydrogen bonds are formed between iG and iC, and iGiC substitutions result in less favorable loop stability. The results provide benchmarks for testing computations of molecular interactions that shape RNA three-dimensional structure.
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