ArticleBiochemistry2006
Consecutive GA pairs stabilize medium-size RNA internal loops.
Article in Biochemistry, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Preferential production of RNA rings by T4 RNA ligase 2 without any splint through rational design of precursor strand.Nucleic acids research · 2020Article
- Random-sequence genetic oligomer pools display an innate potential for ligation and recombination.eLife · 2018Article
- Analysis of RNA nearest neighbor parameters reveals interdependencies and quantifies the uncertainty in RNA secondary structure prediction.RNA (New York, N.Y.) · 2018Article
- Advancing viral RNA structure prediction: measuring the thermodynamics of pyrimidine-rich internal loops.RNA (New York, N.Y.) · 2017Article
- Thermodynamic characterization of RNA 2 × 3 nucleotide internal loops.Biochemistry · 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
- Computational approaches for RNA energy parameter estimation.RNA (New York, N.Y.) · 2010Article
- Stochastic sampling of the RNA structural alignment space.Nucleic acids research · 2009Article
- A CA(+) pair adjacent to a sheared GA or AA pair stabilizes size-symmetric RNA internal loops.Biochemistry · 2009Article
- RNA STRAND: the RNA secondary structure and statistical analysis database.BMC bioinformatics · 2008Article
- Single-molecule mechanical unfolding and folding of a pseudoknot in human telomerase RNA.RNA (New York, N.Y.) · 2007Article
- 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
- Capillary electrophoresis is a sensitive monitor of the hairpin-random coil transition in DNA oligomers.Analytical biochemistry · 2007Article
- An alternating sheared AA pair and elements of stability for a single sheared purine-purine pair flanked by sheared GA pairs in RNA.Biochemistry · 2006Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Internal loops in RNA are important for folding and function. Consecutive noncanonical pairs can form in internal loops having at least two nucleotides on each side. Thermodynamic and structural insights into such internal loops should improve approximations for their stabilities and predictions of secondary and three-dimensional structures. Most natural internal loops are purine rich. A series of oligoribonucleotides that form purine-rich internal loops of 5-10 nucleotides, including kink-turn loops, were studied by UV melting, exchangeable proton and phosphorus NMR. Three consecutive GA pairs with the motif 5' Y GGA/3' R AAG or GGA R 3'/AAG Y 5' (i.e., 5' GGA 3'/3' AAG 5' closed on at least one side with a CG, UA, or UG pair with Y representing C or U and R representing A or G) stabilize internal loops having 6-10 nucleotides. Certain motifs with two consecutive GA pairs are also stabilizing. In internal loops with three or more nucleotides on each side, the motif 5' U G/3' G A has stability similar to 5' C G/3' G A. A revised model for predicting stabilities of internal loops with 6-10 nucleotides is derived by multiple linear regression. Loops with 2 x 3 nucleotides are predicted well by a previous thermodynamic model.
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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.