ArticleNucleic acids research2006
Structural parameters affecting the kinetics of RNA hairpin formation.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed.
- Kinetic Modeling of Target-Amplification-Free CRISPR-Cas-Based Autocatalysis Reactions.bioRxiv : the preprint server for biology · 2026Article
- Utilizing RNA-seq Data to Infer Bacterial Transcription Termination Sites and Validate Predictions.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Clusters of hairpins induce intrinsic transcription termination in bacteria.Scientific reports · 2021Article
- Structure-guided mutational analysis of gene regulation by the Bacillus subtilis pbuE adenine-responsive riboswitch in a cellular context.The Journal of biological chemistry · 2015Article
- Stem-loop structures can effectively substitute for an RNA pseudoknot in -1 ribosomal frameshifting.Nucleic acids research · 2011Article
- Predicting secondary structural folding kinetics for nucleic acids.Biophysical journal · 2010Article
- RNA folding: conformational statistics, folding kinetics, and ion electrostatics.Annual review of biophysics · 2008Review
- Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding.RNA (New York, N.Y.) · 2007Article
- Probing the structural hierarchy and energy landscape of an RNA T-loop hairpin.Nucleic acids research · 2007Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program 'Kinfold'. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem-loop structures.
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