ArticleJournal of the American Chemical Society2009
Motions of the substrate recognition duplex in a group I intron assessed by site-directed spin labeling.
Article in Journal of the American Chemical Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 44 citations in OpenAlex.
- Paramagnetic Chemical Probes for Studying Biological Macromolecules.Chemical reviews · 2022Review
- Do the P1 and P2 hairpins of the Guanidine-II riboswitch interact?Nucleic acids research · 2020Article
- Cobalt-based paramagnetic probe to study RNA-protein interactions by NMR.Journal of inorganic biochemistry · 2017Article
- Shortening the HIV-1 TAR RNA Bulge by a Single Nucleotide Preserves Motional Modes over a Broad Range of Time Scales.Biochemistry · 2016Article
- Dynamic motions of the HIV-1 frameshift site RNA.Biophysical journal · 2015Article
- An Integrated Spin-Labeling/Computational-Modeling Approach for Mapping Global Structures of Nucleic Acids.Methods in enzymology · 2015Article
- A nucleotide-independent cyclic nitroxide label for monitoring segmental motions in nucleic acids.BMC biophysics · 2015Article
- Characterizing the dynamics of the leader-linker interaction in the glycine riboswitch with site-directed spin labeling.Biochemistry · 2014Article
- Roles of long-range tertiary interactions in limiting dynamics of the Tetrahymena group I ribozyme.Journal of the American Chemical Society · 2014Article
- Hierarchy of RNA functional dynamics.Annual review of biochemistry · 2014Review
- A single-stranded junction modulates nanosecond motional ordering of the substrate recognition duplex of a group I ribozyme.Chembiochem : a European journal of chemical biology · 2013Article
- The internal dynamics of mini c TAR DNA probed by electron paramagnetic resonance of nitroxide spin-labels at the lower stem, the loop, and the bulge.Biochemistry · 2012Article
- Nitroxide sensing of a DNA microenvironment: mechanistic insights from EPR spectroscopy and molecular dynamics simulations.The journal of physical chemistry. B · 2012Article
- A role for a single-stranded junction in RNA binding and specificity by the Tetrahymena group I ribozyme.Journal of the American Chemical Society · 2012Article
- A nucleotide-independent nitroxide probe reports on site-specific stereomeric environment in DNA.Biophysical journal · 2010Article
- Precise mapping of RNA tertiary structure via nanometer distance measurements with double electron-electron resonance spectroscopy.Journal of the American Chemical Society · 2010Article
- Site-specific DNA structural and dynamic features revealed by nucleotide-independent nitroxide probes.Biochemistry · 2009Article
- Probing the dynamics of the P1 helix within the Tetrahymena group I intron.Journal of the American Chemical Society · 2009Article
- Studying RNA using site-directed spin-labeling and continuous-wave electron paramagnetic resonance spectroscopy.Methods in enzymology · 2009Article
- RNA dynamics: perspectives from spin labels.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
The Tetrahymena group I intron recognizes its oligonucleotide substrate in a two-step process. First, a substrate recognition duplex, called the P1 duplex, is formed. The P1 duplex then docks into the prefolded ribozyme core by forming tertiary contacts. P1 docking controls both the rate and the fidelity of substrate cleavage and has been extensively studied as a model for the formation of RNA tertiary structure. However, previous work has been limited to studying millisecond or slower motions. Here we investigated nanosecond P1 motions in the context of the ribozyme using site-directed spin labeling (SDSL) and electron paramagnetic resonance (EPR) spectroscopy. A nitroxide spin label (R5a) was covalently attached to a specific site of the substrate oligonucleotide, the labeled substrate was bound to a prefolded ribozyme to form the P1 duplex, and X-band EPR spectroscopy was used to monitor nitroxide motions in the 0.1-50 ns regime. Using substrates that favor the docked or the undocked states, it was established that R5a was capable of reporting P1 duplex motions. Using R5a-labeled substrates it was found that the J1/2 junction connecting P1 to the ribozyme core controls nanosecond P1 mobility in the undocked state. This may account for previous observations that J1/2 mutations weaken substrate binding and give rise to cryptic cleavage. This study establishes the use of SDSL to probe nanosecond dynamic behaviors of individual helices within large RNA and RNA/protein complexes. This approach may help in understanding the relationship between RNA structure, dynamics, and function.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.