ArticleRNA (New York, N.Y.)2006
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA.
Article in RNA (New York, N.Y.), 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 40 citations in OpenAlex.
- Molecular Dynamics Simulations of Protein RNA Complexes by Using an Advanced Electrostatic Model.The journal of physical chemistry. B · 2022Article
- Spliceosomal SL1 RNA binding to U1-70K: the role of the extended RRM.Nucleic acids research · 2022Article
- Article
- Evolutionary plasticity of the NHL domain underlies distinct solutions to RNA recognition.Nature communications · 2018Article
- Impaired spliceosomal UsnRNP assembly leads to Sm mRNA down-regulation and Sm protein degradation.The Journal of cell biology · 2017Article
- Urb-RIP - An Adaptable and Efficient Approach for Immunoprecipitation of RNAs and Associated RNAs/Proteins.PloS one · 2016Article
- Climbing the vertebrate branch of U1A/U2B″ protein evolution.RNA (New York, N.Y.) · 2014Article
- Synthetic RNA recognition motifs that selectively recognize HIV-1 trans-activation response element hairpin RNA.ACS chemical biology · 2014Article
- GraphProt: modeling binding preferences of RNA-binding proteins.Genome biology · 2014Article
- Engineering RNA-binding proteins for biology.The FEBS journal · 2013Review
- Intrinsic flexibility of snRNA hairpin loops facilitates protein binding.RNA (New York, N.Y.) · 2012Article
- U1A protein-stem loop 2 RNA recognition: prediction of structural differences from protein mutations.Biopolymers · 2011Article
- RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.PLoS computational biology · 2010Article
- Article
- Conformationally restricted nucleotides as a probe of structure-function relationships in RNA.RNA (New York, N.Y.) · 2008Article
- Prediction of salt and mutational effects on the association rate of U1A protein and U1 small nuclear RNA stem/loop II.The journal of physical chemistry. B · 2008Article
- Dimerization of FIR upon FUSE DNA binding suggests a mechanism of c-myc inhibition.The EMBO journal · 2008Article
- Interaction of yeast RNA-binding proteins Nrd1 and Nab3 with RNA polymerase II terminator elements.RNA (New York, N.Y.) · 2007Article
- Sequence-specific binding of single-stranded RNA: is there a code for recognition?Nucleic acids research · 2006Review
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
No grant is acknowledged in the PubMed record.
Abstract
The N-terminal RNA Recognition Motif (RRM1) of the spliceosomal protein U1A interacting with its target U1 hairpin II (U1hpII) has been used as a paradigm for RRM-containing proteins interacting with their RNA targets. U1A binds to U1hpII via direct interactions with a 7-nucleotide (nt) consensus binding sequence at the 5' end of a 10-nt loop, and via hydrogen bonds with the closing C-G base pair at the top of the RNA stem. Using surface plasmon resonance (Biacore), we have examined the role of structural features of U1hpII in binding to U1A RRM1. Mutational analysis of the closing base pair suggests it plays a minor role in binding and mainly prevents "breathing" of the loop. Lengthening the stem and nontarget part of the loop suggests that the increased negative charge of the RNA might slightly aid association. However, this is offset by an increase in dissociation, which may be caused by attraction of the RRM to nontarget parts of the RNA. Studies of a single stranded target and RNAs with untethered loops indicate that structure is not very relevant for association but is important for complex stability. In particular, breaking the link between the stem and the 5' side of the loop greatly increases complex dissociation, presumably by hindering simultaneous contacts between the RRM and stem and loop nucleotides. While binding of U1A to a single stranded target is much weaker than to U1hpII, it occurs with nanomolar affinity, supporting recent evidence that binding of unstructured RNA by U1A has physiological significance.
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.