@RNAStructureBot

RNA Structure bot retweeting #RNAStructure & #StructuralRNA Pubmed articles and #bioRxiv #arXiv preprints. Semi-curated by @RhysHParry

Joined March 2022
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Welcome to RNA Structure or Structural RNA bot. Collating RNA structure research. Profile picture from the crystal structure of an exonuclease resistant RNA from Zika virus Akiyama et al., 2016 (doi: 10.1126/science.aah3963) (PDB:5TPY). Any issues please DM @RhysHParry
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Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure dlvr.it/TDdTz7

Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure - PubMed

HIV-1 must generate infectious virions to spread to new hosts and HIV-1 unspliced RNA (HIV-1 RNA) plays two central roles in this process. HIV-1 RNA serves as an mRNA that is translated to generate...

pubmed.ncbi.nlm.nih.gov
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Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect between affinity and activation of ZTP riboswitch ligands dlvr.it/TDclX1

Machine learning-augmented molecular dynamics simulations (MD) reveal insights into the disconnect...

The challenge of targeting RNA with small molecules necessitates a better understanding of RNA-ligand interaction mechanisms. However, the dynamic nature of nucleic acids, their ligand-induced...

pubmed.ncbi.nlm.nih.gov
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Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering dlvr.it/TDclS4

Selective deuteration of an RNA:RNA complex for structural analysis using small-angle scattering -...

The structures of RNA:RNA complexes regulate many biological processes. Despite their importance, protein-free RNA:RNA complexes represent a tiny fraction of experimentally-determined structures....

pubmed.ncbi.nlm.nih.gov
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Datasets for Benchmarking RNA Design Algorithms dlvr.it/TDbH2w
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SHAPE Probing to Screen Computationally Designed RNA dlvr.it/TDbH2v
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Toward Increasing the Credibility of RNA Design dlvr.it/TDbH2s

Toward Increasing the Credibility of RNA Design - PubMed

In the problem of RNA design, also known as inverse folding, RNA sequences are predicted that achieve the desired secondary structure at the lowest possible free energy and under certain constraints....

pubmed.ncbi.nlm.nih.gov
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Sequence Design Using RNAstructure dlvr.it/TDbH2p
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Sequence Design for RNA-RNA Interactions dlvr.it/TDbH1z

Sequence Design for RNA-RNA Interactions - PubMed

The design of RNA sequences with desired structural properties presents a challenging computational problem with promising applications in biotechnology and biomedicine. Most regulatory RNAs function...

pubmed.ncbi.nlm.nih.gov
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Templated 3' terminal fluorescent labeling of RNA using Klenow DNA polymerase dlvr.it/TDNMd0
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Assessment of MIR200B Polymorphisms Association with Sight-Threatening Diabetic Retinopathy dlvr.it/TDLr03
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Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and binding sites dlvr.it/TDDn0V

Genetic polymorphism in untranslated regions of PRKCZ influences mRNA structure, stability and...

This study laid the groundwork for future studies aimed at targeting PRKCZ as a therapeutic target.

pubmed.ncbi.nlm.nih.gov
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Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-causing mechanism dlvr.it/TD9wSz

Alu insertion-mediated dsRNA structure formation with pre-existing Alu elements as a disease-caus...

We previously identified a homozygous Alu insertion variant (Alu_Ins) in the 3'-untranslated region (3'-UTR) of SPINK1 as the cause of severe infantile isolated exocrine pancreatic insufficiency....

pubmed.ncbi.nlm.nih.gov
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Stress less: Viral mastery of the RNA G-quadruplex dlvr.it/TD9wRY

Stress less: Viral mastery of the RNA G-quadruplex - PubMed

RNA G-quadruplexes are dynamically regulated during stress and infection. In this issue of Cell Host & Microbe, Schult et al.1 demonstrate that an RNA G-quadruplex conserved across orthoflaviviruses...

pubmed.ncbi.nlm.nih.gov
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Potential of 6'‑hydroxy justicidin B from Justicia procumbens as a therapeutic agent against coronavirus disease 2019 dlvr.it/TCyNXS

Potential of 6'‑hydroxy justicidin B from Justicia procumbens as a therapeutic agent against...

This research highlights both the antiviral efficacy and safety profile of 6'-HJB, underscoring its potential as a novel COVID-19 treatment option. The potential of 6'-HJB was demonstrated using...

pubmed.ncbi.nlm.nih.gov
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RluA is the major mRNA pseudouridine synthase in Escherichia coli dlvr.it/TCwqcD

RluA is the major mRNA pseudouridine synthase in Escherichia coli - PubMed

Pseudouridine (Ψ) is an ubiquitous RNA modification, present in the tRNAs and rRNAs of species across all domains of life. Conserved pseudouridine synthases modify the mRNAs of diverse eukaryotes,...

pubmed.ncbi.nlm.nih.gov
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Generative artificial intelligence for computational chemistry: a roadmap to predicting emergent phenomena dlvr.it/TCttFh
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Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine-I Riboswitch dlvr.it/TCmr3x
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Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs dlvr.it/TCm0bw
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Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40 dlvr.it/TCm0Y2

Targeting RNA with small molecules, from RNA structures to precision medicines: IUPHAR review: 40 -...

RNA plays important roles in regulating both health and disease biology in all kingdoms of life. Notably, RNA can form intricate three-dimensional structures, and their biological functions are...

pubmed.ncbi.nlm.nih.gov
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Evaluation of the effect of RNA secondary structure on Cas13d-mediated target RNA cleavage dlvr.it/TCjPMh
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