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RNAStructureBot

@RNAStructureBot

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

Joined March 2022
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Photo by RNAStructureBot (@RNAStructureBot)
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

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...

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 -...

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
Datasets for Benchmarking RNA Design Algorithms - PubMed

Datasets for Benchmarking RNA Design Algorithms - PubMed

RNA molecules play vital roles in many biological processes, such as gene regulation or protein synthesis. The adoption of a specific secondary and tertiary structure by RNA is essential to perform...

pubmed.ncbi.nlm.nih.gov
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SHAPE Probing to Screen Computationally Designed RNA dlvr.it/TDbH2v
SHAPE Probing to Screen Computationally Designed RNA - PubMed

SHAPE Probing to Screen Computationally Designed RNA - PubMed

RNA design is a major challenge for the future development of synthetic biology and RNA-based therapy. The development of efficient and accurate RNA design pipelines is based on trial and error...

pubmed.ncbi.nlm.nih.gov
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Toward Increasing the Credibility of RNA Design dlvr.it/TDbH2s
Toward Increasing the Credibility of RNA Design - PubMed

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
Sequence Design Using RNAstructure - PubMed

Sequence Design Using RNAstructure - PubMed

RNA is present in all domains of life. It was once thought to be solely involved in protein expression, but recent advances have revealed its crucial role in catalysis and gene regulation through...

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

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
Templated 3' terminal fluorescent labeling of RNA using Klenow DNA polymerase - PubMed

Templated 3' terminal fluorescent labeling of RNA using Klenow DNA polymerase - PubMed

A long-standing challenge in the study of RNA structure-function dynamics using fluorescence-based methods has been the precise attachment of fluorophores to structured RNA molecules. Despite...

pubmed.ncbi.nlm.nih.gov
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Assessment of MIR200B Polymorphisms Association with Sight-Threatening Diabetic Retinopathy dlvr.it/TDLr03
Assessment of MIR200B Polymorphisms Association with Sight-Threatening Diabetic Retinopathy - PubMed

Assessment of MIR200B Polymorphisms Association with Sight-Threatening Diabetic Retinopathy - PubMed

In silico analysis showed mild changes in MIR200B secondary structure and increased free energy in the presence of one of the identified variants (g.1167183G>A; rs72563729). Increasing the sample...

pubmed.ncbi.nlm.nih.gov
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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...

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...

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

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...

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

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
Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine-I Riboswi...

Atomistic Simulations Reveal Crucial Role of Metal Ions for Ligand Binding in Guanidine-I Riboswi...

Riboswitches are structured ribonucleic acid (RNA) segments that act as specific sensors for small molecules in bacterial metabolism. Due to the flexible nature of these highly charged macromolecul...

pubmed.ncbi.nlm.nih.gov
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Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone mRNAs dlvr.it/TCm0bw
Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone...

Eukaryotic initiation factor 4B is a multi-functional RNA binding protein that regulates histone...

RNA binding proteins drive proliferation and tumorigenesis by regulating the translation and stability of specific subsets of messenger RNAs (mRNAs). We have investigated the role of eukaryotic...

pubmed.ncbi.nlm.nih.gov
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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 -...

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
Evaluation of the effect of RNA secondary structure on Cas13d-mediated target RNA cleavage - PubMed

Evaluation of the effect of RNA secondary structure on Cas13d-mediated target RNA cleavage - PubMed

The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas13d system was adapted as a powerful tool for targeting viral RNA sequences, making it a promising approach for antiviral...

pubmed.ncbi.nlm.nih.gov
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