RNA
No mentions found
This entity hasn't been tracked yet, or Iris is still building its knowledge base.
Related Articles from SNS
De novo mutation of an RNA virus is increased in the presence of engineered synonymous mutations that disrupt RNA structural elements
Using a combination of methods including selective 2?-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq), a complete RNA structure map of the cucumber mosaic virus (CMV) RNA 3 segment was mapped (Watters et al. (2018) Nucleic Acids Research 46, 2573?2584). To explore the effect of structural perturbations on genomic stability, infectious mutants were engineered to contain changes in one of four open reading frame (ORF) stem-loop (SL) structures SL1362, SL1439, SL1745 and...
Nanopore Direct RNA Sequencing Enables Reproducible, Site-Resolved Pseudouridine Quantification in Human Ribosomal RNA
Pseudouridine is the most abundant post-transcriptional modification in human ribosomal RNA, with over 110 annotated sites and variable stoichiometry across biological contexts. Existing quantification methods are low-throughput or constrained to predefined panels. We benchmarked nanopore direct RNA sequencing using the Dorado v5.1 model against mass spectrometry-validated sites in human liver tissue, induced pluripotent stem cells, and HeLa cells.
A phage-encoded small RNA that mimics chimeric guide to inhibit CRISPR-Cas9
CRISPR Cas9 relies on a dual crRNA-tracrRNA guide, yet whether RNA based anti CRISPRs exist for this system has remained unknown. Here we identify a phage encoded small non coding RNA, rAcrIIA1, that adopts an unexpected chimeric crRNA-tracrRNA architecture, faithfully recapitulating the entire single guide RNA (sgRNA) of Cas9. Cryo EM structures of the Cas9-rAcrIIA1 binary complex and the Cas9-rAcrIIA1-DNA ternary complex reveal that rAcrIIA1 engages Cas9 nearly identically to the native...
Continuous stirring made early life-like RNA systems more extinction-prone, experiment shows
Continuous stirring made early life-like RNA systems more extinction-prone, experiment shows Andrew Zinin Lead Editor Recent research showed that an artificially constructed self-replicating RNA system modeling primitive life at the origin of life evolved to become more prone to extinction under certain experimental conditions. Modern life is a complex assembly of numerous molecules with diverse functions. However, it is believed that when life first emerged in ancient times, simple...
The RNA helicase DDX21 cooperates with ETS1 and FLI1 in cell cycle, immune evasion, and snoRNA processing in activated B-cell-like diffuse large B-cell lymphoma cells
Diffuse large B-cell lymphoma (DLBCL) is a clinically and biologically heterogeneous disease, with the activated B-cell-like (ABC) subtype showing inferior outcomes. The ETS transcription factors ETS1 and FLI1 are recurrently gained and functionally relevant in DLBCL, yet their pathogenic role remains to be fully elucidated. Here, we describe their cooperation with the RNA regulatory machinery, demonstrating that the RNA helicase DDX21 is a central effector of the ETS1/FLI1 transcriptional...
RNA-guided transposon mechanics show use of figure-eight intermediate and direct-transfer route
RNA-guided transposon mechanics show use of figure-eight intermediate and direct-transfer route Gaby Clark Scientific Editor Robert Egan Associate Editor IS110 transposons are a large, diverse family of bacterial insertion sequences (IS elements)—small, mobile DNA elements that can move from one genomic location to another. They have recently attracted broad interest due to the finding that some of these transposons use a bridge RNA (bRNA) to recognize both donor DNA and target DNA. Upon...
Structure of a dopamine-binding RNA aptamer reveals metal-mediated ligand recognition
The selection of small-molecule binding RNA aptamers enables the creation of ligand-responsive RNA tools, yet most aptamers fail to operate reliably across diverse environments. Scaffolded selection addresses this limitation by preserving the tertiary architecture of a riboswitch scaffold while driving the evolution of a new ligand-binding pocket. Using the xpt purine riboswitch aptamer, we previously generated dopamine-binding aptamers.
Disentangling RNA evolution and thermodynamics in genomic language models
Genomic language models (gLMs) trained only on large-scale nucleic acid sequence data seem to capture signals of RNA structure, yet the specifics of how remain unclear. Using the categorical Jacobian (CJ) operation, a model-agnostic operation for querying pairwise dependencies, we systematically compared three flagship gLMs: RNA-FM, Evo 2, and gLM2. We found that CJ signals recover base pairs supported by evolutionary covariation analyses, consistent with findings in protein language models.
Conserved structural features of RNA export pores spanning the double membrane of arterivirus and coronavirus replication organelles
Corona- and arteriviruses are distantly related positive-stranded RNA virus families within the order Nidovirales. Both transform intracellular membranes into double-membrane vesicles (DMVs) that serve as replication organelles. Newly made viral RNA presumably exits DMVs through double-membrane-spanning molecular pores formed by coronavirus nsp3-nsp4 and arterivirus nsp2-nsp3.
An Integrating Sphere Based Method for Quantifying RNA Encapsulation Efficiency in Lipid Nanoparticles without Lysis
Encapsulation efficiency (EE) is a critical quality attribute of lipid nanoparticle (LNP)-RNA formulations, determining the fraction of active RNA payload available for delivery and influencing therapeutic potency, dose accuracy, and product consistency. Conventional fluorescence-based EE assays, such as RiboGreen (RG), require detergent-mediated LNP lysis, which can introduce systematic bias arising from incomplete particle disruption and additional sample handling steps. Here, we report a...