Transfer RNA-derived small RNA: an emerging small non-coding RNA with key roles in cancer
Experimental Hematology & Oncology, 2022 Transfer RNAs (tRNAs) promote protein translation by binding to the corresponding amino acids and transporting them to the ribosome, which is essential in protein translation.
Xinliang Gu +5 more
doaj +1 more source
ER Membrane Contact Sites: Key Platforms for Biogenesis of RNA-Containing Extracellular Vesicles
Contact, 2022 The mechanisms by which cytoplasmic cargoes such as RNAs are incorporated into extracellular vesicles (EVs) are poorly understood. In a recent article published in Developmental Cell, we describe a novel function of endoplasmic reticulum membrane contact
Bahnisikha Barman +2 more
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Knowledge from Large-Scale Protein Contact Prediction Models Can Be Transferred to the Data-Scarce RNA Contact Prediction Task [PDF]
arXiv, 2023 RNA, whose functionality is largely determined by its structure, plays an important role in many biological activities. The prediction of pairwise structural proximity between each nucleotide of an RNA sequence can characterize the structural information of the RNA.
arxiv
Mitochondrial DNA. Part B. Resources, 2021 The complete mitogenome sequence of Sinogastromyzon szechuanensis was obtained using next generation sequencing and confirmed via overlap-PCR method.
Wei Li +7 more
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Highly Sensitive Northern Hybridization Using a Rapid Protocol for Downward Alkaline Blotting of RNA
BioTechniques, 1998 A simple and fast RNA gel blot procedureis described that uses 50 mM NaOH tosimultaneously transfer and fix RNA to apositively charged nylon membrane. TheRNA is transferred in a downward direction,and transfer is routinely completedwithin 2.5 h.
Ivan L. Ingelbrecht +2 more
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RNA folding landscapes from explicit solvent all-atom simulations [PDF]
arXiv, 2022 Atomically detailed simulations of RNA folding have proven very challenging in view of the difficulties of developing realistic force fields and the intrinsic computational complexity of sampling rare conformational transitions. To tackle both these issues, we extend to RNA an enhanced path sampling method previously successfully applied to proteins ...
arxiv
Using Guided Transfer Learning to Predispose AI Agent to Learn Efficiently from Small RNA-sequencing Datasets [PDF]
arXiv, 2023 Given the increasing availability of RNA-seq data and its complex and heterogeneous nature, there has been growing interest in applying AI/machine learning methodologies to work with such data modalities. However, because omics data is characterized by high dimensionality and low sample size (HDLSS), current attempts at integrating AI in this domain ...
arxiv
Combining simulations and solution experiments as a paradigm for RNA force field refinement [PDF]
J. Chem. Theory Comput., 2016, 12 (12), pp 6192-6200, 2016 Recent computational efforts have shown that the current potential energy models used in molecular dynamics are not accurate enough to describe the conformational ensemble of RNA oligomers and suggest that molecular dynamics should be complemented with experimental data.
arxiv +1 more source
Characterization of UVA-Induced Alterations to Transfer RNA Sequences
Biomolecules, 2020 Ultraviolet radiation (UVR) adversely affects the integrity of DNA, RNA, and their nucleoside modifications. By employing liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based RNA modification mapping approaches, we identified the transfer RNA (
Congliang Sun +2 more
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Machine learning a model for RNA structure prediction [PDF]
NAR Genom. Bioinform. 2, lqaa090 (2020), 2020 RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and ensemble populations.
arxiv +1 more source