Magnesium Contact Ions Stabilize the Tertiary Structure of Transfer RNA: Electrostatics Mapped by Two-Dimensional Infrared Spectra and Theoretical Simulations [PDF]
J. Phys. Chem. B 2021, 125, 740-747, 2021 Ions interacting with hydrated RNA play a central role in defining its secondary and tertiary structure. While spatial arrangements of ions, water molecules, and phosphate groups have been inferred from X-ray studies, the role of electrostatic and other noncovalent interactions in stabilizing compact folded RNA structures is not fully understood at the
arxiv +1 more source
Annals of Translational Medicine, 2020 Transfer RNA-derived small RNA (tsRNA)s are novel non-coding RNAs, expressed in a variety of tissues and organs. Two subtypes of tsRNAs have been reported: tRNA-derived stress-induced RNA (tiRNA)s and tRNA-derived fragment (tRF)s.
Yanglei Jia, Wei Tan, Yedi Zhou
semanticscholar +1 more source
tRFtarget: a database for transfer RNA-derived fragment targets
Nucleic Acids Res., 2020 Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of ...
Ningshan Li +3 more
semanticscholar +1 more source
A novel mistranslating tRNA model in Drosophila melanogaster has diverse, sexually dimorphic effects [PDF]
, 2022 Transfer RNAs (tRNAs) are the adaptor molecules required for reading the genetic code and producing proteins. Transfer RNA variants can lead to genome-wide mistranslation, the misincorporation of amino acids not specified by the standard genetic code ...
Berg, Matthew D. +6 more
core +2 more sources
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Research, 1997 We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
T. Lowe, S. Eddy
semanticscholar +1 more source
Transfer RNA fragments replace microRNA regulators of the cholinergic poststroke immune blockade
Proceedings of the National Academy of Sciences of the United States of America, 2020 Significance Ischemic stroke triggers peripheral immunosuppression, increasing the susceptibility to poststroke pneumonia that is linked with poor survival.
Katarzyna Winek +14 more
semanticscholar +1 more source
Structural insights into RNA processing by the human RISC-loading complex. [PDF]
, 2009 Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC).
AD Haase +41 more
core +2 more sources
tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes
Nucleic Acids Res., 2016 High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-
T. Lowe, Patricia P. Chan
semanticscholar +1 more source
Broad role for YBX1 in defining the small noncoding RNA composition of exosomes. [PDF]
, 2017 RNA is secreted from cells enclosed within extracellular vesicles (EVs). Defining the RNA composition of EVs is challenging due to their coisolation with contaminants, lack of knowledge of the mechanisms of RNA sorting into EVs, and limitations of ...
Lambowitz, Alan M +6 more
core +1 more source
tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes
bioRxiv, 2019 tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded. With the massive increase in quantity and phylogenetic diversity of genomes, the accurate detection and ...
Patricia P. Chan +3 more
semanticscholar +1 more source