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Role of Non-Canonical Stacking Interactions of Heterocyclic RNA Bases in Ribosome Function.
Biochemistry (Mosc)
December 2024
Faculty of Chemistry, Lomonosov Moscow State University, Moscow, 119991, Russia.
Identification and analysis of repetitive elements (motifs) in DNA, RNA, and protein macromolecules is an important step in studying structure and functions of these biopolymers. Functional role of NA-BSE (non-adjacent base-stacking element, a widespread tertiary structure motif in various RNAs) in RNA-RNA interactions at various stages of the ribosome function during translation has been investigated in this work. Motifs of this type have been described to date that are reversibly formed during mRNA decoding, moving of the ribosome subunits relative to each other, and moving mRNA and tRNA along the ribosome during translocation.
View Article and Find Full Text PDFAssembly and comparative analysis of the complete mitochondrial genome of red raspberry (Rubus idaeus L.) revealing repeat-mediated recombination and gene transfer.
BMC Plant Biol
January 2025
CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, 430074, China.
Background: Red raspberry (Rubus idaeus L.) is a renowned fruit plant with significant medicinal value. Its nuclear genome and chloroplast genome (plastome) have been reported, while there is a lack of genetic information on its mitogenome.
View Article and Find Full Text PDFNuFold: end-to-end approach for RNA tertiary structure prediction with flexible nucleobase center representation.
Nat Commun
January 2025
Department of Biological Sciences, Purdue University, West Lafayette, 47907, Indiana, USA.
RNA plays a crucial role not only in information transfer as messenger RNA during gene expression but also in various biological functions as non-coding RNAs. Understanding mechanical mechanisms of function needs tertiary structure information; however, experimental determination of three-dimensional RNA structures is costly and time-consuming, leading to a substantial gap between RNA sequence and structural data. To address this challenge, we developed NuFold, a novel computational approach that leverages state-of-the-art deep learning architecture to accurately predict RNA tertiary structures.
View Article and Find Full Text PDFRNase P cleavage of pseudoknot substrates reveals differences in active site architecture that depend on residue N-1 in the 5' leader.
RNA Biol
December 2025
Department of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Uppsala, Sweden.
We show that a small biotin-binding RNA aptamer that folds into a pseudoknot structure acts as a substrate for bacterial RNase P RNA (RPR) with and without the RNase P C5 protein. Cleavage in the single-stranded region in loop 1 was shown to depend on the presence of a RCCA-motif at the 3' end of the substrate. The nucleobase and the 2'hydroxyl at the position immediately 5' of the cleavage site contribute to both cleavage efficiency and site selection, where C at this position induces significant cleavage at an alternative site, one base upstream of the main cleavage site.
View Article and Find Full Text PDFEngineered initiator tRNAs can effectively start translation at non-AUG start codons and diversify N-terminal amino acids for mRNA Display.
Nucleic Acids Res
January 2025
Department of Peptide Therapeutics, Genentech, South San Francisco, CA 94080, USA.
mRNA display is an effective tool to identify high-affinity macrocyclic binders for challenging protein targets. The success of an mRNA display selection is dependent on generating highly diverse libraries with trillions of peptides. While translation elongation can canonically accommodate the 61 proteinogenic triplet codons, translation initiation is restricted to the native start codon AUG.
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