22 papers · ranked by Valyu relevance
Andrea Cappannini, Angana Ray, Elżbieta Purta, Sunandan Mukherjee + 7 more
The MODOMICS database was updated with recent data and now includes new data types related to RNA modifications. Changes to the database include an expanded modification catalog, encompassing both natural and synthetic residues identified in RNA structures. This addition aids in representing RNA sequences from the RCSB…
Yaran Liu, Yang Li, Qiang Sun
RNA modifications add a dynamic and versatile regulatory layer to gene expression, influencing RNA stability, splicing, translation, and cellular responses. Despite their importance, traditional detection methods-such as antibody-based enrichment, chemical labeling, or indirect sequencing approaches-often suffer from…
Viktoriia A. Arzumanian, Georgii V. Dolgalev, Ilya Y. Kurbatov, Olga I. Kiseleva + 2 more
'Olga I. Kiseleva' 'Ekaterina V. Poverennaya' 'Chianshiu Chien'] The alphabet of building blocks for RNA molecules is much larger than the standard four nucleotides. The diversity is achieved by the post-transcriptional biochemical modification of these nucleotides into distinct chemical entities that are structurally…
Andrea Vandelli, Laura Broglia, Alexandros Armaos, Riccardo Delli Ponti + 1 more
RNA modifications play a crucial role in regulating gene expression by altering RNA structure and modulating interactions with RNA-binding proteins (RBPs). In this study, we explore the impact of specific RNA chemical modifications—N6-methyladenosine (m⁶A), A-to-I editing, and pseudouridine (Ψ)—on RNA secondary…
Janet Sasso, Barbara Ambrose, Rumiana Tenchov, Ruchira Datta + 3 more
In the last decade, there has been a shift in research, clinical development, and commercial activity to exploit the many roles of RNA in physiology for use in medicine. With the rapid success in the development of lipid-RNA nanoparticles for mRNA vaccines against COVID-19 and with several approved RNA-based drugs, RNA…
Mohammad Burhan Uddin, Zhishan Wang, Chengfeng Yang
More than a hundred chemical modifications in coding and non-coding RNAs have been identified so far. Many of the RNA modifications are dynamic and reversible, playing critical roles in gene regulation at the posttranscriptional level. The abundance and functions of RNA modifications are controlled mainly by the…
Yongji Zou, Mian Umair Ahsan, Joe Chan, Wen Meng + 3 more
Direct RNA sequencing from Oxford Nanopore Technologies (ONT) has become a valuable method for studying RNA modifications such as N6-methyladenosine (m6A), pseudouridine (ψ), and 5-methylcytosine (m5C). Recent advancements in the RNA004 chemistry substantially reduce sequencing errors compared to previous chemistries…
Oguzhan Begik, Morghan C Lucas, Jose Miguel Ramirez, Ivan Milenkovic + 8 more
A broad diversity of modifications decorate RNA molecules. Originally conceived as static components, evidence is accumulating that some RNA modifications may be dynamic, contributing to cellular responses to external signals and environmental circumstances. A major difficulty in studying these modifications, however…
D. W. U. Thilanka, P. S. Warushavithana
Ribosomal RNA modifications are pivotal in bacteria. A method for locating rRNA modification sites and associated enzymes is crucial for understanding ribosome formation, bacterial functionality, and antibiotic resistance correlated with rRNA modifications. ModrRNA1 introduces a bioinformatics approach to streamline…
Shuhua Yang, Nhat Truong Pham, Ziyang Li, Jae Young Baik + 9 more
'Joseph Lee' 'Tianhua Zhai' 'Weicheng Yu' 'Bojian Hou' 'Tianqi Shang' 'Wenping He' 'Duy Duong‐Tran' 'Mayur Naik' 'Li Shen'] Due to the hierarchical organization of RNA structures and their pivotal roles in fulfilling RNA functions, the formation of RNA secondary structure critically influences many biological processes…
Rebecca J. D’Esposito, Christopher A. Myers, Alan A. Chen, Sweta Vangaveti + 2 more
'Sweta Vangaveti' 'Francesca Tuorto' 'Jia Sheng'] RNA is critical to a broad spectrum of biological and viral processes. This functional diversity is a result of their dynamic nature; the variety of three-dimensional structures that they can fold into; and a host of post-transcriptional chemical modifications. While…
Joshua T Burdick, Annelise Comai, Alan Bruzel, Guangxin Sun + 3 more
'Peter C Dedon' 'Vivian G Cheung' 'R Anholt'] Title: Abstract RNA undergoes complex posttranscriptional processing including chemical modifications of the nucleotides. The resultant-modified nucleotides are an integral part of RNA sequences that must be considered in studying the biology of RNA and in the design of RNA…
Argiris Symeonidis, Argyri Chroni, Irene Dereki, Dionysios Chartoumpekis + 2 more
The intracellular topography of RNA molecules, encompassing ribonucleotides with biochemical modifications, such as N6-methyladenosine (m6A), 5-methylcytosine (m5C), adenosine to inosine (A → I) editing, and isomerization of uridine to pseudouridine (Ψ), as well as of non-coding RNA molecules, is currently studied…
Valerio Piomponi, Mattia Bernetti, Giovanni Bussi
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA–protein interactions. Additionally, artificially modified RNAs have been suggested as optimal oligonucleotides for therapeutic purposes. The impact of chemical…
Anna M. Popova, Nikhil Jain, Xiyu Dong, Farshad Abdollah-Nia + 2 more
Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across bacterial phylogeny. B. subtilis is a preeminent model organism for gram-positive bacteria, with a well-annotated and editable genome, convenient for fundamental studies…
Alexander Apostle, Yipeng Yin, Komal Chillar, Adikari M. D. N. Eriyagama + 4 more
Like other viruses, SARS-CoV-2 causes different symptoms and different degrees of harmfulness to different individuals. Potential reasons include an individual's viral dose exposure, the affinity of an individual's ACE2 to the spike protein of the virus, and the ability of the individual's induced immune system to…
Michael Lanzillotti, Jennifer Brodbelt
Recent progress in top-down mass spectrometry analysis of progressively larger nucleic acids has enabled in-depth characterization of intact, modified RNA molecules. Development of methods for desalting and MS/MS fragmentation allows rapid acquisition of high-quality top-down MS/MS spectra of nucleic acids up to 100…
Authors not listed
RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated molecules and complexes with ions, small molecules, or proteins. We highlight how…
Authors not listed
A chemical method suitable for the synthesis of RNAs containing modifications such as N4-acetylcytidine (ac4C) that are unstable under the basic and nucleophilic conditions used by standard RNA synthesis methods is described. The method uses the 4-((t-butyldimethylsilyl)oxy)-2-methoxybutanoyl (SoM) group for the…
Michael Lanzillotti, Jennifer Brodbelt
Mass spectrometry has proven to be a highly effective tool for characterization of RNA post-transcriptional modifications. For both synthetic RNAs and ones from biological sources, mass spectrometry can interrogate multiple, co-occurring covalent modifications at the nucleotide level simultaneously. To expand the…
Sébastien Benizri, Arnaud Gissot, Andrew Martin, Brune Vialet + 2 more
'Mark W. Grinstaff' 'Philippe Barthélémy'] ABSTRACT: Oligonucleotide-based agents have the potential to treat or cure almost any disease, and are one of the key therapeutic drug classes of the future. Bioconjugated oligonucleotides, a subset of this class, are emerging from basic research and being successfully…
Michael Lanzillotti, Jennifer Brodbelt
Broad interest in nucleic acids – both their therapeutic capabilities and understanding the nuances of their structure and resulting function – has increased in recent years. Post-transcriptional modifications in particular have become an important analysis target, as these covalent modifications to the sugars…