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Knowledge of the structural information is essential for understanding the functional details of modified RNA. Cellular non-coding RNA such as rRNA, tRNA and even viral RNAs contain a number of post-transcriptional modifications with varied degree of diversity and density. In this chapter, we discuss the use of a combination of biochemical and analytical tools such as ribonucleases and liquid chromatography coupled with mass spectrometry approaches for characterization of modified RNA. We present the protocols and alternate strategies for obtaining confident modified sequence information to facilitate the understanding of function.
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http://dx.doi.org/10.1016/bs.mie.2021.06.023 | DOI Listing |
Nucleic Acids Res
September 2025
School of Biomedical and Pharmaceutical Sciences, Guangdong University of Technology, No. 100 Waihuanxi Road, Guangzhou 510006, China.
The 5' untranslated region (5'UTR) plays a crucial regulatory role in messenger RNA (mRNA), with modified 5'UTRs extensively utilized in vaccine production, gene therapy, etc. Nevertheless, manually optimizing 5'UTRs may encounter difficulties in balancing the effects of various cis-elements. Consequently, multiple 5'UTR libraries have been created, and machine learning models have been employed to analyze and predict translation efficiency (TE) and protein expression, providing insights into critical regulatory features.
View Article and Find Full Text PDFJ Am Chem Soc
September 2025
Life-like Materials and Systems, University of Mainz, Duesbergweg 10-14, 55128 Mainz, Germany.
Transmembrane signaling is essential for cellular communication, yet reconstituting such mechanisms in synthetic systems remains challenging. Here, we report a simple and robust DNA-based mechanism for transmembrane signaling in synthetic cells using cholesterol-modified single-stranded DNA (Chol-ssDNA). We discovered that anchored Chol-ssDNA spontaneously flips across the membrane of giant unilamellar lipid vesicles (GUVs) in a nucleation-driven, defect-mediated process.
View Article and Find Full Text PDFElife
September 2025
Department of Earth and Environmental Sciences, Paleontology and Geobiology, Ludwig Maximilians-Universität München, Munich, Germany.
The rapid emergence of mineralized structures in diverse animal groups during the late Ediacaran and early Cambrian periods likely resulted from modifications of pre-adapted biomineralization genes inherited from a common ancestor. As the oldest extant phylum with mineralized structures, sponges are key to understanding animal biomineralization. Yet, the biomineralization process in sponges, particularly in forming spicules, is not well understood.
View Article and Find Full Text PDFBasic Clin Pharmacol Toxicol
October 2025
Department of Medical Pharmacology, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey.
Neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrophic lateral sclerosis and frontotemporal dementia represent a significant global health burden with limited therapeutic options. Current treatments are primarily symptomatic and fail to modify disease progression, emphasizing the urgent need for novel, mechanism-based interventions. Recent advances in molecular neuroscience have identified several non-classical pathogenic pathways, including neuroinflammation, mitochondrial dysfunction, impaired autophagy and proteostasis, synaptic degeneration and non-coding RNA dysregulation.
View Article and Find Full Text PDFJ Cancer Res Clin Oncol
September 2025
Drug Inspection Laboratory, Jingzhou Institute for Food and Drug Control, Jingzhou, 434000, China.
Objective: Dipeptidyl peptidase 9 (DPP9) not only regulates tumor progression and drug sensitivity, but also modifies oxidative stress mediated ferroptosis. This study aimed to investigate the effect of DPP9 inhibition on sorafenib sensitivity and its interaction with ferroptosis in hepatocellular carcinoma (HCC).
Methods: Two HCC cell lines (Huh7 and MHCC-97H) were transfected with DPP9 siRNA, followed by detection of reactive oxygen species (ROS), ferrous iron (Fe), malondialdehyde (MDA), and ferroptosis-related proteins, and treated by 0-16 μM sorafenib to calculate half-maximal inhibitory concentration (IC) for sensitivity assessment.