98%
921
2 minutes
20
The computational design of messenger RNA (mRNA) sequences is a critical technology for both scientific research and industrial applications. Recent advances in prediction and optimization models have enabled the automatic scoring and optimization of $5^\prime $ UTR sequences, key upstream elements of mRNA. However, fully automated design of $5^\prime $ UTR sequences with more than two objective scores has not yet been explored. In this study, we present a computational pipeline that optimizes human $5^\prime $ UTR sequences in a multi-objective framework, addressing up to four distinct and conflicting objectives. Our work represents an important advancement in the multi-objective computational design of mRNA sequences, paving the way for more sophisticated mRNA engineering.
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC12103902 | PMC |
http://dx.doi.org/10.1093/bib/bbaf225 | 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 PDFMater Today Bio
October 2025
Department of Laboratory Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China.
Peri-implantitis (PI) is a major cause of implant restoration failure, necessitating therapeutic strategies that integrate bone regeneration and anti-inflammatory effects. Despite advances in treatment, no existing agents simultaneously address both objectives. Exosomes (Exos), as key mediators of intercellular communication, have demonstrated dual anti-inflammatory and osteogenic capacities through microRNA (miRNA) delivery; however, their potential in PI therapy remains unexplored.
View Article and Find Full Text PDFInt J Biol Macromol
September 2025
Supercomputing Facility for Bioinformatics & Computational Biology (SCFBio) & Kusuma School of Biological Sciences, Indian Institute of Technology, Delhi, 110016, India; Department of Chemistry, Indian Institute of Technology, Delhi, 110016, India. Electronic address:
DNA is a dynamic molecule composed of numerous genic and regulatory elements that orchestrate cellular functions. Traditional methods often fail to provide accurate functional genome annotations because they do not effectively account for sequence variability within and across different organisms. To address this, we conducted an extensive genomic physical fingerprinting of ~4.
View Article and Find Full Text PDFExp Cell Res
September 2025
State Key Laboratory of Oral Diseases, National Center for Stomatology, National Clinical Research Center for Oral Diseases, Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology, Sichuan University, Chengdu City 610041, China. Electronic address:
Adipose-derived mesenchymal stem cells (ADSCs) hold great promise for bone tissue repair and regeneration. Circular RNAs (circRNAs) play a crucial role in regulating the osteogenic differentiation and bone remodeling of ADSCs; however, the underlying molecular mechanisms remain unclear. In this study, we conducted whole transcriptome sequencing (WTS) on ADSCs and constructed a competing endogenous RNA (ceRNA) regulatory network to identify the circTTC3/miR-205/mothers against decapentaplegic homolog 3 (Smad3) signaling axis.
View Article and Find Full Text PDFBiophys J
September 2025
Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB, T1K 3M4, Canada; Li Ka Shing Institute of Virology, University of Alberta, Edmonton T6G 2E1, Alberta, Canada; Department of Microbiology, Immunology
The dengue virus (DENV) poses a significant threat to human health, accounting for approximately 400 million infections each year. Its genome features a circular structure that facilitates replication through long-range RNA-RNA interactions, utilizing cyclization sequences located in the untranslated regions (UTRs). To gain new insights into the organization of the DENV genome, we purified the 5' and 3' UTRs of DENV in vitro and examined their structural and binding properties using various biophysical techniques combined with computational methods.
View Article and Find Full Text PDF