Evidence map›Paper›PMID 40384581›Full record

ArticleNucleic acids research2025

mRNAdesigner: an integrated web server for optimizing mRNA design and protein translation in eukaryotes.

Ouyang Mo, Zhuo Zhang, Xiang Cheng, Liqi Zhu, Kaixiang Zhang, Niubing Zhang, Justin Li, Honglin Li, Shixin Fan, Xuan Li and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

11 authors.

Ouyang MoKey Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0009-0000-2364-6021
Zhuo ZhangKey Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.
Xiang ChengCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
Liqi ZhuKey Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.
Kaixiang ZhangKey Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Niubing ZhangKey Laboratory of Synthetic Biology, State Key Laboratory of Plant Trait Design, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
Justin LiDepartment of Mathematics, University of Connecticut, 352 Mansfield Road, Storrs, CT 06269, United States.
Honglin LiInnovation Center for AI and Drug Discovery, School of Pharmacy, East China Normal University, Shanghai 200237, China.
Shixin FanChemPartner PharmaTech Co., Ltd, Shanghai 200237, China.
Xuan LiCollege of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.ORCID 0000-0002-7435-9652
Pei HaoKey Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai 200031, China.ORCID 0000-0002-1498-7059

Funding

Key R&D Program of Jiangsu Province Modern Agriculture BE2023336National Natural Science Foundation of China 32270695National Natural Science Foundation of China 32270719National Natural Science Foundation of China 92451303National Science and Technology 2023ZD0502400
6 · The paper itself

Abstract

Messenger RNA (mRNA) therapy has revolutionized modern medicine through its rapid development capabilities and ability to induce effective immune responses, becoming a powerful weapon against infectious diseases. The expression level of target proteins from mRNA sequences is primarily influenced by translational efficiency and stability, which can be significantly enhanced by modifying the 5' and 3' untranslated regions (UTRs), codon adaptation index, GC content, and secondary structure. To address the challenges of optimizing mRNA design, we have developed mRNAdesigner (https://www.biosino.org/mRNAdesigner/), a web server specifically designed to improve mRNA stability and translational efficiency in eukaryotes. Users can input a coding sequence (CDS) along with optional 5' UTR and 3' UTR, and the tool optimizes the CDS by reducing unpaired regions, minimizing complex stem-loop structures, and mitigating the use of rare codons while adhering to user-defined GC content preferences. Additionally, mRNAdesigner identifies optimal UTR sequences to enhance translation efficiency and stability. As an open-access computational resource, mRNAdesigner supports full-length mRNA design, enabling researchers to generate high-expression mRNA sequences for efficient protein production in eukaryotic expression systems, providing extra support for vaccine development and protein therapeutics. This is the first such tool that was made open accessible to the public.

Indexed as

Protein BiosynthesisRNA, MessengerSoftware3' Untranslated Regions5' Untranslated RegionsBase CompositionCodonEukaryotaHumansInternetRNA Stability3' Untranslated Regions5' Untranslated RegionsCodonRNA, Messenger

Identifiers

PMID40384581
PMCPMC12230703

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.