mRNA Sequence Analysis Service
In the rapidly evolving landscape of the therapeutic nucleic acid development platform, ensuring the fidelity of messenger RNA (mRNA) is paramount. At CD BioGlyco, we recognize that the sequence of an mRNA molecule is the foundational blueprint for its therapeutic efficacy and safety. Any deviation in the primary structure, from single-nucleotide polymorphisms to truncation in the polyadenylated (poly(A)) tail, lead to reduced protein expression or unintended immunogenicity.
Our mRNA sequence analysis service provides a comprehensive solution for researchers within the mRNA-based vaccine development sector. By integrating high-resolution sequencing with advanced mass spectrometry (MS), we deliver an exhaustive structural characterization of your mRNA candidates. Whether you are validating a novel antigen for a prophylactic vaccine or optimizing a therapeutic RNA for gene replacement, our platform ensures that your sequence is exactly what you intended it to be.
Key Technologies
- Next-Generation Sequencing (NGS)
We utilize high-throughput NGS platforms to provide deep coverage of the entire mRNA transcript. This allows for the detection of low-frequency variants, verification of the open reading frame (ORF), and assessment of sequence homogeneity across the entire sample population. - Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS)
For direct sequence mapping that bypasses the biases of reverse transcription, we use LC-MS/MS. This technique is used for identifying modified nucleosides and providing 100% sequence coverage of large RNA molecules through enzymatic digestion and oligonucleotide mass fingerprinting. - Long-Read Sequencing
Utilizing nanopore technologies, we perform end-to-end sequencing of single mRNA molecules. This is particularly effective for accurately measuring the length and composition of the poly(A) tail and identifying complex isoforms or splicing variants that short-read methods might miss.
Unlocking Genetic Precision: Comprehensive mRNA Sequence Mapping
As a critical component of our mRNA structural characterization services, the mRNA sequence analysis service at CD BioGlyco covers every vital segment of the mRNA architecture. We provide a granular analysis that ensures the integrity of the following elements:
- 5' Cap Structure Verification
We confirm the presence and type of the 5' cap (e.g., Cap 0, Cap 1), which is essential for mRNA stability and translation initiation. - Untranslated Regions (UTRs) Analysis
Our service meticulously maps the 5' and 3' UTRs, identifying any mutations that could affect the binding of regulatory proteins or microRNAs. - ORF Fidelity Check
We ensure the coding sequence is free of unintended insertions, deletions, or substitutions, guaranteeing the production of the correct therapeutic protein. - Poly(A) Tail Characterization
We provide precise measurement of the poly(A) tail length and structure, a key determinant of the transcript's half-life and translational efficiency. - Impurity and Degradation Profiling
Our analysis detects truncated transcripts, double-stranded RNA (dsRNA) contaminants, and residual template DNA that could compromise product quality.
Workflow
Initial Sample Quality Control (QC)
Every sample undergoes rigorous QC using capillary electrophoresis and spectrophotometry. We assess the concentration, purity, and RNA integrity number (RIN) to ensure the starting material meets the standards required for downstream analysis.
Tailored Library Construction
We perform either poly(A) selection or ribosomal RNA (rRNA) depletion. We then fragment the mRNA and perform strand-specific library preparation to maintain the directional information of the original transcripts.
High-Resolution Sequencing or Mass Mapping
Samples are processed through our NGS platforms for deep sequence coverage or subjected to LC-MS/MS for direct RNA mapping. This dual-platform capability allows us to cross-validate results and ensure absolute sequence confidence.
Advanced Bioinformatics Processing
Our team of expert bioinformaticians utilizes proprietary pipelines to align reads against your reference sequence. We perform variant calling, identify isoforms, and utilize specialized algorithms to calculate poly(A) tail length distributions.
Sequence Validation and Annotation
We provide a detailed annotation of all functional domains, including the ORF and UTRs. Any identified variants are cross-referenced with biological databases to assess their potential impact on protein folding or mRNA stability.
Comprehensive Reporting and Consultation
The final deliverable is a detailed report containing raw data, processed alignments, and a summary of all findings. Our specialists are available for a follow-up consultation to help you interpret the results in the context of your vaccine or therapy development.
Publication Data
DoI: 10.1371/journal.pone.0332440
Journal: PLoS One
IF: 3.2
Published: 2025
Results: This study investigates the impact of ambient mRNA contamination on droplet-based single-cell RNA-sequencing (scRNA-seq) analysis and validates mitigation strategies. Using two datasets—peripheral blood mononuclear cells (PBMCs) from dengue patients and human fetal liver tissues—the researchers applied CellBender (automated) and SoupX (predefined contaminant genes) correction tools. Uncorrected data showed ambient mRNAs (e.g., immunoglobulins, hemoglobin) distorting differentially expressed genes (DEGs) and enriching irrelevant biological pathways in unexpected cell subpopulations. After correction, ambient mRNA levels decreased, improving DEG identification and revealing cell type-specific pathways. A cross-species validation dataset confirmed reduced false positives post-correction. The findings emphasize the necessity of ambient mRNA correction to enhance scRNA-seq data reliability and biological interpretation accuracy.
Fig.1 Expression profiles of ambient mRNAs before and after correction. (Arora, et al., 2025)
Applications
mRNA Vaccine Development
Our analysis ensures that the mRNA sequence encoding the target antigen is perfectly accurate, which is critical for inducing the desired immune response and maintaining the safety profile of the final vaccine product.
Gene Therapy Research
We help researchers verify the integrity of therapeutic RNA transcripts designed for gene replacement or editing, ensuring that the mRNA remains stable and functional within the target cellular environment for the required duration.
RNA Modification Studies
We allow for the precise mapping of chemical modifications like pseudouridine, which are often incorporated into therapeutic mRNA to reduce innate immune sensing and enhance the overall efficiency of protein translation.
Advantages
Unmatched Sequence Coverage
By combining NGS with LC-MS/MS, CD BioGlyco achieves 100% sequence coverage, ensuring that even the most difficult-to-sequence regions of the mRNA are accurately mapped and verified for your therapeutic projects.
Expert Bioinformatic Support
Our dedicated team uses advanced algorithms specifically optimized for mRNA analysis, providing you with deep insights into transcript isoforms, poly(A) tail dynamics, and low-frequency variants.
State-of-the-Art Services
We utilize the latest sequencing and MS, allowing for high-sensitivity detection of impurities and modifications, which is essential for meeting the strict regulatory requirements of mRNA drug development.
End-to-End Solutions
From initial sample extraction and quality assessment to final data interpretation, we provide a seamless, all-in-one service that accelerates your research timeline and reduces the complexity of managing multiple vendors.
Frequently Asked Questions
Customer Review
"The team at CD BioGlyco provided exceptional clarity during our mRNA vaccine pilot. Their ability to map the entire ORF while simultaneously providing data on the poly(A) tail length."
– A.H., Senior Scientist
"We struggled with sequence verification of our modified mRNA using standard NGS. CD BioGlyco's LC-MS/MS approach finally gave us the 100% coverage we needed to confirm the identity of our candidate."
– A.S., Director of R&D
"The precision of the sequence analysis at CD BioGlyco is unmatched. They identified a low-level point mutation that we had missed, which explained the drop in expression we were seeing in our gene therapy trials."
– E.T., Principal Investigator
Associated Services
CD BioGlyco offers an industry-leading mRNA sequence analysis service that provides the precision and depth required for modern therapeutic nucleic acid development. By leveraging our advanced technological platforms and biological expertise, we help you ensure the safety, stability, and efficacy of your mRNA-based products. Please feel free to contact us for more information and to discuss your project.
Reference
- Arora, J.K.; et al. Understanding and mitigating the impact of ambient mRNA contamination in single-cell RNA-sequencing analysis. PLoS One. 2025, 20(9): e0332440. (Open Access)