mRNA Integrity Analysis ServicemRNA Integrity Analysis Service
Overview
In the rapidly evolving landscape of RNA therapeutics, the molecular integrity of messenger RNA (mRNA) stands as the most critical determinant of translational efficiency and therapeutic potency. CD BioGlyco offers a specialized mRNA integrity analysis service designed to provide high-resolution, quantitative assessments of RNA quality. Even minor fragmentation can lead to truncated protein products, reduced expression levels, and potential immunogenic responses, which can jeopardize the success of preclinical and clinical programs. Our service leverages advanced analytical platforms to distinguish between intact transcripts and degraded fragments, ensuring that your drug substance meets the rigorous standards required for modern medicine. By integrating state-of-the-art electrophoresis and liquid chromatography, CD BioGlyco empowers researchers to optimize IVT processes and maintain the highest quality control over their genetic payloads.
Core Technologies
Our analytical suite is engineered to overcome the challenges posed by the large size and complex secondary structures of therapeutic mRNA.
- Capillary Gel Electrophoresis with Laser-Induced Fluorescence (CGE-LIF)
Recognized as the gold standard for mRNA integrity, CGE-LIF provides exceptional resolution. We utilize optimized denaturing conditions, including formamide and urea, to eliminate secondary structures, allowing for the precise separation of full-length mRNA from smaller degradation products.
- Ion-Pair Reversed-Phase Liquid Chromatography (IP-RPLC)
This high-resolution technique offers an orthogonal approach to electrophoresis. It is particularly effective for assessing purity and identifying specific species within a complex RNA mixture based on hydrophobicity and size.
- Automated Fragment Analysis
For rapid screening and routine quality checks, we utilize automated platforms that provide RNA integrity numbers (RIN) or RNA quality numbers (RQN) through digital electrophoresis.
- Mass Photometry
A cutting-edge, label-free technology that measures the mass of individual molecules in solution. This allows for the direct assessment of the mass distribution of mRNA populations, identifying aggregates and large-scale degradation with minimal sample volume.
Quantifying integrity, ensuring efficacy.
Our service covers the full spectrum of mRNA types and delivery formats:
- IVT mRNA integrity: Assessment of post-synthesis quality for conventional and modified mRNA constructs.
- LNP-encapsulated mRNA analysis: specialized extraction and integrity testing of RNA directly from delivery vehicles.
- Self-amplifying RNA (saRNA) characterization: High-resolution analysis of very large transcripts (up to 15kb) requiring specialized separation matrices.
- Stability study monitoring: Longitudinal integrity tracking under various storage conditions (e.g., -80°C, -20°C, and 4°C).
- Process-related degradation profiling: Identifying specific stages in your manufacturing workflow where RNA integrity might be compromised.
- Comparative integrity mapping: Benchmarking different batches or manufacturing sites to ensure product consistency.
Workflow
Sample Acquisition and Stabilization
Upon receipt, your samples are immediately logged into our secure, trackable system and transferred to a dedicated, strictly RNase-free handling suite. We employ fluorometric quantification assays to accurately verify RNA concentration. This crucial step ensures each sample is within the optimal detection range for our high-resolution platforms, preventing signal saturation or loss, and laying the foundation for reliable, quantitative analysis.
LNP Release and RNA Recovery
For lipid nanoparticle-encapsulated mRNA, we utilize a proprietary, mild detergent-based or buffer-exchange protocol designed to gently disrupt the LNP structure without shearing or chemically modifying the RNA. This non-destructive release method is critical; it ensures that the integrity measurement we obtain authentically represents the state of the encapsulated therapeutic cargo, isolating true product degradation from potential artifacts introduced during the analysis preparation itself.
Denaturation and Secondary Structure Removal
To guarantee that electrophoretic migration reflects true molecular length, samples are treated with high-purity formamide and urea, then subjected to precisely controlled thermal denaturation cycles. This process completely unfolds even the most stable G-C rich hairpins and complex secondary structures, converting all mRNA molecules into a linear, uniform state. This step is paramount for achieving clear separation and accurate sizing, especially for long transcripts.
High-Resolution Separation
Samples are processed through our core analytical platforms: CGE-LIF and/or IP-RPLC. Using specialized, polymer-filled capillaries or columns maintained in a precise temperature-controlled environment, we achieve exceptional separation resolution. This setup maintains the RNA in its denatured, linear conformation throughout the run, allowing us to distinguish the full-length product from degradation fragments that may differ in length by only a few nucleotides.
Digital Data Acquisition and Integration
Advanced detection systems and proprietary software algorithms convert raw fluorescent or UV signals into high-fidelity digital electropherograms or chromatograms. Our software then performs sophisticated peak detection and baseline correction to accurately quantify the area under the curve (AUC) corresponding to the full-length transcript peak versus the broad "smear" of smaller fragments. From this, we calculate an absolute, numerical percentage of intact mRNA, providing an objective and quantifiable integrity metric.
Comprehensive Reporting and Consultation
You receive a detailed, professional report containing high-resolution graphs, tabulated quantitative results (including intact percentage and degradation index), and clear methodological summaries. Beyond the report, our PhD-level scientific team provides a consultative review, helping you interpret the data in the context of your specific process, stability profile, or therapeutic goals, and translating findings into actionable insights for development.
Publication Data
Journal: Molecular Therapy Methods & Clinical Development
DOI: 10.1016/j.omtm.2025.101454
IF: 4.7
Published: 2025
Results: In this comprehensive study, Deslignière and colleagues address the critical analytical challenges in characterizing intact mRNA-based therapeutics, which are large, heterogeneous, and unstable molecules, by developing and optimizing innovative single-particle techniques. They demonstrate that conventional ensemble mass spectrometry fails for mRNAs exceeding 2,000 nucleotides, but Orbitrap-based charge detection mass spectrometry (CDMS) under denaturing conditions enables high-resolution mass measurements of mRNAs up to 9,400 nt (~3 MDa) with significantly improved accuracy by analyzing highly charged ions for enhanced signal-to-noise. Complementarily, mass photometry (MP) provides rapid, in-solution mass determination and detects low-abundance impurities like fragments and dimers, though it requires specialized surface treatments for mRNA adhesion. The authors validate these methods on various mRNAs, including SARS-CoV-2 spike protein encoding sequences, showing that CDMS and MP offer orthogonal, digestion-free strategies for assessing mRNA integrity, heterogeneity, and purity, thereby advancing quality control for next-generation therapeutics.
Applications
Vaccine R&D
Ensuring that every batch of mRNA vaccine contains the maximum amount of intact transcript to drive high-level antigen expression and robust immune responses in target populations.
Gene Editing Applications
Characterizing the quality of mRNA encoding Cas9 or base editors, where even minor degradation can lead to non-functional enzymes and significantly reduced editing efficiency in vivo.
Veterinary Medicine
Supporting the development of high-integrity RNA vaccines and therapeutics for livestock and companion animals, where cost-effectiveness and product stability are critical for field deployment.
Storage and Distribution Validation
Assessing the impact of cold-chain fluctuations on mRNA integrity, helping to define the safe temperature margins for global shipping and long-term storage of RNA products.
Advantages
Expertise in LNP Cargo Recovery
We have developed specialized methods to release mRNA from complex lipid nanoparticles without causing shearing or chemical damage, ensuring the integrity of the data reflects the true state of your drug product.
Stringent Secondary Structure Control
By utilizing high-concentration urea and formamide under precisely controlled temperatures, we ensure total denaturation of even the most complex RNA hairpins, leading to highly accurate length and integrity measurements.
Automated and Reproducible Workflows
Our laboratory utilizes validated, automated systems that minimize human error and ensure that every sample is processed under identical conditions for maximum batch-to-batch comparability.
Quantitative Degradation Metrics
We provide more than just a visual smear; our reports include precise percentages of intact mRNA and a calculated "Degradation Index" that allows for objective decision-making during process development.
Frequently Asked Questions
Customer Review
CD BioGlyco's CGE-LIF service revealed degradation issues that our standard Bioanalyzer missed. Their ability to resolve long transcripts is unmatched, and it's been crucial for our saRNA program.
— By Dr. K.A. Peterson, Principal Scientist, Vaccine Division
We were struggling with inconsistent potency in our LNP batches. CD BioGlyco's integrity analysis of the encapsulated cargo helped us identify a critical shearing issue during the mixing process.
— By Manager of Formulation, Biotech Therapeutics
The level of detail in the characterization reports is exceptional. Having a PhD-level scientist to discuss the results with makes a huge difference in how we pivot our research.
— By Dr. S.D. Takahashi, Lead Researcher, Oncology Dept
Associated Services
Maximize the stability and expression of your construct before you even reach the analysis stage.
High-quality plasmid and linear templates designed for the production of high-integrity mRNA.
Access a wide range of modified nucleotides to enhance the biological half-life and potency of your RNA.
Remove immunogenic impurities and truncated fragments to ensure the highest starting integrity for your drug substance.
CD BioGlyco is dedicated to providing the analytical precision required for the next generation of genetic medicine. Our mRNA integrity analysis service combines deep technical expertise with state-of-the-art technology to ensure your RNA therapeutics are of the highest quality. Whether you are in early-stage discovery or preparing for regulatory submission, contact us!
Reference
- Deslignière, E.; et al. Characterization of intact mRNA-based therapeutics by charge detection mass spectrometry and mass photometry. Molecular Therapy Methods & Clinical Development. 2025, 33(2). (Open Access)