mRNA Sequence Design&Optimization Service
Overview
The effectiveness of mRNA-based therapeutics is inextricably linked to the primary sequence of the nucleic acid. A poorly designed sequence can lead to low protein yield, rapid degradation, or unintended immune activation. CD BioGlyco offers a sophisticated mRNA sequence design & optimization service that transcends simple codon usage tables. We integrate advanced computational algorithms, structural modeling, and regulatory element engineering to create mRNA molecules with peak performance. Our approach focuses on the "three pillars of mRNA excellence": maximizing translation efficiency, extending intracellular half-life, and minimizing innate immunogenicity. By optimizing every component from the 5' cap to the poly(A) tail, we help researchers unlock the full potential of their genetic medicines, ensuring that your therapeutic protein is expressed at the right levels for the right duration.
Core Technologies
Our optimization platform leverages a multi-disciplinary toolkit to refine every nucleotide of your sequence:
- AI-Driven Codon Optimization
Our proprietary algorithms go beyond the codon adaptation index (CAI). We consider tRNA abundance, GC content distribution, and the avoidance of "rare" codons that cause ribosomal stalling.
- Structural MFE Prediction
We utilize minimum free energy (MFE) modeling to predict the secondary and tertiary structures of mRNA. By minimizing stable hairpins in the translation initiation region, we facilitate seamless ribosome loading.
- UTR Library Screening
We maintain a curated library of high-performance 5' and 3' untranslated regions (UTRs). These elements are selected based on their ability to recruit translation factors or prevent exonuclease-mediated decay.
- Immunogenicity Filtering
Our software scans sequences for specific motifs (such as certain uridine-rich sequences) that are known to trigger TLR7/8 or RIG-I sensors, allowing us to design sequences that are "stealthier" in the cellular environment.
mRNA Sequence Design & Optimization: Maximizing Expression and Stability
Our mRNA sequence design & optimization are designed to support a wide array of research and clinical modalities. We provide expert design for prophylactic vaccines, cancer immunotherapies, protein replacement therapies, and gene editing components. Our scope includes the optimization of specialized transcripts such as self-amplifying RNA (saRNA) and circular RNA (circRNA), which require unique structural considerations for replication and translation.
We also offer "sequence-to-synthesis" integration. Once a design is finalized, we facilitate the production of the mRNA using modified nucleosides (such as N1-methylpseudouridine) to further enhance performance. Whether you are working with a novel viral antigen or a complex human enzyme, our service provides the molecular architecture necessary to achieve high-titer protein expression in vivo and in vitro.
Workflow
Requirement Definition
We initiate the process through a collaborative workshop to thoroughly define your project's specific objectives. This includes identifying the target protein, specifying the intended target cell type (e.g., muscle cells for vaccine applications versus hepatocytes for metabolic therapy), and clarifying the required expression kinetics, such as onset, peak level, and duration. This foundational stage ensures the design strategy is precisely aligned with your therapeutic or vaccine goals from the outset.
Initial Sequence Generation
Using your provided amino acid sequence as the template, our proprietary platform algorithmically generates thousands of candidate nucleotide sequences. This is achieved by employing diverse codon-optimization strategies (e.g., species-specific, GC-content balanced, or immune-silent) to maximize translational efficiency while also systematically varying overall GC-content to influence mRNA stability and secondary structure.
In Silico Screening
The large library of candidate sequences is rigorously filtered through our suite of advanced, proprietary predictive models. These models evaluate multiple critical parameters concurrently, including predicted secondary structure stability (which can impede ribosomal scanning), estimated ribosomal transit speed, and the presence of undesirable sequence motifs such as cryptic splice sites, internal ribosome entry sites, or premature start codons that could compromise expression fidelity.
Regulatory Element Integration
We then integrate key non-coding regulatory elements to further enhance mRNA performance. The optimal 5' and 3' untranslated regions (UTRs) are selected from our curated, functionally validated database to promote robust ribosome engagement and regulate mRNA half-life. Concurrently, we engineer a poly(A) tail with a defined length and, if applicable, a segmented structure, specifically designed to maximize cytoplasmic stability and facilitate efficient translation.
Final Structural Validation
The top-performing sequence candidate from the screening process undergoes a final, comprehensive "stress test." This involves advanced computational folding simulations that model the full-length mRNA's behavior under physiological conditions, ensuring the key regions, particularly the start codon and ribosome binding site, remain structurally accessible to the translation machinery and are not occluded by stable intramolecular base-pairing.
Comprehensive Design Report
You receive the final, optimized nucleotide sequence accompanied by a detailed, stand-alone design report. This document provides the complete rationale behind all design choices, presents key predictive stability and secondary structure metrics, includes translation efficiency scores, and offers clear guidance for downstream synthesis and application.
Publication Data
Journal: RNA biology
DOI: 10.1080/15476286.2024.2333123
IF: 3.4
Published: 2024
Results: This comprehensive review by Mochida and Uchida systematically explores the critical design elements of mRNA vaccines, emphasizing the optimization of adjuvanticity and delivery mechanisms to enhance both safety and efficacy. The authors elucidate how contemporary mRNA formulations integrate adjuvant functions directly into nanoparticles, enabling synchronized delivery of antigen-encoding mRNA and immunostimulatory components in a unified system. They detail how the inherent adjuvant properties of mRNA sequences and carrier materials, such as lipids and polymers, can be harnessed but require careful calibration to prevent excessive innate immune activation that may compromise vaccine performance. The article further analyzes various delivery platforms, including lipid nanoparticles and polyplexes, designed to target antigen-presenting cells within lymphoid organs, either through direct nanoparticle trafficking or cellular migration. By synthesizing current mechanistic understandings from in vitro and in vivo studies, the review proposes strategic improvements in chemical modifications, nanoparticle engineering, and administration routes to achieve a superior therapeutic window, ultimately advocating for a balanced approach to adjuvanticity and precise delivery for advancing mRNA vaccine applications against infectious diseases and cancers.
Applications
Prophylactic Viral Vaccines
We optimize viral antigens to ensure rapid and robust expression, facilitating the development of vaccines that induce strong neutralizing antibody titers with lower doses of mRNA.
Cancer Neoantigen Vaccines
Our high-speed pipeline allows for the rapid design of personalized neoantigen sequences, ensuring that patient-specific mutations are expressed efficiently by the immune system.
Protein Replacement Therapy
For genetic diseases like cystic fibrosis or hemophilia, we design mRNA sequences that provide sustained expression of missing proteins, reducing the frequency of administration.
We optimize mRNA encoding chimeric antigen receptors (CARs) for delivery directly into T-cells in vivo, facilitating a transient and safe approach to cell therapy.
Advantages
Multi-Parameter Codon Selection
Unlike basic tools, we optimize for tRNA availability, GC content, and RNA folding simultaneously. This multi-factor approach results in up to a 10-fold increase in protein expression compared to standard codon-optimized sequences.
Strategic Secondary Structure Management
We design sequences with high MFE while ensuring the 5' end remains unstructured. This balance prevents the mRNA from being targeted by cellular nucleases while keeping the "ribosome entry gate" wide open.
Enhanced Intracellular Stability
By optimizing the 3' UTR and poly(A) tail architecture, we delay the onset of deadenylation. Pur optimized tails extend the functional half-life of mRNA by several hours in primary cell cultures.
Minimization of TLR Activation
Our sequences are designed to minimize the presence of pathogen-associated molecular patterns (PAMPs). This reduces the induction of Type I interferons, which otherwise would prematurely shut down protein synthesis.
Frequently Asked Questions
Customer Review
The optimized sequence from CD BioGlyco showed a 5-fold increase in luciferase expression compared to our internal design. Their structural analysis report was incredibly insightful.
— By Dr. A.M., Senior Scientist
We needed a highly stable mRNA for a multi-antigen program. CD BioGlyco delivered optimized designs for all four antigens in record time, and the in vivo results were outstanding.
— By Manager, Vaccine Developmen
CD BioGlyco's expertise in UTR engineering made a huge difference in our protein replacement project. The duration of protein expression was nearly doubled compared to our previous benchmarks.
— By Dr. P.H., Principal Researcher
Associated Services
Ensuring your optimized sequence is synthesized without truncation or degradation.
High-resolution quantification of full-length transcripts and removal of double-stranded RNA contaminants.
Precise verification of transcript size and poly(A) tail distribution using advanced capillary electrophoresis.
Sensitive detection of template DNA to ensure safety and regulatory compliance of your final mRNA product.
CD BioGlyco is committed to helping you design the perfect mRNA for your therapeutic needs. Our mRNA sequence design & optimization service provides the molecular precision required to maximize efficacy and minimize the risks associated with RNA-based drugs. Whether you are in the discovery phase or moving toward clinical trials, CD BioGlyco delivers the data-driven designs you need to succeed, contact us!
Reference
- Mochida, Y.; Uchida, S. mRNA vaccine designs for optimal adjuvanticity and delivery. RNA biology. 2024, 21(1): 422-448. (Open Access)