mRNA Synthesis Custom Order

mRNA synthesis, also known as in vitro transcription (IVT), is commonly used to synthesize mRNA for specific genes or to make RNA molecules for research purposes. IVT is a process of producing gene RNA by combining RNA polymerase with various elements required for transcription.

1. Cap:

• Cap consists of a specific nucleotide located at the 5' end of eukaryotic mRNA.
• Cap is an essential element for protecting mRNA, increasing translation efficiency, and regulating immune responses.
• Cap-0: It consists of a unique nucleotide called 7-methylguanino (m7G) at the 5’ end of mRNA.
• Cap-1: In addition to Cap-0, it refers to a structure in which the 2’-OH group of the first nucleotide is replaced with a methyl group.

2. 5’ & 3’ Untranslated Region (UTR):

• UTR refers to the untranslated region of mRNA. UTRs are located at the 5' end (5' UTR) and 3' end (3' UTR) of mRNA and play an important role in regulating translation efficiency, stability, and localization of mRNA.
• 5' UTR: Located at the 5' end of the mRNA molecule, preceding the coding region (CDS). The 5' UTR performs the following functions:
• Translation initiation: The translation initiation complex (eIF4F) binds to determine where translation begins.
• Modulation of translation efficiency: Certain structural elements within a UTR can increase or decrease translation efficiency.
• Regulation of mRNA stability: Certain structural elements within the UTR can increase or decrease the stability of the mRNA.
• 3' UTR: Located at the 3' end of the mRNA molecule, after the coding region (CDS). The 3' UTR performs the following functions:
• Regulation of mRNA stability: Certain structural elements present within the UTR can increase or decrease the stability of the mRNA.
• Regulation of mRNA localization: Specific structural elements can regulate the movement of mRNA to specific locations within the cell.
• Post-translational regulation: Specific elements within the UTR can regulate the degradation, modification, and transport of mRNA after protein translation.

3. Coding Region Sequence (CDS):

• CDS is the core part that contains genetic information and is the basic unit of protein expression. CDS is expressed as a protein through transcription and translation processes.
• mRNA consists of four bases (A, U, C, G), and three base sequences (codons) code for specific amino acids. It generally consists of a continuous codon sequence starting with a start codon (ATG) and ending with a stop codon (TAA, TAG, TGA). This contiguous codon sequence is also called Open Reading Frame (ORF).
• CDS can design DNA sequences based on desired protein sequences and synthesize desired DNA sequences through gene synthesis technology.

4. Poly(A) tail:

• It refers to a tail in which adenine (A) nucleotides are continuously connected at the 3' end of mRNA.
• The poly(A) tail protects mRNA from nuclease (RNA-degrading enzyme), preventing degradation of mRNA and increasing its stability.

Q1: What is IVT Optimization and why is it necessary?

IVT Optimization is the process of redesigning DNA template sequences to maximize In Vitro Transcription (IVT) process efficiency and in vivo mRNA stability while maintaining the target amino acid sequence. It is a core process technology that goes beyond simple expression enhancement to ensure the production of high-purity, high-yield mRNA for vaccines and therapeutics.

Why Optimization is Needed:

1. T7 Polymerase Processability:
• T7 RNA polymerase can cause Premature Termination upon encountering consecutive T sequences (Poly-T) or Slippage at consecutive G sequences (Poly-G), resulting in incomplete mRNA or byproducts.
• IVTDesigner™ fundamentally removes these "production-hindering sequences" to maximize the yield of full-length mRNA.
2. Balancing mRNA Structural Stability & Translation Efficiency:
   • mRNA requires a stable global structure (Low MFE) for storage stability, but the 5' end where ribosomes bind must remain unstructured for efficient translation.
   • IVTDesigner™ employs a Dual Structure Control strategy to satisfy these conflicting thermodynamic requirements simultaneously.
3. Reduced Immunogenicity:
   • Exogenous mRNA can trigger innate immune responses via sensors like TLRs and RIG-I, reducing efficacy.
   • Safety is ensured by minimizing sequences that form double-stranded RNA (dsRNA) and reducing immuno-stimulatory motifs like CpG/UpA.

Benefits of IVTDesigner™ Optimization:

• High-Purity mRNA Production: Secures GMP-level quality by eliminating error-prone sequences.
• Maximized Protein Expression: Increases translation efficiency via 5' UTR optimization and improved Codon Adaptation Index (CAI).
• Enhanced Safety: Removes risk factors (dsRNA, CpG) that trigger innate immune responses.

Q2: Can I get mRNA optimization services using IVTDesigner™?

Yes. Bioneer provides customized sequence optimization services for mRNA vaccine and therapeutic development using our proprietary IVTDesigner™.

To request the service, please send the following information to mrnaorder@bioneer.co.kr:

1. DNA or Protein Sequence: Target sequence (CDS). Stop codon optimization is included if DNA is provided.
2. Target Organism: The host where the mRNA will be translated (e.g., Homo sapiens, Mus musculus).
3. UTR & Poly-A Options: Selection from our high-efficiency UTR library, custom UTR sequences, or specification of Poly-A tail length.
4. Optimization Goal:
   • Maximize: Maximize protein expression and mRNA stability (Default).
   • Targeting: Customize for specific GC content (%) or CAI values (e.g., for attenuated vaccines).

Q3: What is IVTDesigner™

IVTDesigner™ is Bioneer's next-generation sequence design platform specialized for mRNA synthesis. Combining high-performance Genetic Algorithms with a Numba JIT-based high-speed RNA structure prediction engine, it performs Multi-Objective Optimization to reduce manufacturing defect rates and enhance biological efficacy.

Notably, it employs a proprietary Integrated Structural Strategy to generate structurally stable seed candidates from the very beginning. This technology derives optimal sequences through a four-step algorithm:

1. Viterbi Global Optimization: Searches for globally optimal paths considering Codon Adaptation Index (CAI) and GC content.
2. Local Repair: Removes local instability factors (Bad Motifs) and excessive structural formations.
3. Convergent Stabilizer: Iteratively scans and swaps codons to converge structural stability (MFE) towards the target GC content.
4. 5' RNAInverse: Loosens the structure at the 5' end to enhance translation efficiency.

Q4: What are the differences between conventional codon optimization and IVTDesigner™?

While conventional methods focus primarily on increasing in vivo protein expression (CAI optimization), IVTDesigner™ prioritizes the physical constraints of the mRNA manufacturing process (IVT) and in vivo safety.

Key Differentiators:

1. T7 Process Safety:
• It strictly enforces Hard Filters to block Poly-T (≥8nt) and Poly-G (≥6nt) sequences, which cause IVT failure, while also penalizing moderate repeats (≥5nt) to ensure process stability.
2. Precise Immunogenicity Control:
• Beyond simple codon matching, it precisely detects and removes Inverted Repeats (dsRNA) capable of stimulating immune sensors like RIG-I, and minimizes CpG/UpA dinucleotides.
3. Structural Flexibility:
• It applies Local MFE Control, ensuring global mRNA stability (High GC, Low Energy) while preventing structural folding in the critical 5' start region (first 40bp). This is achieved through the Integrated Strategy, combining Viterbi algorithms with Convergent Repair techniques.
4. Diversity via Clustering:
• Instead of a single result, it uses K-Means Clustering to provide the Top 8 Candidate Clusters with distinct structural characteristics, enabling researchers to screen for the candidate that best fits their experimental needs.

Experience high-quality mRNA with maximized expression and stability via IVTDesigner™'s sophisticated structural optimization.

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The ability to produce large quantities of customized mRNA through in vitro transcription (IVT) allows it to be used for a variety of purposes across a range of applications:

• 1. mRNA vaccine development: This is the fastest growing area with IVT. mRNA encoding viral antigens (foreign molecules that trigger an immune response) can be produced quickly and efficiently through IVT. These mRNA vaccines instruct cells to produce antigens, stimulating the immune system to develop immunity without introducing the entire virus. This method offers several advantages:
  • Faster development: Compared to traditional vaccines, mRNA vaccines can be designed and manufactured much faster and are advantageous for responding to emerging infectious diseases.
  • Safety: Because they do not contain live virus, mRNA vaccines are generally considered safe with minimal side effects.
  • Versatility: mRNA platforms can be easily adapted to target a variety of pathogens by simply modifying the encoded antigen sequence.
• 2. Gene therapy: IVT has tremendous potential to develop new gene therapies for a variety of genetic diseases.
• 3. Protein production: Synthetic mRNA can be used for large-scale production of specific proteins in cell-free systems. Applications include:
  • Research applications: Studying protein function, protein-protein interactions, or drug discovery.
  • Production of difficult-to-obtain proteins: Certain proteins may be difficult to isolate from natural sources or may require complex purification processes. IVT provides an alternative way to obtain these proteins for research or therapeutic purposes.
• 4. Other potential applications: mRNA has additional potential uses in fields such as:
  • Tissue engineering: Stimulating tissue regeneration by delivering mRNA coding for specific growth factors or proteins.
  • Cell reprogramming: Using mRNA to induce changes in cell fate or identity for regenerative medicine applications.
  • Cancer immunotherapy: Designing mRNA vaccines to target cancer antigens or deliver immunostimulatory molecules.

Access the Bioneer homepage (eng.bioneer.com), log in, and follow the form specified on the mRNA synthesis custom order page for Capping, UTR, Poly(A) tail. Please select the availability and type, fill in the Coding Region Sequence, etc. and submit. After confirmation, you will receive detailed guidance on mRNA synthesis.

The optimal RNA transcript size for mRNA synthesis service is 100 to 5,000 nt. If you require a length other than this, service will be provided after consultation.

Template DNA Samples must be sent in a volume of 10 μl or more (at least 1 μg of DNA) at a concentration of 100 to 200 ng/μl.

Please accurately enter your organization and client name in the box, and deliver the sample through the affiliated delivery company below.

Sending address: Bioneer Co., Ltd., 8-11 Munpyeongseo-ro, Daedeok-gu, 34302 Daejeon, Republic of Korea.

Shipping costs: We are responsible for the cost regardless of the number of templates. If the service becomes difficult due to incorrect sample delivery, 50% of the final billing amount will be charged as a set-up charge. When delivering samples, please be sure to check and send carefully.

Gene synthesis of CDS and UTR is possible through our Gene synthesis service.

It's possible. For further information, please contact mrnaorder@bioneer.co.kr.

For 5’ Cap, you can choose Cap-0 or Cap-1. The 3’ poly(A) tail can be selected as 111 nt (105 nt poly-A with 6 nt linker in the middle).

Custom 5’ or 3’ UTR modification is possible. Alternatively, you can choose Bioneer 5’ or 3’ UTR.

If you would like to manufacture RNA-LNP in conjunction with the lipid nanoparticle (LNP) service, please contact us.

The synthesized mRNA is provided in a freeze-dried state, and electrophoresis results and absorbance measurement results using Nanodrop are included.