Q: What is the purpose of heating first and then cooling down in the enzymatic cap addition process? It seems quite difficult to achieve heating followed by cooling during large-scale production.

A: The purpose of preheating is to unfold the secondary structure of RNA and bring it to a single-stranded state. If this step is not carried out, it will affect the efficiency of capping. This part is indeed a current technical challenge in production. Some companies now directly predict the secondary structure of RNA when determining the template sequence. The capping enzyme only recognizes the first few nucleotides of mRNA. If it is determined that this structure will not result in the secondary structure of RNA, then heating can be omitted.

Q: How to choose between cap-like analogues and enzymatic cap addition?

A: In industry, the most commonly used method for enzymatic cap addition is to treat IVT products with vaccinia virus cap-adding enzyme, which can modify them into Cap 0 mRNA. The Cap 0 structure can be further modified into Cap 1 (m7GpppmN) under the action of 2'O-methyltransferase. With enzymatic cap addition, the cap addition efficiency can reach over 95%. The co-transcription cap addition method is simple to operate, but because GTP competes with the cap dimer, the cap addition rate of this method is a little lower; both methods have their own advantages and disadvantages.

Q: What are the methods for optimizing the cap?

A: By increasing the amount of VCE, for example, adding 10 ul of 100 U of enzyme activity to a 100 ul system, the main purpose is to enhance the methyltransferase activity of VCE. It can also be achieved by increasing SAM (0.5 mmol) to enhance the guanine transfer activity and increase the cap formation rate. For instance, our new single-strand cap enzyme has a significantly improved cap formation rate. This is because its guanine transfer activity is better than that of traditional VCE. For traditional VCE, the small subunit D12 is prone to precipitation and polymer formation, which makes purification difficult and leads to loss, thus resulting in higher costs and inability to control batches.

Q: For some mRNAs that do not have caps added, what impact will this have on subsequent experiments, such as those involving the production of biological agents?

A: Currently, the industry has not specifically targeted this aspect. In the industry, the main focus is on the efficiency of the cap application. The current best cap application rate is above 80%. Of course, the higher the better. There is still no absolute standard for this.

For the synthesized mRNA, purification methods can be employed, such as the one-step membrane encapsulation method by Kang*. This significantly reduces the purification process. The traditional method uses Oligo d(T) columns for purification, with good results achieving a recovery rate of 70-80%; poor results have a recovery rate of 40-50%. An additional step of a hydrophobic column can also be added after the Oligo d(T) column.

Q: What are the requirements for the starting position of the template for co-transcriptional cap addition and two-step cap addition?

A: The co-transcription requirement stipulates that the starting position of the template must begin with AGG*.

The two-step method does not have any specific requirements for the position. However, our current products have the highest yield for the AGGG starting position, mainly due to the preference of the T7 enzyme.