Modeling of repeated-batch transcription for production of RNA

Enzymatic transcription for in vitro production of ribonucleic acids (RNA) is typically carried out in small batch reactors which suffer from low yields and high costs due to the formation of abortive RNA transcripts and the disposal of the DNA template and polymerase enzyme after a single use. This work considers repeated-batch transcription in which the DNA template molecules are immobilized on beads which are recovered and reused in multiple rounds. Some of the enzyme binds to the DNA template and is also recovered and reused. A model of this process is presented which employs equilibrium binding between the enzyme and template and which includes a first-order sequential deactivation of the enzyme. The model predicts the yields of RNA product and aborts for each round of repeated-batch transcription with no DNA addition after the first round and only partial enzyme replacement. The yield of RNA product per substrate (nucleoside triphosphates) generally decreases in subsequent rounds, whereas the yields of RNA product per enzyme and per template increase due to their reuse. Experimental data are presented which confirm the model and which show how the model parameters are obtained. A cost analysis shows that the cost of RNA production can be reduced by more than 50% for the system tested by employing an optimum number of rounds of repeated-batch transcription.