a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis

Question

Can the following oversimplified biochemical pathway for DNA synthesis serve as a model for evaluating the degree of the effect that the 3′ to 5′ exonuclease affinity for mismatched base pairs can have on the degree of the fidelity of dsDNA synthesis? Is this idea basically correct to model the relationship?

Thank you for your attention

dna pathway polymerase

Thank you for your attention

e-gabrielyan · Answer

well I tried to implement this pathway in MATLAB and it seems to me that it makes some sense. Here are two versions of the reaction progress simulation, one with low and the other with high affinity of the 3' to 5' exonuclease domain for the mismatches. The violet curve of the simulation corresponds the amount of synthesized dsDNA and the green curve corresponds to the error-free amount of that dsDNA.
The next figure shows that with low affinity of the exonuclease for the mismatches, the error rate is high (12%).

The figure below shows that the dsDNA synthesis error rate decreased with the increase of the affinity of the exonuclease for the mismatches.

The MATLAB code of this simulation is provided
https://matlab.mathworks.com/users/mwa0000016879211/Published/x551/x551.html
Your comments and suggestions are most appreciated.
Thanks,

a biochemical pathway for evaluating the effect of 3' to 5' exonuclease on the proofreading activity of DNA synthesis

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