I was trying to understand the process of how polymerase performs error corrections on DNA. Every paper on this topic mentions what happens during the process, but there's no mention of how it happens. I even looked up the page on enzymes and it only explains enzyme binding sites, enzymes acting as catalysts and the types of reactions the enzymes perform.

It'd be reasonable to theorize that codons on DNA would have chemical properties that can attract certain enzymes to them to start the transcription process. But during transcription when the enzyme makes an error, what incentive does the enzyme have, to move backward to correct the error? I know that sometimes the error correction is performed only after the transcription, but the question is the same: How does the enzyme know what to do? Moreover, if enzymes were mere catalysts, does this mean that even without an enzyme, the DNA would get transcribed at an extremely slow rate? Could this mean that the "software code" that contains instructions of what to do during a transcription, is in the DNA itself?

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    $\begingroup$ Biologists look for mechanisms, not "motivations". No enzyme has "incentives" to do anything. Enzymes perform their functions because they have a chemical propensity to do it (encoded in their primary, secondary, tertiary or quaternary structure). Not because they feel any "obligation" to do so. Error-correcting mechanisms are just a type of propensity encoded in the enzyme's structure. It is a probabilistic event, whether they do or not, favored thermodynamically. Transcription involves many enzymes & proteins, not just polymerases; transcription would certainly not occur without enzymes. $\endgroup$ – TumbiSapichu Apr 14 '20 at 11:28
  • $\begingroup$ Language and personification of enzymes aside, would you be satisfied with an answer to how does polymerase recognise it has made error as oposed to situation when it has integrated correct nucleotide? In other words what is the pysical stimul which triggers exonuclease activity of DNA polymerase? That would be answerable scientific question. $\endgroup$ – BagiM Apr 14 '20 at 13:31
  • $\begingroup$ By motivation/incentive what I meant was the mechanism which makes it perform such a specific action. Codons showed us there was some kind of programming, so perhaps the way enzymes and proteins are folded are a kind of a programming that makes cellular bonds behave in a certain way. Anyway, from your replies it looks like we haven't figured this out yet. @ BagiM: I'd definitely like to know how the polymerase recognizes an error, but the answer would need to explain both the how and why of what happens. I reckon science doesn't yet have that answer. $\endgroup$ – Nav Apr 14 '20 at 15:05
  • $\begingroup$ There are no codons on DNA, only deoxribonucleosides. $\endgroup$ – David Apr 14 '20 at 19:00

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