I’ll mention that your example of a protease is a good counter example — the function of the protein is to bind the larger peptide and cleave it. The evolutionary pressure was to bind the larger molecule and release the smaller (cleaved) ones. Here, the evolutionary pressure was to bind the smaller (unlabeled) nucleotide to build the DNA strand. This is a complex reaction that involves a lot of ligand binding and intermediates. Trying to add a function to preferentially bind a larger fluorophore labeled base seems like it would be overly disruptive or at least reduce the rate of polymerization.
I don’t know enough about the structure of DNA polymerase to say how feasible this really is — but the extra bulk of the fluorophore seems like it would cause issues.
But, is it possible? Sure! This is biology — there is always a way (or three)! I’d expect for there to be a way to generate a polymerase that does this via mutagenesis. But it would be very difficult and probably more expensive than the prize.
If they were able to keep the concentration of fluorescently labeled nucleotides higher, this wouldn’t be an issue. But due to the technology choices (one tube reactions, laser release), they are stuck trying to get a better polymerase.
I certainly wish them luck, I’d love for this to work for more than 5-6 bp.
But this is an obvious issue. With this type of photo-reaction, you’ll get a build up of unlabeled nucleotides. There is still some potential for the technology, but it’s really hard for me to see how this works in one tube without some kind of washing (which also increases costs by a lot).
Maybe there is a way to add multiple moieties to the NTPs, such that removal of the fluorophore would cause a bigger hindrance? (Fluorophore + extra-moiety would bind, but extra-moiety alone would have more trouble binding?)