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How would one calculate the availability of nucleotides to an enzyme like a polymerase ?

I imagine an answer in units like nucleotides per second per enzyme, but I'm also imagining an answer that is not a simple rate of reaction. k_on calculations and k_off do not offer mechanistic explanation.

I'd like to know, specifically, if there is a theoretical approach to this question: how does a polymerase reject an incorrect nucleotide?

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All nucleotides or a specific nucleotide? – Rory M Jan 31 '12 at 15:01
All nucleotides. I will revise the question to reflect better my intention. – Thomas Ingalls Jan 31 '12 at 16:48
The second question on DNA proofreading is probably worth an entire question by itself. You might as well ask it and get more reputation ;) – bobthejoe Feb 24 '12 at 4:40
Wouldn't this be a mass-transport related question? I think that transport rate/flux of nucleotides can be described entirely by the diffusion coefficient given the cellular environment. – bobthejoe Feb 28 '12 at 1:37
@bobthejoe things like temp, pH, salts, etc. should also make a difference to nucleotide incorporation by a polymerase. I think a thorough answer would cover it all, and will be really impressed if we get something that comprehensive. – Richard Smith-Unna Mar 13 '12 at 18:19

I could read this question more than one way. Are you talking about an enzyme in a cell or in a reaction in vitro? Kinetics and mechanical explanations can overlap, but are not entirely the same and are usually dealt with separately - kinetics with watching the rate of reactions in a tube and mechanism in a crystal structure or possibly Nuclear Magnetic Resonance.

Protein structures are usually static- you only get a time lapse snapshot of the reaction in most cases. kinetics allows you to see how fast these things go and can help you understand the order of binding when more than one component is needed for the reaction, etc.

The polymerase has a binding pocket where the template strand and the growing strand are used to build a double helix together. if the base being introduced does not form Watson Crick base pair bonds, the geometry of the reaction will not allow the base to be added to the growing strand.

Hope this helps? If I can make this clearer, can you drop me a comment and I'll revise...

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