A simple reaction for a DNA molecule is the exchange of a DNA base proton with a water pro...

A simple reaction for a DNA molecule is the exchange of a DNA base proton with a water proton. In the DNA base pair shown below, the imino proton (in boldface) exchanges with water at a rate measurable by NMR.

The stoichiometry of the reaction is

A mechanism for its rate of exchange is as follows:

(TH . A)closed represents a closed base pair. (TH…A)open

is the open base pair ready to exchange. B is a base that

catalyzes the transfer of H to H*.

a. Use a steady-state approximation for [(TH … A)open] to obtain an expression for the initial rate of exchange:

Write kex as a function of kop, kcl, ktr, and [B].

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b. Show how the rates of exchange vs. concentrations of [(TH • A)closed] and [B] can be used to obtain kopen (the rate coefficient for base-pair opening).

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c. The imino exchange rate for a synthetic polynucleotide, poly dA-dT, was measured as a function of pH at 27°C. Calculate a value for kop, the rate coefficient for base- pair opening, from the following data: