Mechanism for unwinding of double‐helical polynucleotides by formaldehyde

We have formulated a mathematical model for the unwinding process of polynucleotides induced by formaldehyde by making use of the master equation approach. Our model assumes that the formaldehyde kinetics follows the helix–coil theory of Zimm and Bragg. The model incorporates experimental features such as the interplay between pH‐dependent and ‐independent reactions and the dependence of the initial and final helix stability on the unwinding. That is, our model incorporates the existence of the critical point such that if the pH of the system is high enough (i.e., pH ≳ 7), the unwinding of polynucleotides occurs by means of two separate chemical reactions, either by the HCHO–imino reaction alone or by the HCHO–amino reaction alone. The critical point depends on the ionic strength, temperature, and the formaldehyde concentration satisfying the relation s = 1 + K U λ, where s is the helix stability parameter, K U is the binding constant for the HCHO–imino reaction, and λ is the formaldehyde concentration. Thus above the critical point, i.e., s < (1 + K U λ), the unwinding is due to the reaction of imino groups with formaldehyde, and below the critical point, i.e., s > (1 + K U λ), the unwinding is due to the reaction of amino groups with formaldehyde. Although, below the critical point, the imino group does not participate directly in the rate‐determining step, it participates indirectly in such a manner that it reduces the initial helix stability parameter s to s /(1 + K U λ) by forming a complex. The kinetic constants in the master equation have been determined by making use of the principle of detailed balance and the breathing mechanism proposed in the past. With this model we have quantitatively explained the anomalous temperature dependence observed in the kinetics of formaldehyde‐induced poly[ d (A‐T)] and the salt dependence observed in poly(A·U).