Protonation scheme in acid-induced DNA strand separation

Abstract

The natural DNA double helix undergoes strand separation at low pH. Protonation of the bases is thought to have a weakening effect on the hydrogen bonds between the guanine-cytosine (G-C) and adenine- thymine (A-T) base pairs of the two strands. Some biochemists believe that the first protonation occurs at the amino- nitrogen substituted on the purine and pyrimidine rings. This belief may originate from the fact that several textbooks and authoritative monographs, old and new, attribute pKa values of 24.5 to the amino groups of guanine, cytosine and adenine bases, and their nucleosides and nuc- leotides, and some show explicit illustra- tions of singly protonated bases having the positive charge on the exocyclic nitrogens (Fig. la). Another factor may be that some people consider the amino groups (usually quite basic) substituted on the purine and pyrimidine rings should have pKa values in the same range as that of the amino of aniline which is 4.6. This intuitive estima- tion is not correct. What follows below should show that at pH around 2 to 3.5, where acid-induced DNA denaturation is