Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation

Abstract

Significance Iodine-induced cleavage is widely used for detecting bacterial DNA phosphorothioation in gel electrophoresis, deep sequencing, and single-molecule optical mapping. However, we lack quantitative understanding of the phosphorothioate DNA (PT-DNA) cleavage efficiency and the chemoselectivity of this method for determination of phosphorothioate vs. phosphate. Computational explorations now reveal why iodine selectively attacks at sulfur in phosphorothioate links but not at normal phosphates. The active role of Tris buffer in the PT-DNA cleavage, and the factors controlling cleavage efficiency, were also revealed. Cleavage efficiency is limited by competition between the desired DNA backbone cleavage and unwanted P-S/P-O conversion. These mechanistic studies will guide the development of new methods for iodine-induced specific PT-DNA cleavage.