Different conformations of double‐stranded nucleic acid in solution as revealed by circular dichroism

Abstract

Conformation of two‐stranded DNA in H 2 O–methanol, H 2 O–ethanol, H 2 O–isopropanol, and H 2 O–dioxane solutions at different concentrations of alkaline ions has been studied with the aid of circular dichroism. The following conclusions are drawn: The conformation of DNA in H 2 O and H 2 O–methanol belongs to a family of B forms (B, C, T forms are the representatives of the family). The magnitude of the winding angle between adjacent base pairs (θ) is determined by the concentration and type of the cations. In H 2 O the cation action is nonspecific and leads to an increase in θ value. In 80% methanol the ions act specifically, Cs+ being to stabilize a form with a greater θ value, and Li+ being with a lesser one. The total θ change is likely within the limits of 33° ⩽ θ ⩽ 45°. At high content of ethanol, isopropanol, or dioxane (∼80%), but not with methanol, and in low ionic strength the conformation of DNA belongs to a family of A forms (A form is one of the members of the family) and is specified by the concentration and type of cation involved. The two‐stranded regions of RNA in H 2 O are also of A type and winds with the rise of cation concentration. The range of θ variation is not narrower than 30° ⩽ θ 33°. The conformational transitions within the families (induced by ions) are of non‐cooperative pattern, wheras the transitions between the families (induced by nonpolar component) are of cooperative pattern. The effect of cations, when specific, is discussed on the basis of steric correspondence between the width of DNA narrow groove and the size of a hydrated cation.