Stereochemistry of nucleic acids and their constituents: XIX. Copper binding sites and mechanism of G·C selective denaturation of DNA. Crystal and molecular structures of guanine·copper(II) chloride and cytosine·copper(II) chloride complexes

Abstract

The crystal and molecular structures of the copper(II) chloride complexes of guanine (C 5H 6N 5O·CuCl 3·H 2O) and cytosine (C 4N 3H 5O·CuCl 2) have been determined by the heavy-atom technique and refined by the method of least-squares to R values of 0.052 and 0.078, respectively, using three-dimensional diffractometric data and copper K α radiation. Crystals of guanine copper(II) chloride are monoclinic space group C2/c, with unit cell constants a = 16.952 A ̊ , b = 10.183 A ̊ , c = 13.185 A ̊ , β = 99.97 °. The calculated and observed densities are 2.015 and 2.024 g cm −3, respectively. Crystals of cytosine copper(II) chloride are monoclinic space group P2 1/ c with unit cell constants a = 8.349 A ̊ , b = 13.744 A ̊ , c = 13.660 A ̊ , β = 128.0 °. Calculated and observed densities are, respectively, 1.90 and 1.96 g cm −3. The preferred copper binding sites were found to be N(3) and O(2) (weak) for cytosine and N(9) for guanine. It is significant that the copper binding to cytosine involves two of the three sites which are normally involved in hydrogen bonding to guanine in the Watson-Crick base pairing scheme. The known preference of copper(II) for binding to G·C pairs rather than A · T pairs is shown to be related to the observed copper(II) binding scheme. From other physico-chemical evidence implicating copper binding to N(7) of guanine, probable complexes of copper and cytosine and/or guanine are suggested which can affect denaturation of DNA.