Conformational characteristics of deoxyribonucleic acid-butylamine complexes with C-type circular dichroism spectra. 1. An X-ray fiber diffraction study.
A set of complexes of calf thymus DNA and n-butylamine, covalently cross-linked to the DNA bases with CH2O, has been examined by X-ray diffraction. The attachment of this amine to DNA has been previously shown to result in a profound reduction of the rotational strength of the positive band above 260 nm in the circular dichroism (CD) spectrum in 20 mM NaCl, pH 7, without changing any of the properties which are characteristic of a native base-stacked duplex [Chen, C., Kilkuskie, R., & Hanlon, S. (1981) Biochemistry 20, 4987]. In 20 mM NaCl, pH 7, substitution levels of 0-0.15 mol of amine/mol of nucleotide are sufficient to produce a family of CD spectra which range from the conservative one normally seen for protein-free DNA in this solvent to the nonconservative one ascribed to the C form of DNA [Hanlon, S., Brudno, S., Wu, T. T., & Wolf, B. (1975) Biochemistry 14, 1648-1660]. Fibers of the DNA X amine complexes at 79% relative humidity (rh) and 33% rh do indeed show C-type X-ray patterns whereas the controls exhibit A forms under the same conditions. The same preparations, however, exhibit only B patterns when the fibers are examined at 98% rh and in the wet fiber form. Although we cannot rule out the possibility that molecular interactions in the fiber have imposed conformational restraints on the DNA structure that are not present in solution, these present results suggest that the conformation of DNA giving rise to the "C" CD spectrum is a variant of the B form.