DNase I – DNA interaction alters DNA and protein conformations

Abstract

Human DNase I is an endonuclease that catalyzes the hydrolysis of double-stranded DNA predominantly by a single-stranded nicking mechanism under physiological conditions in the presence of divalent Mg and Ca cations. It binds to the minor groove and the backbone phosphate group and has no contact with the major groove of the right-handed DNA duplex. The aim of this study was to examine the effects of DNase I – DNA complexation on DNA and protein conformations.We monitored the interaction of DNA with DNase I under physiological conditions in the absence of Mg2+, with a constant DNA concentration (12.5 mmol/L; phosphate) and various protein concentrations (10–250 µmol/L). We used Fourier transfrom infrared, UV-visible, and circular dichroism spectroscopic methods to determine the protein binding mode, binding constant, and effects of polynucleotide–enzyme interactions on both DNA and protein conformations. Structural analyses showed major DNase–PO2binding and minor groove interaction, with an overall binding constant, K, of 5.7 × 105± 0.78 × 105(mol/L)–1. We found that the DNase I – DNA interaction altered protein secondary structure, with a major reduction in α helix and an increase in β sheet and random structures, and that a partial B-to-A DNA conformational change occurred. No DNA digestion was observed upon protein–DNA complexation.