Degradation of DNA into 5′-Monodeoxyribonucleotides in the Presence of Mn²⁺ Ions

Abstract

DNA is known to be aggregated by metal ions including Mn²⁺ ions, but analysis of the aggregation process from a chemical viewpoint, which means identification of the product yielded during the process, has not been performed yet. On examination of the kinds of degraded materials that were in the supernatant obtained on centrifugation of a DNA mixture aggregated under conditions of 10 mM Mn²⁺ ions ([Mn]/[P] = 46.3) at 70 °C for 1 h, the degradation products were found to be dAMP, dCMP, dGMP, and TMP. These dNMPs were purified by HPLC on TSKgel ODS-80Ts and identified by LC-TOF/MS. The degradation activity was lost on pretreatment of the DNA with a phenol–chloroform mixture, and the activity was recovered by pretreatment with a mixture of DMSO and a buffer containing surfactants. Mn²⁺, Co²⁺, Ni²⁺, Cu²⁺, Zn²⁺, and Cd²⁺, as transition element metal ions, were effective as to the degradation into dNMP. Mg²⁺, Ca²⁺, Sr²⁺, and Ba²⁺, as alkali earth element metal ions, were not effective as to the degradation. Monovalent anions such as Cl⁻, CH₃OO⁻, and NO₃⁻ were found to increase the degradation rate. Sixty μg of the 120 μg of the starting DNA in 450 μl was degraded into dNMP on reaction for 1 h in the presence of 100 mM NaCl and 10 mM Mn²⁺ ions. In this process, aggregation did not occur, and thus was not considered to be necessary for degradation. The degradation was found not to occur at pH 7.0, and to be very sensitive to pH. The OH⁻ ion should have a critical role in cleavage of the phosphodiester linkages in this case. The dNMP obtained in the degradation process was found to be only 5′-NMP, based on the H¹NMR spectra. This prosess should prove to be a new process for the production of 5′-dNMP in addtion to the exonuclease.