Solvent effect on PCR from a viewpoint of a change of microscopic environment of Mg 2+ in a solution

Abstract

The effect of an organic solvent on PCR (polymerase chain reaction) was studied by measuring the molecular clustering of Mg 2+ and a nucleoside cytidine in an aqueous solution through a mass spectrometry. In the PCR, the addition of 5% methanol (CH 3OH) and dimethyl sulfoxide (DMSO) did not inhibit amplification of a human β-globin DNA fragment, while no amplification was observed in the presence of 5% acetonitrile (CH 3CN). The measurement of the clusters isolated from an aqueous solution including a nucleoside cytidine, Mg 2+, and an organic solvent (CH 3OH, DMSO, or CH 3CN) showed obvious differences in the structures of generated clusters; the self-aggregation of cytidine around Mg 2+ clearly occurred in water, water–methanol mixture and water–DMSO mixture, however, it was not effective in water–acetonitrile mixture. The solvation structure of Mg 2+ also showed dependent on the solvent composition, which suggested that the effective hydration of Mg 2+ seemed to promote cytidine clustering and a positive reaction in PCR. The microscopic structures in a solution depended on the coexisting organic solvent may provide a new insight to rationalize the role of the organic solvent on PCR.