Effects of high-energy ion irradiation on DNA have been investigated for quite a long time. However, the important low-energy irradiation process and its effect on DNA, relevant both in natural phenomena and in experimental work, is much less known. We have carried out research on eV-keV ion irradiation of DNA, both experimentally and through computer simulations, to investigate low-energy irradiation effects on DNA including potential induction of mutations. In the experiments, charged and neutralized ions were used to irradiate naked DNA followed by biological DNA analysis and its transfer into bacterial cells. Results showed that the low-energy ion irradiations may cause DNA conformation changes and induce mutations of the bacteria. The ion charge played an important role in the effects. The molecular dynamics simulations of eV-100eV carbon and nitrogen ion irradiations of A-DNA revealed that the low-energy ion-induced damage preferentially but not randomly affects point sites, bonds, backbones and bases.