In ion implantation in materials, when the ion energy is sufficiently low, the ion interaction with materials is in the nanoscale. When low-energy ion beam irradiates biological living materials such as cells and DNA, the nanoscaled ion interaction with the biological objects is a novelty. Theoretical calculation demonstrates the low-energy ion range in DNA being in the order of nanometer. In experiments, keV ions were applied to irradiate naked DNA to investigate primary effects of the low-energy ion interaction with DNA, which would be served as a basis for further investigations on mechanisms involved in ion beam induced mutation of biological species. Preliminary results showed that the nanoscale low-energy ion interaction with DNA could indeed induce changes in the DNA forms. DNA transfer in bacteria demonstrated mutation occurred after low-energy ion irradiation of the DNA. In computer molecular dynamics simulation, 1-100-eV ions bombarded A-DNA and revealed DNA changes occurring in nanoscale with preferential consequence. ©2010 IEEE.