The compaction of gene-size T4 DNA induced by the action of silica nanoparticles (10-100 nm diameter), the surfaces of which were modified to various degrees by a 3-aminopropylsilyl groups, was monitored by a fluorescent microscope in an aqueous solution. It was found that DNA compaction was facilitated by mono- and divalent cations such as Na(+), K(+), Mg(2+), and Ca(2+). This promotion by cations was the result of charge-neutralization of DNA and was more remarkable in compaction by histone-size nanoparticles (10 nm) than in that by larger ones (> 15 nm). Divalent metal ions were more effective at promoting compaction due to their greater charge-neutralizing character, but a quaternary diammonium derivative of 1,3-propanediamine deactivated DNA compaction by 10-nm nanoparticles. Although metal ions binding to DNA can reduce electrostatic tension on DNA and provide flexibility to create a DNA loop with a small diameter, such ammonium dication does not make DNA sufficiently flexible.