The formation of metal-containing Ag-mercaptoethanol (-Ag-S(R)-)(n) complexes on DNA chain scaffold was studied by UV spectroscopy, zeta potential measurement, and fluorescence and transmission electron microscopies. Experimental results made clear the mechanism of DNA mineralization and compaction, according to which intercalation of silver cations into DNA scaffold and further formation of (-Ag-S(R)-)(n) oligomeric complexes on DNA induce efficient DNA chain compaction by terminal Ag+ cations. By transmission electron microscopy the formation of fiber-like DNA-templated nanostructures was observed. DNA-Ag-thiol complexes are promising for DNA-templated engineering of hybrid ID nanostructures with adjustable chemical functionalities by choosing appropriate thiol ligand.