Desorption and nuclease degradation of DNA on four different colloidal fractions from Brown soil and clay minerals were studied. The structures of native DNA, adsorbed and desorbed DNA were investigated by Fourier-Transform Infrared (FTIR), Circular Dichroism (CD) and fluorescence spectroscopy in order to determine the mechanisms on the resistance of bound DNA to enzymatic degradation in soils. Kaolinite exhibited the highest binding affinity for DNA among the examined colloidal particles. In comparison with organic clays, DNA was tightly adsorbed by inorganic clays. FTIR spectra showed that kaolinite and inorganic clays changed DNA conformation from B-form to Z-form, while montmorillonite and organic clays retained the original conformation of DNA. A structural change from B- to C-form in DNA molecules on kaolinite was observed by CD spectroscopy and further confirmed by fluorescence spectroscopy. Soil colloid or mineral-DNA complexes have stronger protection against nuclease degradation than free DNA. Tightly bound-DNA by kaolinite and inorganic clays was degraded to a greater extent than that loosely bound on montmorillonite and organic clays. According to these findings, we propose that the protection of soil colloids and minerals for DNA against nuclease degradation is not controlled by the binding affinity of DNA molecules for the colloids and the conformational change of adsorbed DNA. It seems that the higher stability of DNA is mainly attributed to the presence of organic matter in the system and the adsorption of nuclease on soil colloids and minerals. The information obtained in this study is of fundamental significance for the understanding of the behavior of extracellular DNA in soil environment.