Analysis of oligonucleotide DNA binding and sedimentation properties of montmorillonite clay using ultraviolet light...

Smectite clays such as montmorillonite form complexes with a variety of biomolecules, including the nucleic acids DNA and RNA. Most previous studies of DNA adsorption onto clay have relied on spectrophotometric analysis after the separation of free nucleic acids from bound complexes by centrifugation. In the current work, we demonstrate that such studies produce a consistent error because of (a) incomplete sedimentation of montmorillonite and (b) strong absorbance of the remaining clay at 260 nm. Clay sedimentation efficiency was strongly dependent on cation concentration (Na+ or Mg2+) and on the level of dispersion of the original suspension. An improved clay-DNA adsorption assay was developed and utilized to assess the impact of metal counterions on the binding of single-stranded DNA to montmorillonite. X-ray diffraction demonstrated, for the first time, the formation of intercalated structures consistent with orientation of the DNA strands parallel to the clay surface. Observed gallery spacings were found to match values calculated using atomistic modeling techniques closely.