A route for long-term DNA preservation through nanoconfinement in smectites

Traces of DNA found in sediments are shifting paradigms in the analysis of past and present ecosystems. DNA is an unstable polymer and conditions at which the millennial stabilization is achieved are unclear. Confinement of DNA in nanopores of clay minerals is a promising route for this long-term stabilization and storage. Using smectites with various layer charges, we measured adsorption capacity for DNA using UV spectroscopy and intercalation capacity using X-ray diffraction. We found that while the smectite adsorption capacity is large, the DNA intercalation, i.e. nanoconfinement, decreases as smectite charge increases. We show that low-charge smectites intercalate DNA at concentrations relevant to aqueous environments even at neutral pH but the nanoconfinement is minimal or absent in high-charge smectites. Different intercalation behaviour in NaCl and CaCl2 solutions imply different mechanisms driven by electrostatic forces. Our results demonstrate that DNA nanoconfinement in smectites is likely an important strategy for DNA preservation and that protocols targeting low-charge smectites might improve the success of ancient and modern DNA extraction even in hot and humid climates so far deemed unfavourable for DNA preservation.