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

Abstract

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.

Importance of eDNA taphonomy and sediment provenance for robust ecological inference: Insights from interfacial geochemistry

“…The concentration of dissolved DNA that minerals can sequester varies widely with adsorption capacity of minerals, the concentration of mineral particles in a suspension (particle loading), and with depositional characteristics of the basin. Yet, the sequestration of dissolved DNA to minerals and the role of sediment mineralogy for DNA preservation have not been given much attention to date (Li et al., 2022; Paar et al., 2021; Staehr et al., 2022), or has the role of sediment mineralogy for DNA preservation (Jelavic et al., 2023; Kjær et al., 2022).…”

The potential of lacustrine sedimentary ancient DNA for revealing human postglacial recolonization patterns in northern Sweden – a review

“…Low‐charged smectites can intercalate DNA at neutral pH, which could protect the DNA from microbial and chemical attack and hence increase the chances of preservation over time (Jelavic et al . 2023). A study confirmed that DNA can be absorbed by calcite minerals and stay preserved (Sarhan et al .…”