Sugar based cationic magnetic core–shell silica nanoparticles for nucleic acid extraction

Nucleic acid (NA) extraction is an essential step in molecular testing for a wide range of applications. Conventional extraction protocols usually suffer from time consuming removal of non-nucleic acid impurities. In this study, a new magnetic nanoparticle (MNP) is presented to simplify the NA extraction. A core-shell design, comprising of a ferromagnetic core coated with mesoporous silica, forms the basis of the functional nanoparticle. Chemical functionalization of the silica coating includes a multistep synthesis, in which an activated nanoparticle is coupled with a triethylene glycol spaced glycosyl imidazole. The molecular design aims for charge interactions between the imidazolium-based positive nanoparticle surface and nucleic acids, with specific hydrogen bonding between the surface bonded carbohydrate and nucleic acid targets to ensure nucleic acid selectivity and avoid protein contamination. Two different carbohydrates, differing in molecular size, were selected to compare the efficiency in terms of NA extraction. A triethylene glycol spacer provides sufficient flexibility to remove particle surface constraints for the interaction. The Brunauer-Emmett-Teller (BET) analysis shows a significantly larger surface area for the disaccharide-based particles NpFeSiImMalt (∼181 m2 g-1) compared to the monosaccharide analogue NpFeSiImGlc (∼116 m2 g-1) at small particles sizes (range ∼ 15 nm) and sufficient magnetization (29 emu g-1) for easy isolation by an external magnetic field. The particles enabled a high DNA particle loading ratio of 30-45 wt% (MNP/DNA ratio), reflecting an efficient extraction process. A high desorption rate (7 min) with more than 86% of unchanged DNA loading was recorded, indicating low damage to the target extract.