Size-controlled mesoporous magnetic silica beads effectively extract extracellular DNA in the absence of chaotropic solutions

Abstract

Due to lack of universally effective extraction methods, the importance of extracellular DNA (exDNA) in natural environments to DNA studies has been largely overlooked in favor of intracellular DNA. In this study, a novel method using size-controlled mesoporous silica magnetic nanoparticles (MSCMNPs) was proposed to extract extracellular DNA from various environments. MSCMNPs have an ordered mesopores structure with homogenous pore size at around 3.0 nm. This structure contributes to superior DNA adsorption of MSCMNPs in the absence of chaotropic solutions in terms of capacity (833.3 mg/g), velocity (0.028/s), and lengths of exDNA that can be extracted, including highly fragmented exDNA (less than 100 bp). This high affinity for DNA also allowed MSCMNPs to resist interference by competitive compounds. Furthermore, exDNA adsorbed onto MSCMNPs could be effectively eluted in Tris-EDTA buffer at 60 ℃ for 5 min. Thus, MSCMNPs are promising for extracting exDNA from various environmental samples including wastewater effluent, activated sludge, freshwater river, and soil samples, with the recovery efficiencies between 83.4% and 95.8%. This study is of importance to advance exDNA research in various environments lacking effective exDNA extraction methods.