Magnetic Nanoparticles to Unique DNA Tracers: Effect of Functionalization on Physico-chemical Properties

Abstract

To monitor and manage hydrological systems such as brooks, streams, rivers, the use of tracers is a well-established process. Limited number of potential tracers such as salts, isotopes and dyes, make study of hydrological processes a challenge. Traditional tracers find limited use due to lack of multiplexed, multipoint tracing and background noise, among others. In this regard, DNA based tracers possess remarkable advantages including, environmentally friendly, stability, and high sensitivity in addition to showing great potential in the synthesis of ideally unlimited number of unique tracers capable of multipoint tracing. To prevent unintentional losses in the environment during application and easy recovery for analysis, we hereby report DNA encapsulation in silica containing magnetic cores (iron oxide) of two different shapes—spheres and cubes. The iron oxide nanoparticles having size range 10–20 nm, have been synthesized using co-precipitation of iron salts or thermal decomposition of iron oleate precursor in the presence of oleic acid or sodium oleate. Physico-chemical properties such as size, zeta potential, magnetism etc. of the iron oxide nanoparticles have been optimized using different ligands for effective binding of dsDNA, followed by silanization. We report for the first time the effect of surface coating on the magnetic properties of the iron oxide nanoparticles at each stage of functionalization, culminating in silica shells. Efficiency of encapsulation of three different dsDNA molecules has been studied using quantitative polymerase chain reaction (qPCR). Our results show that our DNA based magnetic tracers are excellent candidates for hydrological monitoring with easy recoverability and high signal amplification. Graphic Abstract

Settling of superparamagnetic silica encapsulated DNA microparticles in river water

“…The synthesis of SiDNAFe MPs was described in Sharma et al (2021). Briefly, synthetic double‐stranded DNA (dsDNA) was firstly bound with positively charged iron oxide nanoparticles (IONPs), thereafter, these DNA‐tagged IONPs were encapsulated within a silica shell.…”

“…Compared with traditional solute/particulate tracers, such as fluorescent dyes/microspheres, DNA‐tagged tracers enable true multi‐tracing with their engineered identical surface properties but unique synthetic DNA signatures, allowing a theoretically unlimited number of distinguishable tracer varieties without environmental interference. Later, superparamagnetic DNA‐tagged silica microparticles (SiDNAFe MPs) were designed with a magnetite core in order to facilitate easy harvesting and up‐concentration from larger volumes of sample water (Puddu et al, 2014; Sharma et al, 2021).…”

Fine-Tuning of Particle Size and Morphology of Silica Coated Iron Oxide Nanoparticles

“…The synthesis process has been adapted from our previously reported study . IONPs were synthesized via chemical coprecipitation.…”

“…The synthesis process has been adapted from our previously reported study. 21 IONPs were synthesized via chemical coprecipitation. Briefly, 84.6 mg of MQ water was weighed in a beaker, and 15.4 mL of 25% (wt) NH 4 OH solution was added to it to prepare a 1 M solution.…”

Effect of channel bed sediment on the transport behaviour of superparamagnetic silica encapsulated DNA microparticles in open channel injection experiments

“…Therefore, engineered nano‐ or micro‐particles with DNA barcodes could serve as an alternative for particle contaminant environmental tracing, where synthetic ds/ss DNA strands are well protected from DNA degradation due to environmental stressors. To date, hydrologists have explored several engineered particle variants with DNA tags, in which DNA was encapsulated or associated with desired materials, for example, clay particles (Mahler et al, 1998), silica (Paunescu et al, 2013), iron oxides (Puddu et al, 2014; A. Sharma et al, 2021), and organic material (Garnett et al, 2009; McNew et al, 2018; Pang et al, 2020; A. N. Sharma et al, 2012). Such DNA‐tagged micro‐composites have been proven to be detectable and could survive significantly longer than ‘naked’ DNA strands for tracing small‐scale surface and subsurface geographic settings (Bovolin et al, 2014; Dahlke et al, 2015; Foppen et al, 2013; McCluskey et al, 2021; Mikutis et al, 2018; Pang et al, 2020, 2022; Sabir et al, 1999).…”