Development of a Reference Material of a Single DNA Molecule for the Quality Control of PCR Testing

Developing Qualitative Plasmid DNA Reference Materials to Detect Mechanisms of Quinolone and Fluoroquinolone Resistance in Foodborne Pathogens

The aim of this study was to develop homogeneous and stable plasmid DNA reference materials for detecting the mechanisms of resistance to quinolones and fluoroquinolones in foodborne pathogens. The DNA fragments of 11 target genes associated with quinolone and fluoroquinolone resistance were artificially synthesized, inserted into plasmid vectors, and transferred into recipient cells. PCR and sequencing of DNA were performed to assess the genetic stability of the target DNA in recombinant Escherichia coli DH5α cells during subculturing for 15 generations. The limit of detection (LOD) of the target DNA was determined using PCR and real-time qualitative PCR (qPCR). The homogeneity and storage stability of plasmid DNA reference materials were evaluated in terms of plasmid DNA quantity, PCR-measured gene expression, and qPCR threshold cycle. All 11 target DNAs were successfully synthesized and inserted into vectors to obtain recombinant plasmids. No nucleotide mutations were identified in the target DNA being stably inherited and detectable in the corresponding plasmids during subculturing of recombinant strains. When the target DNA was assessed using PCR and qPCR, the LOD was ≤1.77 × 105 and 3.26 × 104 copies/μL, respectively. Further, when the reference materials were stored at 37 °C for 13 days, 4 °C for 90 days, and -20 °C for 300 days, each target DNA was detectable by PCR, and no mutations were found. Although the threshold cycle values of qPCR varied with storage time, they were above the LOD, and no significant differences were found in the quantity of each plasmid DNA at different timepoints. Further, the homogeneity and stability of the materials were highly consistent with the requirements of standard reference materials. To summarize, considering that our plasmid DNA reference materials conformed to standard requirements, they can be used to detect the mechanisms of quinolone and fluoroquinolone resistance in foodborne pathogens.

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

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.

Novel Bioprinting Application for the Production of Reference Material Containing a Defined Copy Number of Target DNA

Nucleic acid amplification methods, such as polymerase chain reaction (PCR), are extensively used in many applications to detect target DNA because of their high sensitivity, good reproducibility, and wide dynamic range of quantification. However, analytical quality control when detecting low copy number target DNA is often missing because of a lack of appropriate reference materials. Recent advances in analytical sciences require a method to accurately quantify DNA at the single molecule level. Herein, we have developed a novel method to produce reference material containing a defined copy number of target DNA (referred to as "cell number-based DNA reference material"). In this method, a suspension of cells carrying a single target DNA sequence was ejected by an inkjet head, and the number of cells in each droplet was counted using highly sensitive cameras. The resulting solutions contained a defined copy number of target DNA and could be used as reference materials. The use of the newly developed reference material was compared with that of diluted solutions of target DNA to evaluate the performance of qualitative real-time PCR in terms of the limit of detection (LOD). Our results demonstrated that cell number-based DNA reference material provides more accurate information regarding performance quality. The reference material produced by this method is a promising tool to evaluate assay performance.