Vortex- and Centrifugation-Free Extraction of HIV-1 RNA

Nucleic acid extraction from complex biofluid using toothpick-actuated over-the-counter medical-grade cotton

Nucleic acid amplification technique (NAAT)-assisted detection is the primary intervention for pathogen molecular diagnostics. However, NAATs such as quantitative real-time polymerase chain reaction (qPCR) require prior purification or extraction of target nucleic acid from the sample of interest since the latter often contains polymerase inhibitors. Similarly, genetic disease screening is also reliant on the successful extraction of pure patient genomic DNA from the clinical sample. However, such extraction techniques traditionally utilize spin-column techniques that in turn require centralized high-speed centrifuges. This hinders any potential deployment of qPCR- or PCR-like NAAT methods in resource-constrained settings. The development of instrument-free nucleic acid extraction methods, especially those utilizing readily available materials would be of great interest and benefit to NAAT-mediated molecular diagnosis workflows in resource-constrained settings. In this report, we screened medical-grade cotton, a readily available over-the-counter biomaterial to extract genomic DNA (gDNA) spiked in 30 %, 45 %, and 60 % serum or cell lysate. The extraction was carried out in a completely instrument-free manner using cotton and a sterilized toothpick and was completed in 30 min (with using chaotropic salt) or 10 min (without using chaotropic salt). The quality of the extracted DNA was then probed using PCR followed by agarose gel analysis for preliminary validation of the study. The qPCR experiments then quantitatively established the extraction efficiency (0.3-27 %, depending on serum composition). Besides, percent similarity score obtained from the Sanger sequencing experiments probed the feasibility of extracted DNA towards polymerase amplification with fluorescent nucleotide incorporation. Overall, our method demonstrated that DNA extraction could be performed utilizing toothpick-mounted cotton both with or without using a chaotropic salt, albeit with a difference in the quality of the extracted DNA.

Isolation of target DNA using synergistic magnetic bead transport and electrokinetic flow

The advent and dissemination of next-generation sequencing (NGS) technologies such as Illumina's sequencing platforms has brought forth vast reductions in the cost, time, and technical difficulties associated with DNA and RNA sequencing. Despite this trend, the workflow required to generate nucleic acid libraries for sequencing remains time-consuming and laborious. The following research proposes a method for simplifying and streamlining this process by replacing the manual washing steps of the common magnetic bead-based cleanup with a novel microfluidic method by integrating magnetic separation and electrokinetic purification (MSEP). Requiring no pumps, pipette mixing, vortexing, or centrifugation, MSEP relies on selective adsorption of target DNA onto the magnetic beads with subsequent transport of beads through a microchannel undergoing an antiparallel electroosmotic flow. The synergetic flow conditions were optimized using a simple electrohydrodynamic flow model. This work demonstrates that MSEP is as effective in eliminating adapter-dimers from the post-ligation library mix as the manual method while also greatly reducing the hands-on time and amount of pipetting required. Although MSEP has been applied specifically toward NGS library preparation at this time, it has the potential to be adapted and employed for any bead-based separation scheme, namely, solid phase extraction, sequence-specific hybridization, and immunoprecipitation on a microscale.

Synergistic use of electroosmotic flow and magnetic forces for nucleic acid extraction

Nucleic acid sample preparation is essential for biological sample-based diagnostics. It is crucial that diagnostic tests be both specific and sensitive as to provide the most accurate diagnosis possible. Inefficient sample preparation can hinder the specificity and sensitivity of these tests since carryover contaminants can inhibit downstream processes, such as amplification. Microfluidic devices have been used previously to extract nucleic acids from a biological sample due to lower reagent volumes and ease of use. A novel microfluidic chip has been designed for nucleic acid sample preparation which combines electroosmotic flow and magnetic bead-based extraction to isolate DNA from a plasma sample. A steady electric field was incorporated into the microfluidic chip design, which when combined with a glass clover slip and a voltage differential, creates electroosmotic flow. With the goal of isolating nucleic acids into a clean, inhibitor free solution, the electroosmotic flow is the driving force and separation mechanism purifying the DNA sample captured on magnetic beads in the microfluidic chip system. Carryover volume, or the volume of unwanted sample contaminants that accompany the nucleic acids into the final elution buffer, was minimized to 0.22 ± 0.03%. In combination with magnetic bead based nucleic acid extraction techniques, a 15% increase in DNA extraction yield is reported for the microfluidic chip with the voltage applied versus without. Although the literature on nucleic acid separation in microfluidic chips is abundant, this is the first to combine microfluidic chip design, magnetic bead-based isolation and electroosmotic flow.