A high-throughput pipeline for DNA/RNA/small RNA purification from tissue samples for sequencing

High-throughput total nucleic acid (TNA) purification methods based on solid-phase reversible immobilization (SPRI) beads produce TNA suitable for both genomic and transcriptomic applications. Even so, small RNA species, including miRNA, bind weakly to SPRI beads under standard TNA purification conditions, necessitating a separate workflow using column-based methods that are difficult to automate. Here, an SPRI-based high-throughput TNA purification protocol that recovers DNA, RNA and small RNA, called GSC-modified RLT+ Aline bead-based protocol (GRAB-ALL), which incorporates modifications to enhance small RNA recovery is presented. GRAB-ALL was benchmarked against existing nucleic acid purification workflows and GRAB-ALL efficiently purifies TNA, including small RNA, for next-generation sequencing applications in a plate-based format suitable for automated high-throughput sample preparation.

On-Chip Nucleic Acid Purification Followed by ddPCR for SARS-CoV-2 Detection

We developed a microfluidic chip integrated with nucleic acid purification and droplet-based digital polymerase chain reaction (ddPCR) modules to realize a 'sample-in, result-out' infectious virus diagnosis. The whole process involved pulling magnetic beads through drops in an oil-enclosed environment. The purified nucleic acids were dispensed into microdroplets by a concentric-ring, oil-water-mixing, flow-focusing droplets generator driven under negative pressure conditions. Microdroplets were generated with good uniformity (CV = 5.8%), adjustable diameters (50-200 μm), and controllable flow rates (0-0.3 μL/s). Further verification was provided by quantitative detection of plasmids. We observed a linear correlation of R² = 0.9998 in the concentration range from 10 to 10⁵ copies/μL. Finally, this chip was applied to quantify the nucleic acid concentrations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The measured nucleic acid recovery rate of 75 ± 8.8% and detection limit of 10 copies/μL proved its on-chip purification and accurate detection abilities. This chip can potentially be a valuable tool in point-of-care testing.

The Development of a 3D Printer-Inspired, Microgravity-Compatible Sample Preparation Device for Future Use Inside the International Space Station

Biological testing on the International Space Station (ISS) is necessary in order to monitor the microbial burden and identify risks to crew health. With support from a NASA Phase I Small Business Innovative Research contract, we have developed a compact prototype of a microgravity-compatible, automated versatile sample preparation platform (VSPP). The VSPP was built by modifying entry-level 3D printers that cost USD 200-USD 800. In addition, 3D printing was also used to prototype microgravity-compatible reagent wells and cartridges. The VSPP's primary function would enable NASA to rapidly identify microorganisms that could affect crew safety. It has the potential to process samples from various sample matrices (swab, potable water, blood, urine, etc.), thus yielding high-quality nucleic acids for downstream molecular detection and identification in a closed-cartridge system. When fully developed and validated in microgravity environments, this highly automated system will allow labor-intensive and time-consuming processes to be carried out via a turnkey, closed system using prefilled cartridges and magnetic particle-based chemistries. This manuscript demonstrates that the VSPP can extract high-quality nucleic acids from urine (Zika viral RNA) and whole blood (human RNase P gene) in a ground-level laboratory setting using nucleic acid-binding magnetic particles. The viral RNA detection data showed that the VSPP can process contrived urine samples at clinically relevant levels (as low as 50 PFU/extraction). The extraction of human DNA from eight replicate samples showed that the DNA extraction yield is highly consistent (there was a standard deviation of 0.4 threshold cycle when the extracted and purified DNA was tested via real-time polymerase chain reaction). Additionally, the VSPP underwent 2.1 s drop tower microgravity tests to determine if its components are compatible for use in microgravity. Our findings will aid future research in adapting extraction well geometry for 1 g and low g working environments operated by the VSPP. Future microgravity testing of the VSPP in the parabolic flights and in the ISS is planned.

A Robust, Safe, and Scalable Magnetic Nanoparticle Workflow for RNA Extraction of Pathogens from Clinical and Wastewater Samples

Molecular diagnosis and surveillance of pathogens such as SARS-CoV-2 depend on nucleic acid isolation. Pandemics at the scale of COVID-19 can cause a global shortage of proprietary commercial reagents and BSL-2 laboratories to safely perform testing. Therefore, alternative solutions are urgently needed to address these challenges. An open-source method, magnetic-nanoparticle-aided viral RNA isolation from contagious samples (MAVRICS), built upon readily available reagents, and easily assembled in any basically equipped laboratory, is thus developed. The performance of MAVRICS is evaluated using validated pathogen detection assays and real-world and contrived samples. Unlike conventional methods, MAVRICS works directly in samples inactivated in phenol-chloroform (e.g., TRIzol), thus allowing infectious samples to be handled safely without biocontainment facilities. MAVRICS allows wastewater biomass immobilized on membranes to be directly inactivated and lysed in TRIzol followed by RNA extraction by magnetic nanoparticles, thereby greatly reducing biohazard risk and simplifying processing procedures. Using 39 COVID-19 patient samples and two wastewater samples, it is shown that MAVRICS rivals commercial kits in detection of SARS-CoV-2, influenza viruses, and respiratory syncytial virus. Therefore, MAVRICS is safe, fast, and scalable. It is field-deployable with minimal equipment requirements and could become an enabling technology for widespread testing and wastewater monitoring of diverse pathogens.

Purification of genomic DNA with minimal contamination of proteins

The purification is based on a set of solutions and a simple centrifugation procedure. Protocols are designed for an easy extraction and purification of genomic DNA from a wide range of samples, including whole blood, buffy coat, bone marrow, body fluids, buccal cells, tissues, mouse tails, etc. RBCs are lysed by dilution into a hypotonic solution. Tissues are broken down and digested by proteinase K in the presence of an anion detergent to release genomic DNA. After precipitation of the detergent and proteins, unique beads that bind proteins, lipids, and RNAs are added to achieve the supreme purity. Genomic DNA is then separated by alcohol precipitation. A proprietary nucleic acid precipitation reagent is used to enhance DNA recovery from low concentration samples. No DNA-binding beads or columns are used in the method, eliminating the problem of low yield and the risk of shearing of genomic DNA. The purified samples are free of proteins, lipids, salts, and RNA contamination. Purified samples are also stable for storage and suitable for all downstream applications.