Nucleic acid capture assay, a new method for direct quantitation of nucleic acids

Evaluation of indirect sequence-specific magneto-extraction-aided LAMP for fluorescence and electrochemical SARS-CoV-2 nucleic acid detection

Nucleic acid amplification tests (NAATs) such as quantitative real-time reverse transcriptase PCR (qRT-PCR) or isothermal NAATs (iNAATs) such as loop-mediated isothermal amplification (LAMP) require pure nucleic acid free of any polymerase inhibitors as its substrate. This in turn, warrants the use of spin-column mediated extraction with centralized high-speed centrifuges. Additionally, the utilization of centralized real-time fluorescence readout and TaqMan-like molecular probes in qRT-PCR and real-time LAMP add cost and restrict their deployment. To circumvent these disadvantages, we report a novel sample-to-answer workflow comprising an indirect sequence-specific magneto-extraction (also referred to as magnetocapture, magneto-preconcentration, or magneto-enrichment) for detecting SARS-CoV-2 nucleic acid. It was followed by in situ fluorescence or electrochemical LAMP. After in silico validation of the approach's sequence selectivity against SARS-CoV-2 variants of concern, the comparative performance of indirect and direct magnetocapture in detecting SARS-CoV-2 nucleic acid in the presence of excess host nucleic acid or serum was probed. After proven superior, the sensitivity of the indirect sequence-specific magnetocapture in conjunction with electrochemical LAMP was investigated. In each case, its sensitivity was assessed through the detection of clinically relevant 10² and 10³ copies of target nucleic acid. Overall, a highly specific nucleic acid detection method was established that can be accommodated for either centralized real-time SYBR-based fluorescence LAMP or portable electrochemical LAMP.

A batch processed titanium-vanadium oxide nanocomposite based solid-state electrochemical sensor for zeptomolar nucleic acid detection

Approaching a nucleic acid amplification test (NAAT) based diagnosis of a pathogen from an electrochemistry pathway is a relatively economical, decentralized, and yet highly sensitive route. This work aimed to construct an electrochemical biosensor with a 2-electrode geometry using a transition metal oxide (TMO) based sensing layer. A series of batch-processed TiO₂-V₂O₅ (TVO) nanocomposite-based electrodes were fabricated to probe their electrochemical performance and attain a highly sensitive dual-electrode electrochemical sensor (DEES) compared to pristine V₂O₅. The XRD analysis of the electrodes confirmed the formation of a nanocomposite, while the XPS analysis correlated the formation of oxygen vacancies with improved electrical conduction measured via EIS and I-V characterization. Furthermore, the work demonstrated the application of the optimized electrode in electrochemical detection of end-point loop-mediated isothermal amplification (LAMP) readout for 10¹-10⁴ copies (0.1 zeptomoles to 0.1 attomoles) of SARS-CoV-2 RNA dependent RNA polymerase (RdRp) plasmid DNA and in vitro transcribed RNA in an aqueous solution. The device achieved a limit of detection as low as 2.5 and 0.25 copies per μL for plasmid DNA and in vitro transcribed RNA, respectively. The DEES was able to successfully detect in situ LAMP performed on magneto-extracted SARS-CoV-2 plasmid and RNA from (a) an aqueous solution, (b) a sample spiked with excess human genomic DNA, and (c) a serum-spiked sample. The DEES results were then compared with those of real-time fluorescence and commercially available screen-printed electrodes (SPEs).

A clone screening method using mRNA levels to determine specific productivity and product quality for monoclonal antibodies

To meet increasing demands for efficient and streamlined production processes of therapeutic antibodies, improved methods of screening clones are required. In this article, we examined the potential of using antibody transcript levels as criteria for clone screening. We evaluated the QuantiGene Plex, a commercially available, high-throughput assay for simultaneously measuring multiple transcripts from cell lysate. Using the development of stable Chinese hamster ovary cell lines as examples, we investigated the relationship between transcript and antibody levels through several rounds of screening. First, we observed that measured heavy chain transcript levels are generally correlated with specific productivity, enabling the identification of high-producing clones from mRNA. Second, we observed that low ratios (< 1.5) of light to heavy chain transcript levels may be indicative of high antibody aggregation levels, allowing for the rapid identification and elimination of clones of questionable product quality. Therefore, an efficient process of identifying high-producing clones of desirable product quality is possible by using QuantiGene Plex assay to measure antibody transcript levels.

Metal-Enhanced Fluorescence-Based RNA Sensing

In this communication, we present the proof-of-principle of a new RNA sensing technique, based on metal-enhanced fluorescence, which may improve the potential of solid substrate-based RNA capture assays. In this regard, the detection of RNA is accomplished by annealing a target RNA tagged with a fluorophore to a DNA anchor probe in a single step on a solid surface, where the fluorescence signal is enhanced by silver nanoparticles. Furthermore, the proposed method is highly amenable to high-throughput screening applications and is capable of detecting less than 25 fmol of RNA at a signal-to-noise ratio greater than 20, in several hours compared to that of reverse transcription-PCR at >24 h.

Correlation of Heavy and Light Chain mRNA Copy Numbers to Antibody Productivity in Mouse Myeloma Production Cell Lines

Manufacturing cell line development at Centocor involves transfection of antibody genes into host cell lines and isolating primary transfectomas that upon subcloning yield high expressing cell lines for the desired antibody. In an attempt to increase productivity of these cell lines, we set out to identify the rate-limiting step in the process of antibody expression and secretion. For this purpose, 30 antibody expressing cell lines with variable antibody expression levels were analyzed for heavy-chain and light-chain mRNA expression levels. Results suggested that the increase in antibody titer of the subclones (compared to their primary clones) was partly due to an increase in heavy-chain and light-chain mRNA levels; higher expressers were associated with approximately 1.0 x 10(7) and 1.5 x 10(7) copies of heavy-chain and light-chain per 10 nanogram of cDNA, respectively. Generally, the level of light-chain mRNA was higher compared to the level of heavy-chain mRNA in a majority of the cell lines, and the difference in their levels was not due to their differential stability. The data generated from all the cell lines tested in this study suggested that there was a correlation of light-chain and heavy-chain transcript levels to antibody productivity, with the coefficient of correlation being 0.59 for light chain and 0.81 for heavy chain. We conclude that transcription of heavy chain and to a lesser extent light chain could be one of the rate-limiting steps in the antibody expression pathway. Hence, methods that would increase these mRNA levels could be beneficial in the attempt to improve the antibody expression level of production cell lines.