Isolation of DNA-free RNA from human bone marrow mononuclear cells: comparison of laboratory methods

Development and validation of a rapid five-minute nucleic acid extraction method for respiratory viruses

BACKGROUND

The rapid transmission and high pathogenicity of respiratory viruses significantly impact the health of both children and adults. Extracting and detecting their nucleic acid is crucial for disease prevention and treatment strategies. However, current extraction methods are laborious and time-consuming and show significant variations in nucleic acid content and purity among different kits, affecting detection sensitivity and efficiency. Our aim is to develop a novel method that reduces extraction time, simplifies operational steps, and ensures high-quality acquisition of respiratory viral nucleic acid.

METHODS

We extracted respiratory syncytial virus (RSV) nucleic acid using reagents with different components and analyzed cycle threshold (Ct) values via quantitative real-time polymerase chain reaction (qRT-PCR) to optimize and validate the novel lysis and washing solution. The performance of this method was compared against magnetic bead, spin column, and precipitation methods for extracting nucleic acid from various respiratory viruses. The clinical utility of this method was confirmed by comparing it to the standard magnetic bead method for extracting clinical specimens of influenza A virus (IAV).

RESULTS

The solution, composed of equal parts glycerin and ethanol (50% each), offers an innovative washing approach that achieved comparable efficacy to conventional methods in a single abbreviated cycle. When combined with our A Plus lysis solution, our novel five-minute nucleic acid extraction (FME) method for respiratory viruses yielded superior RNA concentrations and purity compared to traditional methods. FME, when used with a universal automatic nucleic acid extractor, demonstrated similar efficiency as various conventional methods in analyzing diverse concentrations of respiratory viruses. In detecting respiratory specimens from 525 patients suspected of IAV infection, the FME method showed an equivalent detection rate to the standard magnetic bead method, with a total coincidence rate of 95.43% and a kappa statistic of 0.901 (P < 0.001).

CONCLUSIONS

The FME developed in this study enables the rapid and efficient extraction of nucleic acid from respiratory samples, laying a crucial foundation for the implementation of expedited molecular diagnosis.

Sequential extraction of RNA, DNA and protein from cultured cells of the same group

BACKGROUND

Efficient extraction of nucleic acids and proteins (ENAP) from cells is a prerequisite for precise annotation of gene function, and has become laboratory routine for revealing the mysteries of life. However, cell samples are often from different culture dishes, resulting in inevitable experimental errors and sometimes poor repeatability.

AIM

To explore a method to improve the efficiency of ENAP, minimizing errors in ENAP processes, enhancing the reliability and repeatability of subsequent experimental results.

METHODS

A protocol for the sequential isolation of RNA, DNA, and proteins from the same cultured HepG2 cells using RNAzol reagent is presented here. The first step involves culturing HepG2 cells to the exponential phase, followed by the sequential isolation of RNA, DNA, and proteins from the same cultured cells in the second step. The yield of nucleic acids and proteins is detected in the third step, and their purity and integrity are verified in the last step.

RESULTS

The procedure takes as few as 3-4 d from the start to quality verification and is highly efficient. In contrast to the existing kits and reagents, which are primarily based on independent isolation, this RNAzol reagent-based method is characterized by the sequential isolation of RNA, DNA, and proteins from the same cells, and therefore saves time, and has low cost and high efficiency.

CONCLUSION

The RNA, DNA, and proteins isolated using this method can be used for reverse transcription-polymerase chain reaction, polymerase chain reaction, and western blotting, respectively.

Application of Nucleic Acid-Based Strategies to Detect Infectious Pathogens in Orthopaedic Implant-Related Infection

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Implant-associated infection in orthopaedic surgery remains an enormous and largely unsolved clinical problem with a high rate of persistent or recurrent infection. This may be due, at least in part, to the potential for underdiagnosis by traditional microbial culture or the potential for culture to incompletely identify the microbial species present.

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Nucleic acid-based diagnostic techniques, focused on using the diagnostic information contained in DNA or RNA to identify microbial species, have been developing rapidly and have garnered escalating interest for both clinical and research applications.

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Commonly applied techniques include end-point polymerase chain reaction (PCR), quantitative PCR, Sanger sequencing, and next-generation sequencing. Understanding the specific strengths and weaknesses of each technique is critical to understanding their utility, applying the correct assessment strategy, and critically understanding and interpreting research.

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The best practices for interpreting nucleic acid-based diagnostic techniques include considering positive and negative controls, reads per sample, detection thresholds (for differentiating contaminants from positive results), and the primer set or targeted regions.

Yielding quality viral RNA by using two different chemistries: a comparative performance study

Purity and integrity are two important criteria for any RNA extraction process to qualify the RNA for meaningful gene expression analysis. This study compares four commercially available RNA extraction kits using silica membrane and magnetic bead separation methods. The performance was evaluated in terms of both quantity (total RNA amount in μg/μl) and purity (260/280 ratio). The concentration and purity of each kit was significantly different from those of the others (p < 0.001). Although quantity obtained from Mag MAX is comparatively lower than QIAGEN, the quality is comparable as evident from real-time PCR performance. This study suggests that there are practical differences between these RNA extraction kits that should be taken into account while isolating RNA required for gene expression analysis.

Methods for simultaneous and quantitative isolation of mitochondrial DNA, nuclear DNA and RNA from mammalian cells

The aim of this study was to assess two protocols for their capacities to simultaneously isolate RNA, mtDNA and ncDNA from mammalian cells. We compared the Invitrogen TRIzol-based method and Qiagen DNeasy columns, using the HepG2 cell line and human primary glioblastoma stem cells. Both methods allowed the isolation of all three types of nucleic acids and provided similar yields in mtDNA. However, the yield in ncDNA was more than tenfold higher on columns, as observed for both cell types. Conversely, the TRIzol method proved more reproducible and was the method of choice for isolating RNA from glioblastoma cells, as demonstrated for the housekeeping genes RPLP0 and RPS9.