SPINeasy® DNA/RNA Kit for Soil

Humic acids, heavy metals, and other aromatic components are among the most notorious PCR inhibitors found in the soil, leading to false negative or underestimated results. Non‑optimized nucleic acid extraction protocol often co‑purify inhibitors. The SPINeasy^® DNA/RNA Kit for Soil integrates our proprietary inhibitor removal expertise and our new technology for selective binding of DNA and RNA. The SPINeasy^® DNA/RNA Kit for Soil allows simultaneous isolation of pure microbiome genomic DNA and RNA from challenging soil types, including those with low biomass or those that are highly contaminated. The isolated nucleic acid products showed no contaminants and were immediately ready for use in downstream applications, including qPCR and RT-qPCR without the need of further inhibitor removal step.

Performance

Nucleic acid was extracted from challenging soil samples: High biomass, High contaminant, and Low biomass. The SPINeasy^® DNA/RNA Kit for Soil kit consistently delivered a higher amount of DNA and RNA than the commercially available competitor Z.

 

Figure 1. The SPINeasy^® DNA/RNA Kit for Soil gives higher yield of nucleic acid than that of Competitor Z. Three types of soil samples (250 mg each) were used for DNA/RNA extraction. Yields were measured by fluorometric quantification. Each dot on the plot represents a single extraction.

The extracted DNA and RNA were subsequently analyzed using an Agilent Tapestation 4150 to examine their integrity and yield. The DNA integrity (DIN) and RNA integrity (RIN) values were equivalent for samples extracted from both kits; nonetheless, the nucleic acid yield was higher when extracted with the SPINeasy^® DNA/RNA Kit for Soil, as indicated by the more intense bands on the virtual gels. The difference was especially more significant for the challenging low biomass sample (Figure 2, bottom panel).

 

 The SPINeasy^® DNA/RNA Kit for Soil is designed to tackle challenging samples with large amount of contaminant. When DNA/RNA samples obtained from high biomass / contaminant soils were examined using UV spectrophotometer, only the samples extracted with SPINeasy^® DNA/RNA kit for Soil showed optimal A260/A280 ratios (~1.8 for DNA, ~2.0 for RNA), as well as the highest A260/A230 ratios (Figure 3, top panel). Unlike the RNA extracted using SPINeasy^® DNA/RNA Kit for Soil, the RNA samples obtained using the competitor Z displayed a brownish coloration for all soil types, this is in line with the quantification result of the humic acid level using a spectrophotometer @ 400 nm (Figure 3, medium panel). The phenomenon was especially significant for the challenging high contaminant soil with overall contamination levels of up to 10x higher for the competitor Z as compared to SPINeasy^® DNA/RNA Kit for Soil (Figure 3, medium panel). The level of PCR inhibitors in DNA/RNA extracted from high biomass/contaminant soils was also examined using the inhibitor-sensitive qPCR and RT-qPCR. RNA samples obtained from competitor Z kit showed significant PCR inhibition, in line with the purity and humic acid level data. The difference was especially drastic for the samples obtained from high contaminant soil in which a complete inhibition was observed (Figure 3, bottom panel). 

Overall, these results indicate a superior inhibitor removal ability of SPINeasy^® DNA/RNA Kit for Soil.

 

 

Application Notes

The SPINeasy^® DNA/RNA Kit for Soil integrates our proprietary inhibitor removal expertise and our new technology for selective binding of DNA and RNA. The SPINeasy^® DNA/RNA Kit for Soil allows simultaneous isolation of pure microbiome genomic DNA and RNA from challenging soil types, including those with low biomass or those that are highly contaminated. The isolated nucleic acid products showed no contaminants and were immediately ready for use in downstream applications, including qPCR and RT-qPCR without the need of further inhibitor removal step.

Key Applications

Genomic, Molecular Biology, PCR, qPCR