Using pfALBA3 to Check for Genomic DNA Contamination in Plasmodium RNA Extractions
When working with Plasmodium falciparum, extracting high-quality RNA is crucial for downstream applications like qRT-PCR, transcriptomics, and gene expression analysis. However, one common challenge is genomic DNA (gDNA) contamination in RNA samples—which can lead to false positives or skewed expression data.
To tackle this issue, researchers often use a control gene to confirm whether RNA samples are truly free from DNA contamination. One such reliable control is the Plasmodium falciparum gene pfALBA3 (gene ID: PF3D7_1006200).
What is pfALBA3?
pfALBA3 belongs to the ALBA (Acetylation Lowers Binding Affinity) family of RNA-binding proteins. In P. falciparum, ALBA proteins are thought to play key roles in:
RNA metabolism and regulation
Stage-specific gene expression
Possibly even translational control during the parasite's complex lifecycle
Because pfALBA3 is consistently transcribed in blood-stage parasites, it serves as a stable internal reference gene—a feature that makes it ideal for use in RNA quality control assays.
How pfALBA3 Detects DNA Contamination
The typical approach involves using primers that span exon-exon junctions in the pfALBA3 mRNA transcript. Here's how it works:
By comparing reactions with and without reverse transcriptase (RT), you can easily tell whether your RNA sample is clean. If the –RT control yields no amplification of pfALBA3, you're in the clear.
Why pfALBA3 Works Well
Exon-spanning primers reduce the chance of gDNA amplification.
Abundant expression makes it easy to detect in RNA samples.
It’s a housekeeping gene, so expression is relatively stable across lifecycle stages.
This makes pfALBA3 not just a marker of RNA integrity, but also a reliable check for DNA-free extractions—a must for high-confidence transcriptomics.
Best Practices
Always include a –RT control when using pfALBA3 in qPCR.
Perform DNase treatment after RNA extraction to remove any residual gDNA.
Run a no-template control (NTC) to check for primer-dimer or environmental contamination.
Conclusion
Using pfALBA3 as a sentinel gene for RNA quality is a smart move when working with Plasmodium falciparum. It enables you to detect and eliminate gDNA contamination early—saving time, resources, and the integrity of your gene expression data.
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