mRNA quality control

Abstract

Outline Any extracted RNA must be devoid of contaminants such as salt, protein, solvents and genomic DNA. Poor quality RNA will lead to problems when performing the reverse transcription and labelling and might affect data quality. We quality control our extracted RNA using gel electrophoresis and optical density measurements. Gel electrophoresis is used to check for Genomic DNA contamination and RNA decay. Optical density is used to assay the RNA yield and to check for contamination by salt, solvent, protein, etc. Gel electrophoresis to check for genomic DNA: Genomic DNA from D. melanogaster will be visible as a tight DNA band of high molecular weight. Whereas rRNA will be visible as two sharp bands half way down the gel the mRNA is the smear in the background. Presence or absence of genomic DNA is easy to detect. mRNA decay is inferred from fuzzy rRNA bands and the presence of low molecular weight smearing (from the rRNA band and below). The following is an example of good quality D. melanogaster RNA. Gel electrophoresis of D. melanogaster RNA