DNA Quality Control of PCR products and native DNA by Agarose Gel Electrophoresis v1

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This protocols is part of the ANU Biosecurity mini-research project #1 "Plant Pathogen Diagnostics: Visuals, subcultures, and genomics". You will be provided four pots of 3-4 week old wheat plants that have been infected with different wheat pathogens. Each pot has been infected with one major pathogen. You will not know which pot has been infected with which pathogen. However, you will be provided a compendium of 10-15 wheat pathogens that will guide you to identify the infective agent for each treatment group. The fifth treatment group will be uninfected wheat plants which will be clearly identified. You can use treatment group #5 as negative control for your experiments. In total, each group will obtain five pots each: This specific protocol is a step by step guide to assess DNA quality via agarose gel electrophoresis. Agarose gel electrophoresis lets you assess the size of DNA molecules. In addition, you can estimate DNA concentrations and impurities of RNA. During agarose gel electrophoresis DNA gets linearised. Larger molecules take longer to migrate through the gel when migration is driven by a electric potential at the specific pH of the buffer. When running a standard DNA ladder with bands of known molecular size, one can compare the DNA size of ones DNA or PCR sample with the known standards. The final goal is to achieve the following: To assess DNA length of molecules in total DNA stock samples and for all PCR reactions. To approximately estimate relative DNA concentrations. To test if negative PCR controls did not amplify anything as appropriate. To test if whole DNA extracts contain RNA in addition to DNA. Select samples from three research groups to be sequenced in the practical of week 6. This protocol is applicable for week 5. Protocols progress overview: Week 5 Run a 1% Agarose Gel electrophoresis for all samples of each research group. Some useful explainers and resources: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4846332/ https://en.wikipedia.org/wiki/Agarose_gel_electrophoresis https://www.youtube.com/watch?v=ZDZUAleWX78