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Using Automated Electrophoresis to Assess RNA Quality

Bio-Rad
17 Mar 2008

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Bio-Rad Laboratories, Inc., a multinational manufacturer and distributor of life science research and clinical diagnostic products, announced today the availability of a technical note (#5315A), which describes the use of Bio-Rad’s Experion™ automated electrophoresis system to assess RNA quality and quantity in siRNA-induced gene silencing experiments.

An awareness of the quality of an RNA sample is essential to the success of experiments designed to study gene expression. Failure to evaluate the state of RNA samples before their use in downstream applications, such as validation of siRNA gene silencing using RT-qPCR, can yield faulty conclusions.

The Experion system has been shown to be a useful tool in this regard, accurately quantitating RNA as well as providing information on the overall quality and integrity of the RNA that will ultimately be analyzed in various downstream applications.

In this paper, it is discussed how the Experion system, which uses microfluidics technology, can be incorporated into an RNAi experimental workflow. Further, it is shown that the qualitative and quantitative RNA sample information that is obtained using this system is beneficial to the successful evaluation and validation of the efficacy of siRNA-mediated gene silencing.

Supported be numerous graphs, figures and tables, the four-page technical note provides the methods, results, and discussion for assessing RNA quality and quantity, as well as illustrating that RNA quality is critical to downstream results.

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ElectrophoresisElectrophoresis equipment is used to separate mixtures of protein, DNA or RNA, based on their electric charge, size and other physical characteristics, by passing them through a medium such as a polyacrylamide gel, an agarose gel or a capillary tube. Electrophoresis equipment includes horizontal and vertical gel electrophoresis chambers, isoelectric focusing systems, 2D electrophoresis and capillary electrophoresis instruments. Precast gels with a gradient can be used or gels can be hand cast. Samples are run alongside ladders or markers to identify the approximate size of a molecule. Separated proteins and nucleic acids in the gel can be stained or probed with fluorescent markers and then imaged and detected using gel documentation instruments, transilluminators, densitometers and scanners. Find the best electrophoresis equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Genome AnalysisGenomics, the study of genomes, includes functional genomics, evolutionary genomics and comparative genomics. There are many genomic technologies such as DNA sequencing of whole genomes, computational biology and bioinformatics. DNA and nucleic acids must be isolated and concentrated from cells for analysis with kits, automated analyzers and software. Other useful technologies for studying genomics include PCR, microarrays and electrophoresis.PCR and Thermal CyclingPolymerase chain reaction (PCR) kits and thermal cyclers are used for the in vitro amplification of DNA permitting subsequent analysis and experimental procedures. Explore a range of high-quality polymerase, primers and nucleotides or simplify your workflow with a PCR mastermix. Find reverse transcription PCR (RT-PCR) and cDNA synthesis kits for RNA products and libraries. Quantitatively measure the amplification of DNA with real-time PCR (qPCR) and droplet digital PCR (ddPCR) kits and systems, and discover automated PCR setup solutions to increase throughput. Alternative DNA amplification methods also include recombinase polymerase amplification (RPA) kits. Find the best PCR kits and thermal cyclers and purification equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.RNA InterferenceRNA interference (RNAi) uses siRNA or miRNA for transcriptional silencing, gene knockdown and regulation of gene expression. RNAi requires chemical synthesis, introduction of DNA vectors into cells, an assay of RNAi effects and RNAi quantification or analysis. Consider target sequence selection, reagent preparation, controls, high specificity and effectiveness and low non-specific gene knockdown.

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Using Automated Electrophoresis to Assess RNA Quality