RNA spike-in
From Wikipedia, the free encyclopedia
An RNA spike-in is an RNA transcript of known sequence and quantity used to calibrate measurements in RNA hybridization assays, such as DNA microarray experiments, RT-qPCR, and RNA-Seq.[1]
A spike-in is designed to bind to a DNA molecule with a matching sequence, known as a control probe.[2][3][4] This process of specific binding is called hybridization. A known quantity of RNA spike-in is mixed with the experiment sample during preparation.[2] The degree of hybridization between the spike-ins and the control probes is used to normalize the hybridization measurements of the sample RNA.[2]
Nucleic acid hybridization assays have been used for decades to detect specific sequences of DNA or RNA,[5] with a DNA microarray precursor used as early as 1965.[6] In such assays, positive control oligonucleotides are necessary to provide a standard for comparison of target sequence concentration, and to check and correct for nonspecific binding; that is, incidental binding of the RNA to non-complementary DNA sequences.[7] These controls became known as "spike-ins".[1] With the advent of DNA microarray chips in the 1990s[8] and the commercialization of high-throughput methods for sequencing and RNA detection assays, manufacturers of hybridization assay "kits" started to provide pre-developed spike-ins.[1] In the case of gene expression assay microarrays or RNA sequencing (RNA-seq), RNA spike-ins are used.
Manufacturing
RNA spike-ins can be synthesized by any means of creating RNA synthetically, or by using cells to transcribe DNA to RNA in vivo (in cells).[1] RNA can be produced in vitro (cell free) using RNA polymerase and DNA with the desired sequence.[1] Large scale biotech manufacturers produce RNA synthetically via high-throughput techniques and provide solutions of RNA spike-ins at predetermined concentration.[1] Bacteria containing DNA (usually on plasmids) for transcription to spike-ins are also commercially available.[1] The purified RNA can be stored long-term in a buffered solution at low temperature.[1]
