Measuring transcription _in vitro:

Background / Usage:

Broccoli and Spinach are two versions of an RNA aptamer tag that fluoresces with similar spectral properties to GFP when properly folded. Both require a small-molecule fluorophore (DFHBI); the Barrick lab has a stock of fluorophore, and it can be purchased from a number of vendors (as of 5/2017). These aptamers can be used for a variety of applications; this protocol covers using them to measure transcriptional output from T7 RNA Polymerase / promoter mutants in vitro, but they can also be used to measure transcription in vivo in bacteria or eukaryotic cells or (by using the aptamer as a fusion tag) to determine subcellular localization of RNA transcripts.

For in vitro experiments, we have had most success using linear templates ~120bp. These can be produced either by subjecting overlapping oligos to an extension reaction, or by using shorter primers to amplify the template from a plasmid. Note that both of these methods can be used to swap promoters if needed.

Designing and Amplifying Templates

in vitro Transcription Assay

-- Main.ColinBrown - 25 May 2017

Edit | Attach | Watch | Print version | History: r2 < r1 | Backlinks | Raw View | More topic actions...

 Barrick Lab  >  ProtocolList  >  ProtocolsBroccoliAptamerInVitroAssays

Contributors to this topic Edit topic ColinBrown
Topic revision: r1 - 2017-05-25 - 19:57:09 - Main.ColinBrown
This site is powered by the TWiki collaboration platform Powered by Perl This site is powered by the TWiki collaboration platformCopyright ©2021 Barrick Lab contributing authors. Ideas, requests, problems? Send feedback