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Open Access Highly Accessed Methodology article

A novel, non-radioactive eukaryotic in vitro transcription assay for sensitive quantification of RNA polymerase II activity

Cristina Voss1*, Brita Schmitt1, Susanne Werner-Simon2, Christian Lutz3, Werner Simon2 and Jan Anderl1

Author Affiliations

1 Department of Biochemistry and Cell Biology, Heidelberg-Pharma GmbH, Schriesheimer Str. 101, Ladenburg D-68526, Germany

2 Department of Chemistry, Heidelberg-Pharma GmbH, Schriesheimer Str. 101, Ladenburg D-68526, Germany

3 Department of Analytical Chemistry, Heidelberg-Pharma GmbH, Schriesheimer Str. 101, Ladenburg D-68526, Germany

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BMC Molecular Biology 2014, 15:7  doi:10.1186/1471-2199-15-7

Published: 3 April 2014

Abstract

Background

Many studies of the eukaryotic transcription mechanism and its regulation rely on in vitro assays. Conventional RNA polymerase II transcription assays are based on radioactive labelling of the newly synthesized RNA. Due to the inefficient in vitro transcription, the detection of the RNA involving purification and gel electrophoresis is laborious and not always quantitative.

Results

Herein, we describe a new, non-radioactive, robust and reproducible eukaryotic in vitro transcription assay that has been established in our laboratory. Upon transcription, the newly synthesized RNA is directly detected and quantified using the QuantiGene assay. Alternatively, the RNA can be purified and a primer extension followed by PCR detection or qPCR quantification can be performed. When applied to assess the activity of RNA polymerase II inhibitors, this new method allowed an accurate estimation of their relative potency.

Conclusions

Our novel assay provides a non-radioactive alternative to a standard in vitro transcription assay that allows for sensitive detection and precise quantification of the newly transcribed, unlabelled RNA and is particularly useful for quantification of strong transcriptional inhibitors like α-amanitin. Moreover, the method can be easily adapted to quantify the reaction yield and the transcription efficiency of other eukaryotic in vitro systems, thus providing a complementary tool for the field of transcriptional research.