Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR
In transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were transfected with a vector containing the complete &...
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doaj-fb60dfdcc86345de98c8161a74a1fefc2020-11-25T03:18:27ZengMDPI AGMethods and Protocols2409-92792020-05-013404010.3390/mps3020040Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCRBarbara Ahlemeyer0Claudia Colasante1Eveline Baumgart-Vogt2Institute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University, Aulweg 123, 35385 Giessen, GermanyInstitute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University, Aulweg 123, 35385 Giessen, GermanyInstitute for Anatomy and Cell Biology, Division of Medical Cell Biology, Justus Liebig University, Aulweg 123, 35385 Giessen, GermanyIn transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were transfected with a vector containing the complete <i>Pex11β</i> cDNA (plasmid DNA). The <i>Pex11β</i> mRNA level, as calculated using the RT-qPCR product, was unrealistically higher (>1000-fold) in transfected compared to non-transfected cells, and we assumed that there were large amounts of contaminating plasmid DNA in the RNA sample. Thus, we searched for a simple way to distinguish between plasmid-derived mRNA, endogenous genome-derived mRNA and plasmid DNA, with minimal changes to standard RT-PCR techniques. We succeeded by performing a plasmid mRNA-specific reverse transcription, and the plasmid cDNA was additionally tagged with a nonsense tail. A subsequent standard qPCR was conducted using appropriate PCR primers annealing to the plasmid cDNA and to the nonsense tail. Using this method, we were able to determine the specific amount of mRNA derived from the transfected plasmid DNA in comparison to the endogenous genome-derived mRNA, and thus the transfection and transcription efficiency.https://www.mdpi.com/2409-9279/3/2/40endogenous genome-derived mRNAgenomic DNADNA contaminationnonsense-tail reverse transcriptionnonsense-tail PCR primeroverexpression experiments |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Barbara Ahlemeyer Claudia Colasante Eveline Baumgart-Vogt |
spellingShingle |
Barbara Ahlemeyer Claudia Colasante Eveline Baumgart-Vogt Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR Methods and Protocols endogenous genome-derived mRNA genomic DNA DNA contamination nonsense-tail reverse transcription nonsense-tail PCR primer overexpression experiments |
author_facet |
Barbara Ahlemeyer Claudia Colasante Eveline Baumgart-Vogt |
author_sort |
Barbara Ahlemeyer |
title |
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR |
title_short |
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR |
title_full |
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR |
title_fullStr |
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR |
title_full_unstemmed |
Analysis of the Level of Plasmid-Derived mRNA in the Presence of Residual Plasmid DNA by Two-Step Quantitative RT-PCR |
title_sort |
analysis of the level of plasmid-derived mrna in the presence of residual plasmid dna by two-step quantitative rt-pcr |
publisher |
MDPI AG |
series |
Methods and Protocols |
issn |
2409-9279 |
publishDate |
2020-05-01 |
description |
In transfection experiments with mammalian cells aiming to overexpress a specific protein, it is often necessary to correctly quantify the level of the recombinant and the corresponding endogenous mRNA. In our case, mouse calvarial osteoblasts were transfected with a vector containing the complete <i>Pex11β</i> cDNA (plasmid DNA). The <i>Pex11β</i> mRNA level, as calculated using the RT-qPCR product, was unrealistically higher (>1000-fold) in transfected compared to non-transfected cells, and we assumed that there were large amounts of contaminating plasmid DNA in the RNA sample. Thus, we searched for a simple way to distinguish between plasmid-derived mRNA, endogenous genome-derived mRNA and plasmid DNA, with minimal changes to standard RT-PCR techniques. We succeeded by performing a plasmid mRNA-specific reverse transcription, and the plasmid cDNA was additionally tagged with a nonsense tail. A subsequent standard qPCR was conducted using appropriate PCR primers annealing to the plasmid cDNA and to the nonsense tail. Using this method, we were able to determine the specific amount of mRNA derived from the transfected plasmid DNA in comparison to the endogenous genome-derived mRNA, and thus the transfection and transcription efficiency. |
topic |
endogenous genome-derived mRNA genomic DNA DNA contamination nonsense-tail reverse transcription nonsense-tail PCR primer overexpression experiments |
url |
https://www.mdpi.com/2409-9279/3/2/40 |
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