Broccoli aptamer allows quantitative transcription regulation studies in vitro
Amanda van der Sijs, Thomas Visser, Pepijn Moerman, Gert Folkers, Willem Kegel, Jianhui Liu, Jianhui Liu, Jianhui Liu
TL;DR
This paper introduces a method using Broccoli aptamers to study transcription regulation without needing protein translation.
Contribution
The use of Broccoli aptamers enables quantitative transcription studies without a translational step.
Findings
Broccoli aptamers agree well with previous studies when analyzing transcription regulation scenarios.
Non-coding DNA can significantly affect transcription levels, similar to the lac repressor's effect.
The method has limitations due to delays caused by aptamer folding.
Abstract
Quantitative transcription regulation studies in vivo and in vitro often make use of reporter proteins. Here we show that using Broccoli aptamers, quantitative study of transcription in various regulatory scenarios is possible without a translational step. To explore the method we studied several regulatory scenarios that we analyzed using thermodynamic occupancy-based models, and found excellent agreement with previous studies. In the next step we show that non-coding DNA can have a dramatic effect on the level of transcription, similar to the influence of the lac repressor with a strong affinity to operator sites. Finally, we point out the limitations of the method in terms of delay times coupled to the folding of the aptamer. We conclude that the Broccoli aptamer is suitable for quantitative transcription measurements.
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Taxonomy
TopicsAdvanced biosensing and bioanalysis techniques · RNA and protein synthesis mechanisms · DNA and Nucleic Acid Chemistry