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.
| Original language | English |
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| Article number | e0304677 |
| Number of pages | 15 |
| Journal | PLoS One |
| Volume | 19 |
| Issue number | 6 |
| DOIs | |
| Publication status | Published - Jun 2024 |
Bibliographical note
Publisher Copyright:© 2024 van der Sijs et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding
Dutch Research Council (NWO) KLEIN grant. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
| Funders |
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| Dutch Research Council (NWO) KLEIN grant |