van der Sijs Amanda, Visser Thomas, Moerman Pepijn, Folkers Gert, Kegel Willem
Van 't Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.
Self-Organizing Soft Matter, Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.
PLoS One. 2024 Jun 13;19(6):e0304677. doi: 10.1371/journal.pone.0304677. eCollection 2024.
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.
体内和体外的定量转录调控研究常常使用报告蛋白。在此我们表明，利用西兰花适体，无需翻译步骤即可在各种调控情形下对转录进行定量研究。为探索该方法，我们研究了几种调控情形，并使用基于热力学占据的模型对其进行分析，发现与先前研究结果高度吻合。接下来我们表明，非编码DNA可对转录水平产生显著影响，这类似于与操纵子位点具有强亲和力的乳糖阻遏物的影响。最后，我们指出该方法在与适体折叠相关的延迟时间方面的局限性。我们得出结论，西兰花适体适用于转录的定量测量。
