Broccoli aptamer allows quantitative transcription regulation studies in vitro.

Amanda van der Sijs, Thomas Visser, Pepijn Moerman, Gert Folkers, Willem Kegel

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Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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1 · What the graph read from it

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3 · Its place in the literature

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4 · The record

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5 · Who and what money

Authors and funding

5 authors.

Amanda van der SijsVan 't Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.ORCID 0009-0003-6227-0778

Thomas VisserVan 't Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.ORCID 0009-0007-0942-4933

Pepijn MoermanSelf-Organizing Soft Matter, Chemical Engineering and Chemistry, Eindhoven University of Technology, Eindhoven, The Netherlands.

Gert FolkersUtrecht NMR Group, Bijvoet Centre fo Biomolecular Research, Utrecht University, Utrecht, The Netherlands.

Willem KegelVan 't Hoff Laboratory for Physical and Colloidal Chemistry, Debye Institute for Nanomaterials Science, Utrecht University, Utrecht, The Netherlands.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

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.

Indexed as

Aptamers, NucleotideBrassicaTranscription, GeneticGene Expression RegulationThermodynamicsAptamers, Nucleotide

Identifiers

PMID38870160

DOI10.1371/journal.pone.0304677

PMCPMC11175446

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.