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. 2021 Oct 6;12:5856. doi: 10.1038/s41467-021-25973-x

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Co-crystal structure showing interaction of compound 11 with the Tt-preQ₁-RS aptamer (ab_13-14) solved at 1.57 Å resolution. S1, S2, L1, L2, and L3 are colored green, cyan, pink, gray, and orange, respectively. The mF_o – DF_c electron density maps for the compound are colored blue and contoured at 3.0 σ. b Detail of ligand:RNA interaction showing conservation of contacts seen with unmodified PreQ₁. The nucleotides that interact with the compound are labeled, and hydrogen bonds are indicated as dotted lines. Residues at the site of the interaction are labeled to show the proximity of G5 and G11 to the diazirine. The mF_o – DF_c electron density maps for the compound are also shown as in a. c Bar graph representing the photocrosslinking efficiency of wild-type Tt-preQ₁-RS aptamer (Tt-WT) and three different mutant aptamers (Tt-G4A, Tt-G5A, and Tt-G11A) to Probe 11. d Single-round transcription termination assay results for compound 11. Quantification of transcription termination efficiency with increasing concentrations of 11 was calculated based on the band intensity of read-through transcription product (RT) and terminated transcription product (T). Data are presented as the mean ± SEM (n = 3) of three independent experiments. Statistical significance was calculated by two-tailed t-test analysis. Source data are provided as a Source Data file.