Abe Shunsuke, Aburaya Shino, Koyama Takaki, Usui Takashi, Yoshino Junro, Matsumura Shigeyoshi, Ikawa Yoshiya
Graduate School of Science and Engineering, University of Toyama, Gofuku 3190, Toyama 930-8555, Japan.
Graduate School of Pharma-Medical Sciences, University of Toyama, Sugitani 2630, Toyama 930-0152, Japan.
Molecules. 2025 Apr 15;30(8):1777. doi: 10.3390/molecules30081777.
The 17-3 RNA aptamer recognizes DMHBI and induces its fluorescence. We showed that the 17-3 RNA aptamer predominantly induced emission of the phenolate form of DMHBI. We also demonstrated that the active structure of the minimal form of the 17-3 aptamer possessed three stem elements and two large loop elements, which we named Karashi and its sequence-optimized variant, Jigarashi, respectively. Chemical modification experiments suggested that the two loop regions formed tertiary interactions and/or non-Watson-Crick base pairs, and no remarkable structural alterations occurred upon DMHBI binding. AlphaFold3 also predicted a tertiary structure of the ligand-free form of Jigarashi RNA, which was consistent with the results of chemical modification experiments.
17-3 RNA适配体识别DMHBI并诱导其产生荧光。我们发现17-3 RNA适配体主要诱导DMHBI酚盐形式的发射。我们还证明了17-3适配体最小形式的活性结构具有三个茎元件和两个大环元件，我们分别将其命名为“Karashi”及其序列优化变体“Jigarashi”。化学修饰实验表明，两个环区域形成三级相互作用和/或非沃森-克里克碱基对，并且在DMHBI结合后没有发生明显的结构改变。AlphaFold3还预测了Jigarashi RNA无配体形式的三级结构，这与化学修饰实验的结果一致。
