Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany.
Molecules. 2017 Dec 13;22(12):2213. doi: 10.3390/molecules22122213.
We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences-an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase-GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH. The more rigid conjugate showed a specific fluorescence increase for poly A only at pH 7, whereby this response could be reversibly switched-off at pH 5. The more flexible derivative revealed selective fluorescence quenching by poly G at pH 7 but no change for poly A, whereas its recognition of poly AH⁺ can be switched-on at pH 5. The computational analysis confirmed the important role of the GCP fragment and its protonation states in the sensing of polynucleotides and revealed that it is affected by the intrinsic dynamical features of conjugates themselves. Both conjugates showed a negligible response to uracil and cytosine ss-RNA as well as ds-RNA at pH 7, and only weak interactions with ds-DNA. Thus, nucleobase-GCP conjugates can be considered as novel lead compounds for the design of ss-RNA or ss-DNA selective fluorimetric probes.
我们在这里首次证明胍基羰基-吡咯（GCP）单元可用于精细识别单链 RNA 序列-这是一个直观上出乎意料的结果，因为到目前为止，GCP 单元与 ds-DNA 或 ds-RNA 的结合强烈依赖于小沟或大沟相互作用，如前所述工作。两种新型核苷-GCP 等排体在 GCP 单元的灵活性上有所不同，它们对各种单链 RNA 具有荧光识别能力，并且可以通过 pH 值进一步调节。刚性更强的共轭物仅在 pH 7 时对 poly A 显示出特异性荧光增加，而在 pH 5 时可以将这种响应可逆关闭。更灵活的衍生物在 pH 7 时对 poly G 显示出选择性荧光猝灭，但对 poly A 没有变化，而其对 poly AH⁺的识别可以在 pH 5 时开启。计算分析证实了 GCP 片段及其质子化状态在多核苷酸传感中的重要作用，并表明它受自身内在动态特征的影响。两种共轭物在 pH 7 时对尿嘧啶和胞嘧啶 ss-RNA 以及 ds-RNA 均无明显反应，仅与 ds-DNA 有微弱相互作用。因此，核苷-GCP 共轭物可以被认为是设计 ss-RNA 或 ss-DNA 选择性荧光探针的新型先导化合物。
