Laboratory for Biomolecular Interactions and Spectroscopy, 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.
Int J Mol Sci. 2024 Apr 29;25(9):4866. doi: 10.3390/ijms25094866.
Three new phenanthridine peptide derivatives (, , and ) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (, ) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring () exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 10 M was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
合成了三种新的菲啶肽衍生物（、和），以探索它们作为 DNA 和 RNA 的分光光度探针的潜力。紫外/可见和圆二色（CD）光谱、质谱和计算分析证实了所有三种化合物中都存在分子内相互作用。计算分析表明，化合物在弯曲和开环构象之间交替，突出了后者对成功识别多核苷酸的关键影响。在两个非对映异构体（、）中将一个甘氨酸替换为赖氨酸，与 DNA 和 RNA 的结合相互作用比含有两个甘氨酸的化合物（）更强，因此强调了赖氨酸的重要性。靠近菲啶环的赖氨酸非对映异构体（）对非交替的 AT 和 ATT 多核苷酸表现出双重和选择性的荧光响应，并诱导 AT 双链体形成三聚体。与 AT 和 ATT 多核苷酸相互作用的最佳结合常数（K）值为 2.5×10 M。此外，除了区分不同类型的 ds-DNA 和 ds-RNA 外，同一种化合物还可以通过独特的诱导 CD 信号识别富含 GC 的 DNA。
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