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Carbazole modified oligonucleotides: synthesis, hybridization studies and fluorescence properties.
Organic & Biomolecular Chemistry ( IF 2.9 ) Pub Date : 2020-08-24 , DOI: 10.1039/d0ob01553a Alaa S Gouda 1 , Łukasz Przypis , Krzysztof Walczak , Per T Jørgensen , Jesper Wengel
Organic & Biomolecular Chemistry ( IF 2.9 ) Pub Date : 2020-08-24 , DOI: 10.1039/d0ob01553a Alaa S Gouda 1 , Łukasz Przypis , Krzysztof Walczak , Per T Jørgensen , Jesper Wengel
Affiliation
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Synthesis of the novel thiophenyl carbazole phosphoramidite DNA building block 5 was accomplished in four steps using a Suzuki–Miyaura cross-coupling reaction from the core carbazole and it was seamlessly accommodated into a 9-mer DNA-based oligonucleotide by incorporation at the flanking 5′-end in combination with a central insertion of an LNA-T nucleotide. The carbazole-containing oligonucleotide was combined in different duplex hybrids, which were characterized by thermal denaturation, circular dichroism and fluorescence studies. The carbazole monomer modulates the duplex stability in various ways. Thus, monomer Z increased the thermal stability of the 9-mer towards the complementary 9-mer/15-mer DNA duplex by 4.2 °C. Furthermore, indications of its intercalation into the duplex were obtained by modeling studies and robust decreases in fluorescence emission intensities upon duplex formation. In contrast, no clear intercalating tendency was corroborated for monomer Z within the DNA/RNA hybrid duplex as indicated by moderate quenching of the fluorescence and similar duplex thermal stabilities relative to the corresponding control duplex. The recognition efficiencies of the carbazole modified oligonucleotide toward single nucleotide mismatches were studied with two 15-mer model targets (DNA and RNA). For both systems, mismatches positioned at the juxtaposition of the carbazole monomer showed pronounced deceases in thermal denaturation temperature. Steady-state fluorescence emission studies of all mismatched duplexes with incorporation of Z monomer typically displayed efficient fluorescence quenching.
中文翻译：
咔唑修饰的寡核苷酸：合成、杂交研究和荧光特性。
新型噻吩基咔唑亚磷酰胺 DNA 构件5的合成通过核心咔唑的 Suzuki-Miyaura 交叉偶联反应分四步完成，并通过在侧翼 5' 处掺入而无缝地融入基于 9 聚体 DNA 的寡核苷酸中-末端与LNA-T核苷酸的中心插入组合。含咔唑的寡核苷酸被组合成不同的双链体杂交体，并通过热变性、圆二色性和荧光研究对其进行了表征。咔唑单体以多种方式调节双链体稳定性。因此，单体Z将 9 聚体对互补 9 聚体/15 聚体 DNA 双链体的热稳定性提高了 4.2 °C。此外，通过建模研究和双链体形成时荧光发射强度的大幅降低获得了其嵌入双链体的迹象。相反，DNA/RNA杂合双链体中的单体Z没有明显的嵌入趋势得到证实，如荧光的适度猝灭和相对于相应对照双链体的类似双链体热稳定性所表明的。使用两个 15 聚体模型靶标（DNA 和 RNA）研究了咔唑修饰寡核苷酸对单核苷酸错配的识别效率。对于这两个系统，咔唑单体并置处的错配显示出热变性温度的显着降低。对掺入Z单体的所有错配双链体的稳态荧光发射研究通常显示出有效的荧光猝灭。
更新日期：2020-09-16
中文翻译：
咔唑修饰的寡核苷酸：合成、杂交研究和荧光特性。
新型噻吩基咔唑亚磷酰胺 DNA 构件5的合成通过核心咔唑的 Suzuki-Miyaura 交叉偶联反应分四步完成，并通过在侧翼 5' 处掺入而无缝地融入基于 9 聚体 DNA 的寡核苷酸中-末端与LNA-T核苷酸的中心插入组合。含咔唑的寡核苷酸被组合成不同的双链体杂交体，并通过热变性、圆二色性和荧光研究对其进行了表征。咔唑单体以多种方式调节双链体稳定性。因此，单体Z将 9 聚体对互补 9 聚体/15 聚体 DNA 双链体的热稳定性提高了 4.2 °C。此外，通过建模研究和双链体形成时荧光发射强度的大幅降低获得了其嵌入双链体的迹象。相反，DNA/RNA杂合双链体中的单体Z没有明显的嵌入趋势得到证实，如荧光的适度猝灭和相对于相应对照双链体的类似双链体热稳定性所表明的。使用两个 15 聚体模型靶标（DNA 和 RNA）研究了咔唑修饰寡核苷酸对单核苷酸错配的识别效率。对于这两个系统，咔唑单体并置处的错配显示出热变性温度的显着降低。对掺入Z单体的所有错配双链体的稳态荧光发射研究通常显示出有效的荧光猝灭。
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