Sur Souvik, Pujari Suresh, Ranjan Nihar, Azankia Temgoua Lidivine, Wicks Sarah L, Conner Andrea, Arya Dev P
Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States.
ACS Bio Med Chem Au. 2024 Apr 16;4(3):154-164. doi: 10.1021/acsbiomedchemau.3c00074. eCollection 2024 Jun 19.
Synthetic modification of oligodeoxynucleotides (ODNs) via conjugation to nucleic acid binding small molecules can improve hybridization and pharmacokinetic properties. In the present study, five Hoechst 33258 derived benzimidazoles were conjugated to T rich ODNs and their hybridization effectiveness was tested. Thermal denaturation studies revealed significant stabilization of complementary duplexes by ODN-benzimidazole conjugates, with the extent of stabilization being highly dependent on the length of the linker between DNA and benzimidazole. The increases in thermal stability were determined to be due to the binding of the benzimidazole moiety to the duplex. Circular dichroism and molecular modeling studies provided insights toward the influence of conjugation on duplex structure and how linker length impacts placement of the benzimidazole moiety in the minor groove. Furthermore, thermal denaturation studies with the complementary strand containing a single base mismatch or being RNA revealed that covalent conjugation of benzimidazoles to an ODN also enhances the sequence specificity. The fundamental studies reported herein provide a strategy to improve the stability and specificity properties of the ODN probes, which can be of use for targeting and diagnostics applications.
通过与核酸结合小分子共轭对寡脱氧核苷酸（ODN）进行合成修饰，可以改善杂交和药代动力学特性。在本研究中，将五种源自Hoechst 33258的苯并咪唑与富含T的ODN共轭，并测试了它们的杂交效果。热变性研究表明，ODN-苯并咪唑共轭物可显著稳定互补双链体，稳定程度高度依赖于DNA与苯并咪唑之间连接子的长度。热稳定性的增加被确定是由于苯并咪唑部分与双链体的结合。圆二色性和分子模拟研究为共轭对双链体结构的影响以及连接子长度如何影响苯并咪唑部分在小沟中的位置提供了见解。此外，对含有单个碱基错配或为RNA的互补链进行的热变性研究表明，苯并咪唑与ODN的共价共轭也增强了序列特异性。本文报道的基础研究提供了一种改善ODN探针稳定性和特异性特性的策略，可用于靶向和诊断应用。
