School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
Institut Pasteur, Laboratory for Bioorganic Chemistry of Nucleic Acids, Department of Structural Biology and Chemistry, CNRS UMR-3523, 75015 Paris, France.
Proc Natl Acad Sci U S A. 2020 Jul 21;117(29):16790-16798. doi: 10.1073/pnas.2003267117. Epub 2020 Jul 6.
Nucleic acid aptamers selected through systematic evolution of ligands by exponential enrichment (SELEX) fold into exquisite globular structures in complex with protein targets with diverse translational applications. Varying the chemistry of nucleotides allows evolution of nonnatural nucleic acids, but the extent to which exotic chemistries can be integrated into a SELEX selection to evolve nonnatural macromolecular binding interfaces is unclear. Here, we report the identification of a cubane-modified aptamer (cubamer) against the malaria biomarker lactate dehydrogenase (PvLDH). The crystal structure of the complex reveals an unprecedented binding mechanism involving a multicubane cluster within a hydrophobic pocket. The binding interaction is further stabilized through hydrogen bonding via cubyl hydrogens, previously unobserved in macromolecular binding interfaces. This binding mechanism allows discriminatory recognition of over lactate dehydrogenase, thereby distinguishing these highly conserved malaria biomarkers for diagnostic applications. Together, our data demonstrate that SELEX can be used to evolve exotic nucleic acids bearing chemical functional groups which enable remarkable binding mechanisms which have never been observed in biology. Extending to other exotic chemistries will open a myriad of possibilities for functional nucleic acids.
通过指数富集的配体系统进化（SELEX）筛选出的核酸适体与具有多种翻译应用的蛋白质靶标形成精致的球状结构。改变核苷酸的化学性质可以进化出非天然核酸，但将外来化学物质整合到 SELEX 选择中以进化非天然大分子结合界面的程度尚不清楚。在这里，我们报告了针对疟疾生物标志物乳酸脱氢酶（PvLDH）的立方烷修饰适体（cubamer）的鉴定。复合物的晶体结构揭示了一种前所未有的结合机制，涉及疏水性口袋内的多立方烷簇。通过立方氢的氢键进一步稳定结合相互作用，这在大分子结合界面中从未观察到。这种结合机制允许区分 与乳酸脱氢酶，从而区分这些高度保守的疟疾生物标志物用于诊断应用。总之，我们的数据表明，SELEX 可用于进化带有化学官能团的外源性核酸，从而实现生物学中从未观察到的非凡结合机制。扩展到其他外来化学物质将为功能核酸开辟无数可能性。
