Evolution of abiotic cubane chemistries in a nucleic acid aptamer allows selective recognition of a malaria biomarker

• Published in: Proceedings of the National Academy of Sciences - PNAS 2020-07, Vol.117 (29), p.16790-16798
• Main Authors: Cheung, Yee-Wai, Röthlisberger, Pascal, Mechaly, Ariel E., Weber, Patrick, Levi-Acobas, Fabienne, Lo, Young, Wong, Alvin W. C., Kinghorn, Andrew B., Haouz, Ahmed, Savage, G. Paul, Hollenstein, Marcel, Tanner, Julian A.
• Format: Article
• Language: English
• Subjects: Acids; Aptamers; Aptamers, Nucleotide; Aptamers, Nucleotide - chemistry; Binding; Biomarkers; Biomarkers - blood; Biomarkers - chemistry; Chemical Sciences; Crystal structure; Cubane; Dehydrogenase; Dehydrogenases; Diagnostic software; Diagnostic systems; Evolution; Functional groups; Humans; Hydrogen Bonding; Hydrophobicity; Interfaces; L-Lactate Dehydrogenase; L-Lactate Dehydrogenase - blood; L-Lactate Dehydrogenase - chemistry; Lactate dehydrogenase; Lactic acid; Macromolecules; Malaria; Malaria - blood; Malaria - diagnosis; Molecular Diagnostic Techniques; Molecular Diagnostic Techniques - methods; Molecular Dynamics Simulation; Nucleic acids; Nucleotides; Organic chemistry; Physical Sciences; Plasmodium falciparum; Plasmodium vivax; Plasmodium vivax - enzymology; Protein Binding; Protein folding; Protozoan Proteins; Protozoan Proteins - chemistry; Recognition; Vector-borne diseases
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.2003267117

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 Plasmodium vivax 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 P. vivax over Plasmodium falciparum 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.