9RTD
Crystal structure of DNA aptamer C8N5t in complex with Plasmodium falciparum lactate dehydrogenase
Summary for 9RTD
| Entry DOI | 10.2210/pdb9rtd/pdb |
| Descriptor | L-lactate dehydrogenase, DNA (32-MER) (3 entities in total) |
| Functional Keywords | aptamer, lactate dehydrogenase, plasmodium falciparum, oxidoreductase |
| Biological source | Plasmodium falciparum (malaria parasite P. falciparum) More |
| Total number of polymer chains | 5 |
| Total formula weight | 155741.03 |
| Authors | Tars, K. (deposition date: 2025-07-02, release date: 2026-07-15, Last modification date: 2026-08-05) |
| Primary citation | Kunrade, L.,Pleiko, K.,Sproge, L.,Goluba, K.,Pantelejevs, T.,Wright, N.T.,Akopjana, I.,Bogans, J.,Tars, K.,Riekstina, U. Selection and validation of novel DNA aptamer panel co-specific to Plasmodium falciparum and Plasmodium ovale lactate dehydrogenase. Mol Ther Nucleic Acids, 37:102977-102977, 2026 Cited by PubMed Abstract: Malaria remains a major global health concern. The development of point-of-care diagnostic aptasensors could improve malaria detection, patient management, and eradication efforts. We selected and validated single-stranded DNA aptamers against lactate dehydrogenase (Pf-LDH), using systematic evolution of ligands by exponential enrichment (SELEX). The five most abundant aptamers were validated with an enzyme-linked oligonucleotide assay (ELONA). The aptamer binding affinities to Pf-LDH varied between 0.35 and 3.08 nM. Truncation of aptamers enhanced binding affinities in most cases, with all truncated aptamers showing comparable or improved dissociation constants (Kd) relative to full-length aptamers, except Pf-LDH5t, which lost its binding affinity. Selectivity analysis against LDH from , , and showed that Pf-LDH1 and Pf-LDH1t specifically recognized Pf-LDH (Kd = 2.74 ± 0.28 and 1.13 ± 0.26 nM, respectively), while Pf-LDH2, Pf-LDH3, Pf-LDH4, and their truncated forms, as well as Pf-LDH5, recognized both Pf-LDH and LDH (Po-LDH). Crystallography of Pf-LDH4t revealed a binding site overlapping that of the previously characterized aptamer 2008 but involving distinct molecular interactions. These findings demonstrate the structural versatility of LDH-specific aptamers and provide a novel Pf- and Po-LDH co-specific aptamer panel with strong potential for next-generation aptamer-based malaria diagnostics. PubMed: 42381705DOI: 10.1016/j.omtn.2026.102977 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (2.1 Å) |
Structure validation
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