Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer

Abstract

Significance Aptamers are oligonucleotides selected and evolved to bind tightly and specifically to molecular targets. Aptamers have promise as diagnostic tools and therapeutic agents, but little is known about how they recognize or discriminate their targets. In this study, X-ray crystallography together with several other biophysical techniques reveal how a new DNA aptamer recognizes and discriminates Plasmodium lactate dehydrogenase, a protein marker that is a diagnostic indicator of infection with the malaria parasite. We also demonstrate application of the aptamer in target detection. This study broadens our understanding of aptamer-mediated molecular recognition and provides a DNA aptamer that could underpin new innovative approaches for point-of-care malaria diagnosis.

Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor

“…Pi stacking interactions reminiscent of the SOMAmer zipper motif are also observed in traditional DNA/RNA aptamer protein structures (Cheung et al, 2013;Convery et al, 1998;Huang et al, 2003Huang et al, , 2009Nomura et al, 2010;Russo Krauss et al, 2011), where an extruded base interacts with a side chain on the protein. Unlike SOMAmers, the expelled nucleotides are disengaged from the primary DNA/RNA structure, exhibiting few if any intramolecular interactions, but like the SOMAmers, the extrusion appears to be necessary, not only for interactions with the target but to accommodate tight turns or other aspects of the folded structure.…”

Aromatic Surfactant as Aggregating Agent for Aptamer-Gold Nanoparticle-Based Detection of Plasmodium Lactate Dehydrogenase

“…The selectivity information of the previously developed PvLDH aptasensor for the major interfering agent hLDH B was absent [17] for comparative analyses with the present work. The detection limits obtained by us (38 pg/ll with BCK and 55 pg/ll with NaCl) with P38 are marginally superior to the similar assay developed by Cheung et al [14]. A number of variations have been included in the present detection protocol.…”

“…The aptamer P38 developed by us against PfLDH is significantly different from the other reports with no common discernible motifs [14,16]. Unlike the Plasmodium LDH aptamer reported previously [16], the aptamer P38 was developed by incorporating the counter screening against hLDH A and hLDH B in the SELEX process considering the fact that these human enzymes are homologous to PfLDH.…”

“…Unlike covalently conjugating the PfLDH aptamer with AuNPs [14], P38 was physically adsorbed on the nanoparticles, and thereby, we omitted additional steps of preparing the detection probe. Moreover, the SELEX method has been performed here on PVDF membrane instead of expensive Ni-NTA magnetic beads used by both the previous studies [14,16] as proteinimmobilization supports. Hence, the method reported by us is simpler and has potential economical implications.…”

“…Several biomarkers for diagnosis of malaria have been investigated [13] among which Plasmodium-specific lactate dehydrogenase has emerged as a promising biomarker for malaria detection owing to its subtle structural and kinetic differences from the mammalian counterpart, leading to an increased interest in development of sensors that target this enzyme [14][15][16][17][18]. Here, we report a novel ssDNA aptamer developed against Plasmodium falciparum lactate dehydrogenase and its application potential to detect this biomarker through an aromatic cationic surfactant-based assay using gold nanoparticles as the optical sensing platform.…”