Publication: Generation of in-silico DNA-aptamer as synthetic bioreceptor targeting PIVKA-II for early liver cancer detection
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Date
2026-01
Authors
Pranto, Shivnath Das
Journal Title
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Abstract
Protein induced by vitamin K absence or antagonist-II (PIVKA-II) is a clinically validated
biomarker for hepatocellular carcinoma; however, its selective detection remains
challenging due to structural homology among prothrombin-derived proteins. In this study,
an in silico strategy was employed to design and evaluate DNA Aptamers of varying
lengths (30-mer, 40-mer, and 50-mer) for selective recognition of PIVKA-II. Aptamer
structural stability, binding affinity, and specificity were systematically investigated using
secondary structure prediction, molecular docking, and molecular dynamics simulations.
Binding interactions were assessed at Pv6268 and Pv4n, representing distinct PIVKA-II
binding sites, while Pv0 (prothrombin) was used as a non-target protein to evaluate crossreactivity.
The 30-mer and 40-mer DNA Aptamers formed compact and conformationally
stable structures and exhibited strong binding at the Pv4n sites with negligence crossreactivity
toward Pv0. In contrast, the 50-mer DNA Aptamer displayed increased
conformational flexibility, resulting in less selective in distinguishing between PIVKA-II
protein variants and cross-reacted towards Pv0. These findings highlight the critical role of
Aptamer conformational adaptability in achieving high disease specificity and provide a
rational framework for the computational design of highly selective PIVKA-II-targeted
Aptamers for hepatocellular carcinoma diagnostics..