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Computational Selectivity Analysis of Aptamer toward Oxidized Low-Density Lipoprotein
Suticha Chunta1, Soemwit Khongwichit1,2, Napat Prompat1,3
1Faculty of Medical Technology, Prince of Songkla University, Songkhla 90110, Thailand.
ACS Omega
|May 18, 2026
Summary
Aptamer AP11 shows high selectivity for oxidized low-density lipoprotein (oxLDL), confirmed by computational and experimental methods. This finding enhances aptamer applications in diagnostics and therapeutics.
Area of Science:
- Biochemistry
- Molecular Biology
- Computational Chemistry
Background:
- Aptamer selectivity is vital for their practical use.
- Oxidized low-density lipoprotein (oxLDL) is a key biomarker.
Purpose of the Study:
- To evaluate the selectivity of four DNA aptamers (AP07, AP11, AP25, AP29) for oxLDL.
- To identify aptamers with high affinity and specificity for oxLDL.
Main Methods:
- Computational prediction using molecular dynamics simulations and MM/GBSA analysis.
- Experimental validation via aptamer-based electrochemical assays.
- Assessing binding against various lipoproteins and albumin.
Main Results:
- Aptamer AP11 demonstrated the highest predicted affinity and selectivity for oxidized apolipoprotein B100 (apoB100).
- Experimental results confirmed AP11's high selectivity for oxLDL with <6% cross-reactivity.
- AP11 maintained key conformational motifs during oxLDL interaction.
Conclusions:
- The integrated computational-experimental approach effectively evaluates aptamer selectivity.
- AP11 is a promising candidate for oxLDL detection and related applications.
- This framework aids in optimizing aptamers for complex targets.
