The concentration
of 8-oxo-7,8-dihydro-2′-deoxyguanosine
(8-oxo-dG) in urine or serum is associated with the degree of oxidative
damage of DNA and broadly used as a sensitive biomarker for various
diseases. However, determination of a low concentration of 8-oxo-dG
in biosamples is not an easy task owing to the complexity of coexisting
substances. Herein, we design an aptasensor based on aptamer-mediated
aggregation of cysteamine-capped gold nanoparticles (Cyst/AuNPs) for
the detection of 8-oxo-dG by molecular dynamics simulation. Our simulations
reveal that a positively charged Cyst modified onto the surfaces of
AuNP exists in two conformers including gauche and trans. The trans conformer was prevalent
on the AuNP surfaces and can stabilize AuNPs in the aqueous solution,
even in the presence of 8-oxo-dG. Molecular recognition between 8-oxo-dG
and the aptamer was demonstrated and bonding between these biomolecules
was thoroughly elucidated. During the complex formation, van der Waals
stacking interactions between 8-oxo-dG molecules were observed and
found to play a significant role in the binding stability. The sensing
mechanism of the colorimetric aptasensor was studied and the feasibility
study of the proposed aptasensor was assessed by experimental validation.
The experimental results are in good agreement with the computational
study. Our in silico design can pave the way for,
but is not limited to, a highly sensitive aptasensor for the naked-eye
detection of 8-oxo-dG.
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