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.