Conformational study of aptamer and its interaction with aflatoxin B1 using surface-enhanced Raman spectroscopy

Aptamers are single-stranded DNA or RNA oligonucleotides with a unique secondary structure. Target binding induces conformational changes in the secondary structure. Conformation-induced changes in some characteristic Raman bands of DNA aptamer, upon binding to aflatoxin B1 (AFB1), were probed using surface enhanced Raman spectroscopy (SERS). The self-assembled monolayers of thiol-linked DNA aptamer on gold nanoparticles (AuNPs) surface provided a direct, label-free detection method through three adenine bases close to the surface of an AuNPs SERS substrate. The spectra of the DNA aptamer were dominated by the adenine ring breathing mode at 734 cm^-1. Upon binding to AFB1 and conformational changes of the aptamer, the 5'-end of the aptamer with three adenine bases moved away from the surface of AuNPs, resulting in the decreased Raman intensity of the adenine band at 734 cm^-1 (I₇₃₄). In addition to the adenine band, the deoxyribose phosphate backbone (O-P-O) band at 1004 cm^-1 (I₁₀₀₄) was decreased after aptamer binding to AFB1. The change of I₇₃₄, corresponding to the AFB1 concentration, was employed for quantitative measurement of AFB1 in the range of 0.1-5000 pg mL^-1. The aptamer-based SERS assay exhibited high sensitivity with a limit of detection (LOD) of 0.24 pg mL^-1 for I₇₃₄ calibration curve.