Hybrid femtosecond laser processing, which consists of femtosecond laser assisted wet etching, selective metallization, and laser induced periodic surface structure (LIPSS) formation, has enabled fabricating three-dimensional microfluidic surface enhanced Raman scattering (SERS) chips for highly sensitive sensing. To investigate the dependence of laser wavelength on the period of LIPSS which strongly affects the sensitivity of SERS substrate, two different wavelengths (515 nm and 1030 nm) of femtosecond laser beams have been employed. We observed the morphology of nanoripple on the metal layers under different laser parameters to optimize laser parameters, resulting in fabrication of homogenous LIPSS. The nanoripple with narrower groove (~40 nm) fabricated by 515 nm femtosecond laser induced stronger Raman scattering to achieve the SERS analytical enhancement factor exceeding 1 × 108. Furthermore, we introduced a novel method termed liquid-interface assisted SERS (LI-SERS) to realize extremely sensitive sensing, which achieved the detection limit of aM with analytical enhancement factor exceeding 1 × 1014 for R6G detection. We found the LI-SERS was able to locally aggregate the analyte molecules by Raman excitation laser irradiation at the interface of air and analyte solution containing the analytes in a microchannel. The aggregation forced the analyte molecules to enter into the “hot-spots” by Marangoni effect, which extraordinarily increased the SERS intensity. Furthermore, we employed LI-SERS to detect DNA bases which realized the DNA discrimination in the microfluidic channel by LI-SERS.
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