Microarray biochip fabricated on silicon nanowires/carbon dots heterostructures for enhanced viral DNA detection

Abstract

Recent studies have shown that human oncoviruses are responsible for 10% of cancer cases worldwide. While PCR assays are highly sensitive and specific, microarrays offer outstanding performance for detecting multiple targets simultaneously. However, in microarray systems, accurate detection of DNA viruses relies on the type of microarray platform, while obtaining high-quality, fluorescent-labelled single-stranded DNA bares an equal contribution.Our study demonstrates a proof-of-concept of a microarray platform for enhanced DNA detection. First, we assembled 3D microarray chips on silicon nanowires (SiNWs) substrates using a one-step metal-assisted chemical etching (1-MACE) technique, coated them with SU-8 polymer, and ornated with carbon quantum dots (CDs) in either poly(diallyldimethylammonium) PDDA or poly(ethyleneimine) PEI solutions. Second, we obtained high-quality labelled HPV 16 target ssDNA through classic PCR and asymmetric PCR with a nested primer labelled with Cy5, then hybridised the ssDNA on the SiNWs/SU-8/CDs platforms.The fluorescent signal of hybridised DNA was strongest on the SiNWs/SU-8 substrates, and adding CDs further enhanced the signal. The best signal intensities (4.303, 3.7) and coefficients of variation (3.12%, 2.59%) were achieved by combining HPV 16 probes co-immobilised with CDs functionalised with PDDA. Our study conclusively demonstrates the vast potential of this microarray platform for improved DNA detection.