Enhanced nucleotide mismatch detection based on a 3D silicon nanowire microarray

Abstract

We explored the capacity of a nanostructured silicon substrate to be used in microarray technology for nucleotide mismatch detection. The aim of our study was to investigate single nucleotide polymorphisms (SNPs) with pathological significance within breast cancer 1, early onset gene (BRCA1). Herein, we report an easy, one step and low cost method to obtain a layer of silicon nanowires (SiNWs) as a starting point for the development of a microarray platform. The experimental analyses indicate that, in comparison with the usually employed commercial glass support, the new microarray support significantly improves the hybridization signal quality and also the sensitivity of SNP detection. More accurately, the developed platform allows a statistically significant discrimination of the hybridization signal intensities when the DNA probes differ by the presence of one mismatch in a selected position. These achievements are attributed to the facilitated target molecules' access to the attached probes due to the three-dimensional (3D) architecture of the support and to the antireflective properties of the SiNWs substrate.