A DNA tetrahedral structure-mediated ultrasensitive fluorescent microarray platform for nucleic acid test

Abstract

Microarrays are key platforms for biomolecule detection owing to their parallelizability and amenability for high-throughput. However, conventional fluorescent microarrays still suffer from low specificity and sensitivity, therefore are unsuitable for detection of low abundance nucleic acids. In this study, we demonstrate a universal microarray platform with high specificity and ultra-sensitivity for fluorescent detection of DNA and micro RNA (miRNA), which employs a DNA tetrahedral structured probe (DTSP) together with a hybridization chain reaction (HCR) based signal amplification technique. By precisely modulating the number of base pairs on each tetrahedron side, we developed three different sized DTSPs: 17 base pairs, 26 base pairs, and 37 base pairs (DTSP-17, DTSP-26 and DTSP-37, respectively). A low detection limit of 10 aM was obtained by DTSP-26, notably much lower than detection limits of prior methods. Furthermore, our microarray platform can distinguish single base DNA mismatches and thus exhibits single nucleotide specificity. Lastly, our microarray platform can be implemented for miRNA detection, as we demonstrate in a mimic medium, demonstrating potential for its use in clinical diagnosis.