Label-free quantitative detection of nucleic acids based on surface-immobilized DNA intercalators

Abstract

We present a label-free biosensor for the detection of nucleic acids from PCR amplicons based on the surface plasmon resonance (SPR) with novel DNA intercalators. These intercalators can specifically bind to double-stranded DNA (ds-DNA), allowing ds-DNA to be quantitatively monitored by angle shifts of SPR following mass changes on the SPR sensor surface. Pyrenyl intercalator compounds that were synthesized consisted of pyrenyl groups as intercalating moieties, ethylene glycol hexamer linkers that resist non-specific binding events and thiol groups that formed self-assembled monolayers (SAMs) on a gold substrate. Also, hydroxyl group terminated compound instead of pyrenyl group was synthesized to ensure adequate separation between adjacent pyrene groups. The molar concentration ratio of mixed SAMs on SPR sensor surface was selected for maximum mass sensitivity on the basis of experimental results from various mixed ratios. Finally, we investigated the sensor responses due to intercalations on various concentrations of applied pure ds-DNA and demonstrated the capability for the analysis of PCR amplicons in the reaction product mixtures without any purification process. These results show that the proposed label-free biosensor devised based on strong binding interactions between DNA intercalators and base pairs of any ds-DNA can quantitatively analyze ds-DNA in accordance. (C) 2016 Elsevier B.V. All rights reserved.