Label-free DNA hybridization detection and single base-mismatch discrimination using CE-ICP-MS assay

Abstract

Detecting a specific DNA sequence and discriminating single base-mismatch is critical to clinical diagnosis, paternity testing, forensic sciences, food and drug industry, pathology, genetics, environmental monitoring, and anti-bioterrorism. To this end, capillary electrophoresis (CE) coupled with the inductively coupled plasma mass spectrometry (ICP-MS) method is developed using the displacing interaction between the target ssDNA and the competitor Hg²⁺ for the first time. The thymine-rich capture ssDNA 1 is interacted with the competitor Hg²⁺, forming an assembled complex in a hairpin-structure between the thymine bases arrangement at both sides of the capture ssDNA 1. In the presence of a target ssDNA with stronger affinity than that of the competitor Hg²⁺, the energetically favorable hybridization between capture ssDNA 1 and the target ssDNA destroys the hairpin-structure and releases the competitor as free Hg²⁺, which was then read out and accurately quantified by CE-ICP-MS assay. Under the optimal CE separation conditions, free Hg²⁺ ions and its capture ssDNA 1 adduct were baseline separated and detected on-line by ICP-MS; the increased peak intensity of free Hg²⁺ against the concentration of perfectly complementary target ssDNA was linear over the concentration range of 30–600 nmol L⁻¹ with a limit of detection of 8 nmol L⁻¹ (3s, n = 11) in the pre-incubated mixture containing 1 μmol L⁻¹Hg²⁺ and 0.2 μmol L⁻¹ capture ssDNA 1. This new assay method is simple in design since any target ssDNA binding can in principle result in free Hg²⁺ release by 6-fold Hg²⁺ signal amplification, avoiding oligonucleotide labeling or assistance by excess signal transducer and signal reporter to read out the target. Due to element-specific detection of ICP-MS in our assay procedure, the interference from the autofluorescence of substrata was eliminated.