Information Derived from Cluster Ions from DNA-Modified Gold Nanoparticles under Laser Desorption/Ionization: Analysis of Coverage, Structure, and Single-Nucleotide Polymorphism

In this study, we employed laser desorption/ionization mass spectrometry (LDI-MS) to explore the interactions between thiolated DNA (HS-DNA) and gold nanoparticles (Au NPs). Under nanosecond-pulsed laser irradiation (Nd:YAG, 355 nm), the efficiency of Au cluster ion formation from the Au NPs decreased in the presence of HS-DNA. At the optimal laser power density (2.1 × 104 W cm–2), the intensity of the Au cluster signal was sensitive to the DNA coverage and the length of the DNA strands on the Au NPs (diameter: 13 nm). Using this information, we developed a simple and specific DNA sensor that operates through analysis of the Au cluster ions formed from the fragmentation of Au NPs under LDI conditions. The coverage of the thiolated probe DNA (pDNA) on the Au NPs increased in the presence of its perfectly matched DNA (DNApm). As a result, the intensity of the signal of Au cluster ions decreased upon increasing the concentration of DNApm. Coupling these pDNA–Au NPs with LDI-MS allowed the detection of DNApm at concentrations down to the nanomolar regime. Furthermore, we applied this pDNA–Au NP probe to the detection of single-nucleotide polymorphisms (SNPs) of the Arg249Ser unit in the TP53 gene. To the best of our knowledge, this paper provides the first example of the use of LDI to analyze the coverage and structure of DNA strands on metal NPs. This simple, rapid, high-throughput detection system, based on the coupling of biofunctional Au NPs with LDI-MS, appears to hold great practicality for bioanalyses of oligonucleotides and proteins.