Development towards label- and amplification-free genotyping of genomic DNA

Peptide nucleic acid (PNA) microarrays have been used for the analysis of unlabelled DNA molecules by time-of-flight secondary mass spectrometry (ToF-SIMS). PNAs were synthesised with an automated system in multi-well plates followed by the spotting full-length molecules only onto derivatised silicon surfaces using a common split-pin contact printing instrument. After DNA hybridisation, phosphate specific signals were detected and visualised by ToF-SIMS imaging. Because phosphorus is entirely missing in PNAs but is an integral part of nucleic acids, specific signals were only detected on spots at which DNA bound to complementary PNA probes. Combining PNA microarrays with ToF-SIMS detection enables the sensitive analysis of DNA or RNA targets without the need for introducing labels like fluorescent groups.