Ultra-specific detection of nucleic acids by intramolecular referencing

Nucleic acid detection has to be sensitive and specific. Especially with respect to (epigenetic) modifications, methods involving molecular amplification can be blind to subtle variations. Single-molecule methods are becoming increasingly promising for direct and specific nucleic acid detection. Recently, we showed that single-molecule binding times of a short oligonucleotide can report on the subtle influence of cytosine modifications on the binding time when the binding time is compared to an internal reference to account for environmental variations such as temperature changes. Here, we advance the assay by also integrating the imager strand into the DNA origami nanostructure on which target and reference strands are arranged. This full molecular integration of the assay can increase the speed and the robustness of single-molecule nucleic acid detection while improving specificity.