Intercalating Nucleic Acids with Pyrene Nucleotide Analogues as Next‐Nearest Neighbors for Excimer Fluorescence Detection of Single‐Point Mutations under Nonstringent Hybridization Conditions

Fluorescence and hybridization specificity is reported for intercalating nucleic acids (INAs), which are here oligodeoxynucleotides (ODNs) synthesized with insertions using (S)‐1‐[bis(4‐methoxyphenyl)(phenyl)methoxy]‐3‐[(pyren‐1‐yl)methoxy]propan‐2‐ol phosphoramidites. It is shown that an INA with two insertions placed as next‐nearest neighbors can be used for discrimination between nucleic acids and their single‐point mutants. Quenching of an excimer band at 480 nm is observed upon hybridizing to a complementary sequence, whereas the excimer band is present when the nucleobase pair between the two pyrene moieties is mismatched. It is the first example of a solution based on fluorescence detection of single‐point mutants that uses excimer formation and does not rely on stringent hybridization conditions. Furthermore, it is shown that INAs with pyrene insertions retain their sequence specificity in thermal melting.