2′,4′-BNA bearing a 2-pyridine nucleobase for CGbase pair recognition in the parallel motif triplex DNA

Abstract

We succeeded in the synthesis of triplex-forming oligonucleotides (TFOs) that contain a deoxyribonucleotide (Py) bearing a 2-pyridine nucleobase or the 2′,4′-BNA congener (Py^B). By UV melting experiments, it was found that 2-pyridine was a very promising nucleobase for the sequence-selective recognition of a CG base pair within double-stranded DNA (dsDNA) in a parallel motif triplex. Moreover, Py^B in TFOs showed stronger affinity to a CG base pair than Py with further increase in the selectivity. Using TFO including multiple Py^B units, triplex formation with dsDNA containing three CG base pairs was observed.