Development of Functional Bridged Nucleic Acids, 5'-amino-BNAs, for Rapid and Convenient DNA Sensing

Abstract

Conventional DNA-templated organic synthesis (DTS) involves hybridization of two oligonucleotide probes with each other or with a template strand, followed by a bond-forming reaction between reactive substituents conjugated on each strand. Bond cleavage reactions promoted by hybridization of DNA templates comprise a new class of DTS and should be useful for novel genome technologies. Here, we report the site-specific bond cleavage of the oligonucleotide probe triggered by hybridization with a dsDNA template. Oligonucleotides bearing a P3'-N5' phosphoramidate linkage are well known to undergo P-N bond cleavage under acidic conditions. We found that the acid-mediated P-N bond cleavage is significantly accelerated by sequence-selective triplex formation with the dsDNA template. By incorporation of a fluorophore and a quencher into the oligonucleotide probe, we successfully achieved sequence-specific dsDNA sensing.