Synthesis and properties of a novel bridged nucleic acid analogue bearing a P3'-->N5' phosphoroamidate linkage, 5'-amino-3', 5'-BNA.

We have designed and successfully synthesized a novel bridged nucleic acid analogue with a P3'-->N5' phosphoramidate linkage, 5'-amino-3',5'-BNA. X-ray crystallographic analysis demonstrated that the 5'-amino-3',5'-BNA had C1-exo-O4-endo sugar puckering and a constrained gamma dihedral angle of 22.8 degrees. The oligonucleotides containing 5'-amino-3',5'-BNA exhibited strong binding affinity towards complementary strands. In addition, the 5'-amino-3',5'-BNA oligonucleotide was easily hydrolyzed at its phosphoramidate linkage under mild acidic conditions.