A physico-chemical study of triple helix formation by an oligodeoxythymidylate with N3'->P5' phosphoramidate linkages

Non-denaturing gel retardation assay, DNA melting experiments and FTIR spectroscopy were used to characterize the triple helix formed by a 15mer 2'-deoxythymidylate with N3'-->P5' phosphoramidate linkages with its target sequence. The results indicate that: (i) the pentadecadeoxythymidylate with phosphoramidate linkages [dT(15)(np)] is highly potent to form a triple helix with a dT(15).dA(15) target duplex through Hoogsteen base-pairing; (ii) it forms a dT(15)(np).dA(15)xdT(15)(np) tripler with the single-stranded oligo-2'-deoxyadenylate (dA(15)) without detectable double-helical intermediate; (iii) it does not only form a triple helix on the dT(15).dA(15) target duplex, but also partially displaces the dT(15) strand from the dT(15).dA(15) duplex to form a dT(15)(np).dA(15)xdT(15)(np) complex.