Modulation of DNA triplex stability through nucleobase modifications

Spermine conjugation at N-4 of 5-Me-dC in oligonucleotides (sp-ODNs) reduces the net negative charge and these as HG strands form triplexes with foremost stability at neutral pH (7.3), in contrast to unmodified ODNs which form stable triplexes at pH 5.5. The stability of sp-ODN triplexes is shown to arise from improved association with duplex caused by electrostatic interaction of polycationic spermine sidechain with anionic phosphate backbone of DNA and N3 protonation is not a pre-requirement for triplexes constituted from sp-ODNs. The amplification of electrostatic component of interaction can be achieved by transformation of primary amino group of polyamines to corresponding guanidinium functions leading to improved binding and stabilization of DNA triplexes even at pH 7.0. %-Amino-dU ODNs are shown to be compatible as a central strand in formation of triplexes in which pyrimidine would be in the middle position of a triad.