Deoxynucleic guanidine (DNG), a DNA analogue in which positively charged guanidine replaces the phosphodiester linkages, tethering to Hoechst 33258 fluorophore by varying lengths has been synthesized. A pentameric thymidine DNG was synthesized on solid phase in the 3' --> 5' direction that allowed stepwise incorporation of straight chain amino acid linkers and a bis-benzimidazole (Hoechst 33258) ligand at the 5'-terminus using PyBOP/HOBt chemistry. The stability of (DNA)(2)(.)DNG-H triplexes and DNA(.)DNG-H duplexes formed by DNG and DNG-Hoechst 33258 (DNG-H) conjugates with 30-mer double-strand (ds) DNA, d(CGCCGCGCGCGCGAAAAACCCGGCGCGCGC)/d(GCGGCGCGCGCGCTTTTTGGGCCGCGCGCG), and single-strand (ss) DNA, 5'-CGCCGCGCGCGCGAAAAACCCGGCGCGCGC-3', respectively, has been evaluated by thermal melting and fluorescence emission experiments. The presence of tethered Hoechst ligand in the 5'-terminus of the DNG enhances the (DNA)(2)(.)DNG-H triplex stability by a DeltaT(m) of 13 degreesC. The fluorescence emission studies of (DNA)2.DNG-H triplex complexes show that the DNG moiety of the conjugates bind in the major groove while the Hoechst ligand resides in the A:T rich minor groove of dsDNA. A single G:C base pair mismatch in the target site decreases the (DNA)(2)(.)DNG triplex stability by 11 degreesC, whereas (DNA)(2)(.)DNG-H triplex stability was decreased by 23 degreesC. Inversion of A:T base pair into TA base pair in the center of the binding site, which provides a mismatch selectively for DNG moiety, decreases the triplex stability by only 5-6 degreesC. Upon hybridization of DNG-Hoechst conjugates with the 30-mer ssDNA, the DNA(.)DNG-H duplex exhibited significant increase in the fluorescence emission due to the binding of the tethered Hoechst ligand in the generated DNA(.)DNG minor groove, and the duplex stability was enhanced by DeltaT(m) of 7 degreesC. The stability of (DNA)2-DNG triplexes and DNA(.)DNG duplexes is independent of pH, whereas the stability of (DNA)(2)(.)DNG-H triplexes decreases with increase in pH.