DNG cytidine: synthesis and binding properties of octameric guanidinium-linked deoxycytidine oligomer

The synthesis of guanidinium-linked cytidyl oligomer (DNG-C(8)), a cationic DNA analog, and the corresponding cytidine monomers is described. The DNG monomer synthesis was streamlined to produce a shorter route to the final monomer than previously reported for thymidine and subsequent solid-phase synthesis produced an octameric cytidyl DNG strand. Because octameric deoxyguanosine would be used as the complementary strand in our studies, it was necessary to investigate guanosine self-association. Singular value decomposition was used to mathematically deconvolve the spectral data and confirm the presence of transitions due to DNA-G(8) self-association. Job plots show the binding stoichiometry of DNG-C(8) with DNA-G(8) to be 1:1. Thermal denaturation studies of the DNG-C(8).DNA-G(8) duplex established a T(m) > or = 90 degrees and a DeltaG degree = -13.3 kcal mol(-1), indicating the DNG-C(8).DNA-G(8) duplex is over 1000 times more stable than that of DNA-C(8).DNA-G(8).