Physicochemical Properties of Phosphoramide <i>N</i>-Benzimidazole Oligonucleotides in the Presence of Cosolvents

Phosphoramide benzoazole oligonucleotides (PABAOs) are a recently developed class of phosphate-modified nucleic acid derivatives. In this study, we investigated the physicochemical properties of <i>N</i>-benzimidazole oligodeoxyribonucleotides and their duplexes with complementary DNA in the presence of low-molecular-weight cosolvents. For this purpose, we analyzed the effects of ethanol (EtOH), ethylene glycol (EG), glycerol, trifluoroethanol (TFE), and dimethyl sulfoxide (DMSO) on the structure, dynamics, hybridization properties, and solvation of PABAOs. The presence of 20% cosolvents did not alter the secondary structures of native or modified oligonucleotides and duplexes, as confirmed by circular dichroism data. Molecular dynamics simulations revealed structural similarities between the native and modified duplexes as well as hydrogen bond formation with water. The addition of cosolvents reduced differences in the thermal stability of native and modified duplexes, which was most pronounced in ethanol and DMSO. The <i>N</i>-benzimidazole moiety altered the hydrophobic interactions during DNA duplex formation. These findings advance our understanding of nucleic acid interactions and will facilitate the application of PABAOs in biotechnology and biomedicine.