Thermal Stability of Modified i‐Motif Oligonucleotides with Naphthalimide Intercalating Nucleic Acids

In continuation of our investigation of characteristics and thermodynamic properties of the i‐motif 5′‐d[(CCCTAA) 3 CCCT)] upon insertion of intercalating nucleotides into the cytosine‐rich oligonucleotide, this article evaluates the stabilities of i‐motif oligonucleotides upon insertion of naphthalimide (1 H ‐benzo[ de ]isoquinoline‐1,3(2 H )‐dione) as the intercalating nucleic acid. The stabilities of i‐motif structures with inserted naphthalimide intercalating nucleotides were studied using UV melting temperatures ( T m ) and circular dichroism spectra at different pH values and conditions (crowding and non‐crowding). This study indicated a positive effect of the naphthalimide intercalating nucleotides on the stabilities of the i‐motif structures compared to the wild‐type structure which is in contrast to a previous observation for a pyrene‐intercalating nucleotide showing a decrease in T m values.