Tethered naphthalene diimide intercalators enhance DNA triplex stability

Naphthalene diimides function as effective intercalators and when tethered to the 5'-terminus of a pyrimidine-rich oligonucleotide can contribute significantly to the overall stabilization of DNA triplexes. This stabilization can be further enhanced by alterations to the linker tethering the DNA sequence and the intercalator. Less flexible linkers, and particularly one with a phenyl ring present, appear to permit the stabilization afforded by the bound intercalator to be transferred more effectively to the three-stranded complex. The conjugate containing the phenyl linker exhibits a T(M) value that is increased by 28 degrees C relative to the unconjugated triplex. That the linker itself contributes to the observed stabilization is clear since introduction of the phenyl linker increases the observed T(M) by 11 degrees C relative to a simple flexible linker.