Intercalating Nucleic Acids Containing Insertions of Naphthalimide

Abstract

In a study of linker-length dependence, we evaluated naphthalimide (= 1H-benzo[de]isoquinoline-1,3(2H)-dione) and 4-bromonaphthalimide as intercalating nucleic acids. We used a vicinal dihydroxy system when incorporating the six different naphthalimide monomers into DNA, and found the minimum linker-length to be five C-atoms. With this length of the linker, naphthalimide was discriminating between DNA and RNA – stabilizing DNA, while destabilizing RNA. Furthermore, naphthalimide showed universal base character by hybridizing to the four natural bases with a range as narrow as 1.4°. When compared to pyrene, naphthalimide with the same linker-length gave significantly higher thermal meltings when hybridized to DNA.