Intercalating Nucleic Acids Containing Insertions of Naphthalimide by MichaelC.Wamberg, KrzysztofWalczak 1 ), LarsAndersen, AllamA.Hassan 2 ),and ErikB.Pedersen* Nucleic Acid Center 3 ), Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, DK-5230 Odense M (phone: + 4565502555; fax: + 4566158780; e-mail: ebp@chem.sdu.dk) 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 mini- mum 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 1.48.Whencomparedtopyrene,naphthalimidewiththesamelinker-lengthgavesignificantlyhigherther- mal meltings when hybridized to DNA. 1. Introduction. – Naphthalimide (= 1H-benz[de]isoquinoline-1,3(2H)-dione) belongs to a group of promising DNA-targeting anticancer agents [1]. Bisnaphthal- ACHTUNGTRENNUNGimides Elinafide (1) [2] and Bisnafide (2) [3][4] consisting of two naphthalimide resi- dues connected by an aminoalkyl linker have been reported to inhibit topoisomerase II [5] by acting as bisintercalators in the major groove of DNA [6][7]. These symmet- rical compounds are currently undergoing clinical trials [8–10]. The most active mononaphthalimides Amonafide (3) and Mitonafide (4) [1][11] have also been reported to inhibit topoisomerase II [12][13]. They were selected for clinical trials. However, the development of Mitonafide was stopped in phase II due tolackinefficacyinthesolidtumorsthatweretested[14],while Amonafide completed clinicalphaseIandIItrials[1]. Amonafide (3)and Mitonafide (4)differonlyinthesub- stituent at C(5), having an NH 2 and a NO 2 group, respectively. The potency as antitumor agents made it interesting for us to test naphthalimide as an intercalating nucleic acid, which we define as an oligonucleotide with a covalently bound intercalator. Besides the type of aromatic compound used as intercalator, impor- tant factors to consider, when using intercalating nucleic acids for hybridization, are the structure of the backbone and the length of the linker. Ikeda et al. [15] used PNA [16] when incorporating naphthalimide as an intercalator into DNA. We chose a vicinal dihydroxy system for bulge incorporations, which we have previously described for pyr- 1 ) On leave from: Department of Organic Chemistry, Biochemistry and Biotechnology, Silesian Uni- versity of Technology, Krzywoustego 4, PL-44-100 Gliwice. 2 ) Current address: Faculty of Education, Suez Canal University, Egypt. 3 ) A research center funded by The Danish National Research Foundation for studies on nucleic acid chemical biology. # 2006 Verlag Helvetica Chimica Acta AG, Zürich Helvetica Chimica Acta – Vol. 89 (2006) 1826