A Programmed DNA Marker Based on Bis(4-ethynyl-1,8-naphthalimide) and Three-Methane-Bridged Thiazole Orange.

Two large conjugated naphthalimide derivatives with or without three-methane-bridged thiazole orange (TO3; i.e., compounds 1 a and 2 a, respectively) were designed and synthesized. The fluorescence of the naphthalimide group in compound 1 a at λ=532 nm initially decreased and that for the TO3 group at λ=655 nm increased sequentially upon adding Salmon testes (St) DNA. In contrast, without the TO3 group, the fluorescence intensity of compound 2 a monotonously decreased in response to the addition of DNA. The non-monotonic change in the fluorescence for compound 1 a could be divided into two linear sections with two different wavelengths in the range of 0<Rb/1 a <1.2 and 1.2 <Rb/1 a <6.0 (Rb/1 a =[base pair]/[1 a]). Thus, compound 1 a can be regarded as a programmed responding molecule for DNA, which can semi-quantitatively determine the concentration of DNA over a large concentration range from the standard fluorescence curve of compound 1 a at different wavelengths when bound with DNA. Furthermore, the binding modes of compounds 1 a and 2 a with StDNA were studied by using CD spectroscopy and melting temperature (Tm ) testing. The results showed that compound 1 a interacts with StDNA through multi-interactions including weak intercalation, weak minor groove binding, and inter-dye interactions, whereas compound 2 a bound with DNA through simultaneous intercalation and minor groove binding.