Molecular recognition of DNA by rigid [n]-polynorbornane-derived bifunctional intercalators: synthesis and evaluation of their binding properties

We have exploited the concept of multivalency in the context of DNA recognition, using novel chemistry to synthesize a new type of bis-intercalator with unusual sequence-selectivity. Bis-intercalation has been observed previously, but design principles for de novo construction of such molecules are not known. Our compounds feature two aromatic moieties projecting from a rigid, polynorbornane-based scaffold. The length and character of the backbone as well as the identity of the intercalators were varied, resulting in mono- or divalent recognition of the double helix with varying affinity. Our lead compound proved to be a moderately sequence-selective bis-intercalator with an unwinding angle of 27 and a binding constant of about 8 M. 9-Aminoacridine rings were preferred over acridine carboxamides or naphthalimides, and a rigid [3]-polynorbornane scaffold was superior to a [5]-polynorbornane. The flexibility of the linker connecting the rings to the scaffold, although less influential, could affect the strength and character of the DNA binding.

Electrostatic complex of didodecyldimethylammonium and DNA: Langmuir monolayer, Langmuir–Blodgett film and dye recognition at air/water interface

DNA–didodecyldimethylammonium (DNA–DDDA) electrostatic complex was prepared and characterized through Fourier transformation infrared (FT-IR), 1H NMR and circular dichroism (CD) spectroscopy. When the dye molecule aqueous solutions were used as the subphase, the interaction between three dye molecules, acridine orange (AO), ethidium bromide (EB) and 5,10,15,20-tetrakis(4-N-methylpyridyl)porphine tetra(p-toluenesulfonate) (TMPyP) and the complex at air/solution interface were investigated through the surface pressure–area (π–A) isotherms, Brewster angle microscopy and UV-Vis spectroscopy, respectively. Our investigation indicates that the interaction capabilities of the three dyes to DNA–DDDA complex are different and present an order of TMPyP>AO>EB. For the interaction forms, we believe that TMPyP intercalates into the double helix of DNA, and AO adsorbs onto the surface of the DNA. As for EB, the measured signal is too weak to give a definite interaction form in the present experiment.