Interaction of aromatic imides with DNA. 1. Spectrophotometric and viscometric studies

Insights into the Relative DNA Binding Affinity and Preferred Binding Mode of Homologous Compounds Using Isothermal Titration Calorimetry (ITC)

“…However, the chapter will mainly focus on the naphthalene diimide series. The NDI scaffold has been used by several researchers to design therapeutically significant candidates [12][13][14][15][16][17][18][19][20] and are used in our studies as model systems to gain additional insight into the binding of "threading" intercalators to DNA. These symmetrical molecules have two substituents on either side of the intercalating moiety, thus necessitating the threading through or involvement of the side chain during binding (Figure1).…”

“…These symmetrical molecules have two substituents on either side of the intercalating moiety, thus necessitating the threading through or involvement of the side chain during binding (Figure1). [13,14,[17][18][19] In this geometry, one side chain occupies the minor groove, while the other lies in the major groove. According to some researchers, a threading intercalator has a number of potential advantages since the contact with both DNA grooves provide additional potential sites for recognition and targeting.…”

“…According to some researchers, a threading intercalator has a number of potential advantages since the contact with both DNA grooves provide additional potential sites for recognition and targeting. [12][13][14][15][16][17][18][19][20] The NDI scaffold has provided a versatile template for the design of many promising derivatives. [12][13][14][15][16][17][18][19][20] (R = ethyl-or propyl-amino side chain) Figure 1.…”

“…[26] As mentioned above, the NDI scaffold has been used by several groups to design biologically significant compounds. [12][13][14][15][16][17][18][19][20] In the current series, the quaternary amino group in each side chains is close enough (ethyl-and propyl-amino linker) to the naphthalene core group to allow electrostatic contact with the DNA. Therefore, the cationic quaternary amino groups are close to the DNA when the core ring system intercalates between DNA base pairs.…”

“…These molecules are threading intercalators in which side chains on either side of the main intercalating moiety provides the potential for specific recognition sites on the DNA. [12][13][14][15][16][17][18][19] The specific roles of a variety of substituents will be studied with a focus on identifying differential contributions from each moiety. A quaternary amino group will also be incorporated into each NDI side chain to provide electrostatic interaction with the negatively charged DNA backbone.…”