Threading DNA Polyintercalators

While studying the electron-deficient, aromatic 1,4,5,8-napthalenetetracarboxylic diimide(NDI) group and its role in stacking as an aedamer, we learned that it could also be utilized as a DNA intercalator. Based on this observation, we developed a new class of polyintercalating molecules by using a flexible linker to fix NDI units in a head-to-tail fashion. The NDI units are considered to be threading polyintercalators, in which the placement of the linkers alternates between the major and minor grooves of the DNA. This is important, because this realizes the potential to bind specific sequences of DNA, which could potentially be used to further research in cancer therapy, as well as anti-bacterial drugs.
After screening a combinatorial library of different peptide linkers, we discovered that we could design bisintercalators that would selectively bind to specific dG-dC rich sequences of DNA. This also lead to the development of a record-breaking octakis-intercalation molecule, which contained eight intercalating NDI units that was capable of preferentially binding to a 16 base pair (bp) sequence of dG-dC rich DNA.
Further investigation in NMR structural analysis revealed a bisintercalator that would bind specific sequences of DNA d (5’-CG|GTAC|CG-3’) through a binding mode which places the linker (Lys-(Gly)3) in the major groove. A second derivative, containing a Lys-(β-Ala)3 linker, specifically bound to a similar sequence of DNA d(5’-CG|ATAA|GC-3’), however, it proceeded to place the linker in the minor groove. By altering the peptide linkers between the NDI units, we can tune the bisintercalator’s mode of binding to place the linker in either the major or minor groove of DNA. These results enable the creation of DNA polyintercalators that contain groove-specific linkers, which are ideal for the threading intercalation of our molecules.
More recently, we have exploited this programmability in the design of a tetraintercalator that alternates peptide linkers in a pattern specific to a minor groove, major groove, minor groove threading of the molecule (shown below). This allows for the sequence specific binding to a 14 bp site on DNA.

We have also developed a system where we use a more rigid, functionalizable, tricyclic spiro linker for a bisintercalator. This system was designed in such a way that because of the increased rigidification of the linker, the molecule will bind with higher affinity and selectivity to a specific sequence of DNA d(5’-CG|GTAC|CG-3’). This system also shows selectivity for binding in the minor groove of DNA. A topic of key interest, is that this rigidified dimer specifically binds the same sequence of DNA that the dimer with Lys-(Gly)3 linker binds, however the binding modes of the two prefer opposite grooves.
Therefore, it isn’t without reason that we could potentially create cyclic bisintercalating molecules, such that one linker is specific to the minor groove, while the other is specific to the major groove. The capability of this ongoing project continues to further our knowledge of the binding modality of differing NDI intercalators with DNA, as well as fostering potential uses in anti-cancer and anti-bacterial drugs.