DNA threading intercalation: building sequence-specific linear rigidified and cyclic bisintercalators

The threading polyintercalators are based on a 1,4,5,8-naphthalenetetracarboxylic diimide (NDI) unit that binds DNA via threading intercalation with two imide groups situated in different DNA grooves. In order to extend this strategy to bind DNA with higher affinity and more programmable specificity, it was envisioned that the linkers connecting the NDI units had to be rigidified. Thus a rigid, spiro-cyclic linker was designed and synthesized in the context of a bisintercalator, C1. The new linker has several sites for possible addition of functional groups as recognition elements. DNAse I footprinting results showed that C1 has a higher binding affinity (K[subscript D] ~ 10⁻⁷ M) toward 5'-GGTACC-3' sequence than the previously developed dimer G₃K, which has a flexible linker. NMR structural analysis of the C1-d(CGGTACCG)₂ complex has revealed the versatility of threading polyintercalation based on NDI moieties by verifying the binding of the C1 linker in the minor groove with two NDI units intercalating between GpG steps. The observed binding specificity of C1 is the result of interplay of different factors, such as overall linker length, electrostatic and hydrophobic complementarity to their preferred grooves. The fact that C1 and G₃K can target the same DNA sequence via different grooves, but with different linker structures, prompted us to explore the possibility of creating cyclic bisintercalating molecules. The first example, CBI-1, has been efficiently synthesized through a solid phase synthesis strategy, in which Gly₃Lys, a major groove recognition element for d(GGTACC)₂, was linked at one side and ([Beta]-Ala)₃Lys, a perfect match for a 4-base pair span in the minor groove, was connected on the other side. A dissociation kinetics study on poly(dGdC) indicated a slow dissociation process for CBI-1. Data from DNAse I footprinting and NMR structural studies confirmed that CBI-1 forms a tightly bound complex with DNA d(CG GTAC CG)₂, in which two NDI units intercalate between GC pairs, with linkers interacting with the major and minor grooves simultaneously. CBI-1 also exhibits improved sequence specificity compared to the linear dimer G₃K by only binding 5'-GGTACC-3' sequence. All the results demonstrate that cyclic threading intercalation is a new and effective approach to specifically target DNA sequences.