Threading Polyintercalators with Extremely Slow Dissociation Rates and Extended DNA Binding Sites

Abstract

The development of small molecules that bind DNA sequence specifically has the potential to modulate gene expression in a general way. One mode of DNA binding is intercalation, or the insertion of molecules between DNA base pairs. We have developed a modular polyintercalation system in which intercalating naphthalene diimide (NDI) units are connected by flexible linkers that alternate between the minor and major grooves of DNA when bound. We recently reported a threading tetraintercalator with a dissociation half-life of 16 days, the longest reported to date, from its preferred 14 bp binding site. Herein, three new tetraintercalator derivatives were synthesized with one, two, and three additional methylene units in the central major groove-binding linker. These molecules displayed dissociation half-lives of 57, 27, and 18 days, respectively, from the 14 bp site. The optimal major groove-binding linker was used in the design of an NDI hexaintercalator that was analyzed by gel-shift assays, DNase I footprinting, and UV-visible spectroscopy. The hexaintercalator bound its entire 22 bp binding site, the longest reported specific binding site for a synthetic, non-nucleic acid based DNA binding molecule, but with a significantly faster dissociation rate compared to the tetraintercalators.

Developing Bivalent Ligands to Target CUG Triplet Repeats, the Causative Agent of Myotonic Dystrophy Type 1

“…Importantly, it was found that the chloro- and methoxy-groups in 1 could be replaced with a 2- or 4-carboxamido group (see 2 and 3 in Figure 1, respectively) without reducing its affinity for CUG repeats or its inhibition of the MBNL1·CUG complex. Although modeling was not carried out, it appeared that dimeric ligands interconnected at the 2- and 4-positions would have the linker and triaminotriazine recognition units located on the same or the opposite sides of the acridine unit, thereby likely requiring a non-threading or threading 54 mechanism of binding, respectively. This simple analysis suggested that these two isomeric dimers would significantly increase the diversity of our library, especially when considering the ultimate RNA-ligand complex.…”

Exploiting the interactions of aromatic units for folding and assembly in aqueous environments

“…Not mentioned here is our extensive work with DNA-binding oligo-NDI molecules. 74-76 Considering the complex nature of aromatic interactions, the predictable stacking geometry of DAN and NDI in water provides a well-defined recognition motif to achieve higher order architectures. Because the stacking of electrostatically complementary aromatic units is driven in part by polar solvents, the construction of aromatic foldamers and more complex aromatic assemblies in water can be more rationally designed.…”

A DNA-NDI Hybrid to Efficiently Detect Histone in Parts per Trillion (ppt) Level

“…To this end, naphthalene diimides (NDI) with appropriate functionalization were found to be an excellent probe to intercalate with DNA double strands . Several detailed studies on NDI‐DNA interaction have been reported by Iverson and Wilson . A direct consequence of DNA‐binding by all these NDI derivatives is the drastic fall in fluorescence quantum yield of NDIs .…”

“…Several detailed studies on NDI‐DNA interaction have been reported by Iverson and Wilson . A direct consequence of DNA‐binding by all these NDI derivatives is the drastic fall in fluorescence quantum yield of NDIs . We envisioned that this quenching of emission upon binding with DNA can be utilized to create new sensor for proteins capable of binding with DNA, such as histone.…”