Some DNA-Binding Enzymes Prefer Fake DNA to the Real Thing

They’re not DNA molecules, but they have the curves and folds they need to fool DNA-binding enzymes. If these DNA mimics can be twisted just so, they may turn out to be useful decoys, capable of misleading the enzymes deployed by human immunodeficiency virus (HIV) and other viruses.

A class of DNA mimics consisting of foldamers, or helical aromatic oligomers, is being tweaked and molded by scientists based at Ludwig-Maximilians-Universitaet (LMU) in Munich. These scientists, led by Ivan Huc, Ph.D., a professor of pharmacy, report that in their hands, foldamers are being shaped into novel inhibitors of pharmacologically or therapeutically relevant protein–DNA interactions.

The Huc team’s latest work appeared in the journal Nature Chemistry, in an article entitled “Single Helically Folded Aromatic Oligoamides That Mimic the Charge Surface of Double-Stranded B-DNA.” This article describes a synthetic molecule that not only folds into a helical structure, but also adjusts its shape in subtle ways when it is adorned with various substituents.

“…we report the design, synthesis and structural characterization of aromatic oligoamides that fold into single helical conformations and display a double helical array of negatively charged residues in positions that match the phosphate moieties in B-DNA,” wrote the article’s authors. “These molecules were able to inhibit several enzymes possessing non-sequence-selective DNA-binding properties, including topoisomerase 1 and HIV-1 integrase, presumably through specific foldamer–protein interactions….”

Unlike naturally occurring, DNA-mimicking proteins, the synthetic foldamers designed by Dr. Huc and colleagues can be easily tuned. Besides allowing experimenters to imitate the shape of natural DNA, these foldamers can be adjusted to present certain distributions of negative charge. In the current study, foldamers imitated DNA so convincingly that they acted as a decoy for two DNA-binding enzymes, including the HIV integrase, which readily bind to it and are essentially inactivated.

Dr. Huc and colleagues, however, added that their foldamers worked only with non-sequence-selective DNA-binding enzymes. “Sequence-selective enzymes,” the scientists admitted, “were not inhibited.”

Nonetheless, the current study addresses a crucial question—whether foldamers can effectively compete for the enzymes in the presence of their normal DNA substrate. “If the enzymes still bind to the foldamer under competitive conditions, then the mimic must be a better binder than the natural DNA itself,” Dr. Huc explained. And indeed, the study demonstrated that the HIV integrase binds more strongly to the foldamer than to natural DNA.

“Although initially designed to resemble DNA, the foldamer owes its most useful and valuable properties to the features that differentiate it from DNA,” Dr. Huc emphasized.

The new paper builds on advances described in two previous publications in Nature Chemistry already published this year. In the first of these papers, Dr. Huc and his colleagues developed a pattern of binding interactions required to enable synthetic molecules to assume stable forms similar to the helical backbones of proteins. In the second, they worked out the conditions required to allow their synthetic helix to be appended to natural proteins during synthesis by cellular ribosomes.

In the current study, Dr. Huc and his colleagues have focused on enzymes that are generically capable of binding to DNA, irrespective of its base sequence. However, it may also be possible to use the foldamer approach to develop DNA mimics that can block the action of the many important DNA-binding proteins whose functions depend on the recognition of specific nucleotide sequences. “Such modular and synthetically accessible DNA mimics provide a versatile platform to design novel inhibitors of protein–DNA interactions,” the current study concluded.