Researchers at the University of British Columbia (UBC) have developed an improved system for finding sequences of DNA that can selectively bind and destroy certain RNA sequences. The new molecules could be used in ‘gene silencing’ therapies to combat cancer or HIV.

DNAzymes — short sequences of DNA with the ability to catalyse reactions such as cleavage of RNA — have been known since the mid-1990s. Unfortunately, most DNAzymes discovered so far rely on cofactors like magnesium ions, which need to be present at higher concentrations than are found inside cells. “The available magnesium inside a cell is only about 0.5 millimoles per litre, something the DNAzyme community mostly ignores,” says Dave Perrin, a bio-organic chemist at UBC. The protein-based enzyme called ribonuclease A (RNaseA) easily cleaves RNA without metal ions, but it does so indiscriminately; the advantage of DNAzymes is that they can target a given sequence.

Perrin and his team have developed a strategy to create DNAzymes that more closely resemble RNaseA. They do this by modifying nucleotides with imidazole, ammonium and guanidinium groups similar to those found in the protein. Then, using combinatorial chemistry, they build up trillions of random DNA sequences made of these modified nucleotides. A process called ‘systematic evolution of ligands by exponential enrichment’ (SELEX) is used to zero in on the DNAzymes that target specific RNA sequences.

In a recently published paper in ACS Combinatorial Science, the team showed that a sequence known as Dz12-91 could selective cleave an all-RNA target without metal ions; in this case, a sequence from HIV. Such tools could work to ‘silence’ the genes of the virus and prevent it from spreading. They could also work to block the transmission of genes associated with cancer. Perrin cautions that Dz12-91’s efficiency might not yet be high enough to become a therapeutic. Nonetheless, the team is “now in a unique position to test catalysts that will be fully operative in the low Mg2+ regime found in cells.” His team is further refining the SELEX process to recover better DNAzymes, as well as looking at how to get cells to take up the new molecules.