Triplex DNA: The next platform for oligonucleotide drug development

Therapeutic oligonucleotides have started to deliver on their promise to treat a myriad of diseases with >10 oligonucleotides recently approved for clinical use.

They act by hybridising to mRNA and modulating protein expression levels inside cells, through antisense or RNAi mechanisms.

However, a strategy with more therapeutic benefit would be to utilise oligonucleotides that hybridise with genomic DNA directly and prevent the expression of specific genes at the transcriptional level.

Since there are just two copies of genomic DNA per diploid cell this would substantially reduce oligonucleotide dose, limiting off-target binding and unwanted toxicity. However, until now the efficacy of these molecules has been hampered by their low binding affinity at physiological pH.

We have recently overcome this problem by using oligonucleotides containing a commercially available nucleobase: 6-amino-5-nitropyridin-2-one.

The nucleobase not only enables stable and selective triplex formation at physiological pH but can also be incorporated into oligonucleotides by primer extension.

This will enable the enzymatic assembly of our modified oligonucleotides on a solid support and facilitate their assembly, in vitro screening and subsequent in vivo validation.

Consequently, the goal of this project is to: (i) develop a pipeline of these technologies to produce bioactive TFOs capable of mediating gene silencing in living cells, and (ii) to validate the pipeline by demonstrating the targeted knockdown of the c-myc oncogene.

This will put in place expertise and infrastructure to seek funding to exploit our new oligonucleotide platform for the development of drugs targeted to specific diseases and microbial infections.