Novel Applications of DNA and RNA Molecules Identified by In Vitro Selection

Using molecular biology techniques, it is possible to create libraries of 100 trillion random DNA or RNA molecules in a milliliter of buffer. These single-stranded molecules fold into 100 trillion shapes. By chance, some of these shapes can do amazing things, far beyond our current ability to predict or engineer. The Maher lab is exploiting this powerful in vitro selection technique to identify nucleic acid sequences that might inhibit gene-regulatory proteins or sneak into specific intracellular compartments without help from viruses, proteins or other added chemicals.

It was once believed possible that all genes were regulated by the binding of RNA molecules to the DNA double helix. This model is not generally true, but it provides a foundation to explore whether artificial RNA molecules can be selected for the ability to control genes in cells. The Maher lab is studying several approaches to this question.

The historical observation that transcription factor IIIA (TFIIIA) can bind both DNA and RNA made Maher's team curious to determine if artificial tight-binding RNAs could be selected for other transcription factors. Expression of such RNA inhibitors in cells might down-regulate genes that respond to the target transcription factor. As a model, the Maher lab studied small RNAs that the team selected for binding and inhibition of the NF-kappaB transcription factor. Inhibition of this protein could be of value against HIV-1 replication and inflammation and in enhancing tumor cell suicide after chemotherapy, all processes involving NF-kappaB.

Ongoing studies seek to identify potential RNA aptamer inhibitors for hundreds of human transcription factors and to explore transcription factor inhibition in mammalian cells. Understanding how RNA molecules fold to imitate DNA will provide insights into detailed computational prediction of RNA folding.

In new work, the lab is developing methods to select nucleic acid sequences capable of homing to intracellular compartments. Such aptamers might direct cargo for therapeutic or engineering purposes.