When most people hear "dye," they likely think of colorful fabrics and Easter eggs. But for synthetic chemist and NYU Abu Dhabi Postdoctoral Associate Matthew O'Connor, dyes are a tool to study genetic development in organisms.

At NYUAD's Dore Laboratory, a multidisciplinary research group studying complex biological systems, O'Connor creates synthetic dyes that bind to molecules called morpholinos. Morpholinos can inhibit gene expression in cells, a process researchers call "gene knockdown."

Normally, molecules of ribonucleic acid (RNA) are responsible for protein synthesis in cells. These proteins are one of the ways in which genes are expressed in biological organisms. Morpholinos insert themselves into this process, blocking the RNA from directing the formation of proteins and thereby preventing the expression of certain genetic characteristics.

Morpholinos have enabled researchers to identify the role those proteins play in development. Normally, these molecules act immediately. But when bound to the dye molecules that O'Connor synthesizes, morpholino activity shuts off. These "caged" morpholinos can then be released when light is applied to the photosensitive dye molecules. The process enables researchers to observe the effects of gene knockdown at different stages of development.

In zebrafish, for example, if the gene for glutamate decarboxylase (GAD1) is surpressed early in the fish's development, the change will lead to fatal jaw and brain malformations. But by employing dye-caged morpholinos to knock down the GAD1 gene later in development, only non-lethal seizures are observed.

While his colleagues study the biological mechanisms behind these effects, O'Connor is developing a simpler, higher-yield process for synthesizing dye molecules. "From a synthetic standpoint," he said, "there are certain craft challenges" left to address.

This article originally appeared in NYUAD's 2013-14 Research Report (13MB PDF).