Molecular machine to aid drug discovery

The technology is set to have uses in academic pharmaceuticals, biotechnology companies and government-sponsored projects with applications in prokaryotic functional genomics, systems biology and genetic engineering.

Researchers froze one of these molecular machines, which are chemical complexes known as a Group I intron, at mid-point in its work cycle. When frozen, crystallised introns reveal their structure and the sites at which they bind with various molecules to cause biochemical reactions.

Introns are bits of DNA that can activate their own removal from RNA, which translates DNA's directions for gene behaviour. Introns then splice the RNA back together. Scientists are just learning whether many DNA sequences previously believed to have no function actually may play specialised roles in cell behaviour.

It is becoming increasingly clear that successful drug discovery requires an understanding of complex biological contexts. Splicing adds another important dimension of complexity to the proteomic world. Although information on splicing has been accumulating at a rapid rate during the last four years, the core drug discovery processes entail techniques that cannot distinguish between splice variants and are therefore trapped in the 'one gene, one mRNA, one protein' method.

"In terms of human health, Group I introns re interesting because they cause their own removal and also splice the ends of the surrounding RNA together, forming a functional gene,"​ said Barbara Golden, associate professor of biochemistry at Purdue University.

Many pathogens that cause human diseases have Group I introns, including the HIV opportunistic infections pneumocystis, a form of pneumonia. This makes introns a potential target for therapeutics against these diseases by using a strategy called targeted trans-splicing in which introns are manipulated to cut out malfunctioning genes.

"It's thought that RNA, or a molecule related to RNA, possibly were the first biomolecules, because they are capable of both performing work and carrying around their own genetic code,"​ Golden added.

The research team used an intron from a bacteriophage, a molecule that attacks bacteria, to obtain an intron crystal structure trapped in the middle of the cutting and pasting cycle. As introns proceed through their work cycle, they change shape by folding and bending. By crystallising the complex at various stages, the scientists can determine and study its three-dimensional structure and learn how it is able to carry out its biochemical work.

The Group I intron at its work cycle's mid-point, which Golden crystallised, is unreactive but reveals many of the interactions between the RNA and the molecules that it activates, she said.

"It's very hard to find targets in cells because cells are organized in ways we still don't fully understand,"​ Golden said. "This crystal structure shows us where the best targets are for modifying genetic defects."​

The crystal structure of this Group I intron also will allow scientists to form models of hundreds of other introns in the same family and provide possibilities for new treatments for a wide variety of diseases, she added.

Introns were unknown until the late 1970s, and scientists are still investigating their function. Crystallisation of the complex is one tool to determine their purpose.

Two intron structures in different stages of the cycle have been crystallised previously, and the targeted trans-splicing technique has been used to repair haemoglobin infected with sickle cell anaemia. The new structure provides scientists with tools to expand on ways to harness this molecular machine.