DNA can fold into complex shapes to execute new functions

In a study by scientists at Weill Cornell Medicine and the National Heart, Lung, and Blood Institute, a division of the National Institutes of Health, DNA was found to fold into complex, three-dimensional structures and replicate the functions of proteins.

The DNA molecule they constructed to replicate the function of a protein called green fluorescent protein (GFP) was shown to have a novel and complicated structure by the researchers in their paper, which was published in Nature. GFP, a jellyfish-derived protein that serves as a fluorescent tag or beacon in cells, has developed into a crucial scientific tool.

The discoveries increase our understanding of how DNA may be made to fold into complicated shapes and will aid in the development of DNA molecules with these complex configurations for a range of laboratory and therapeutic uses.

For example, an all-DNA fluorescent tag that mimics GFP would frequently be perfect for labelling specific DNA segments in biological investigations and in diagnostic test kits and would be reasonably easy to produce.

"These findings really change our understanding of what we can do with DNA," said study co-author Dr Samie Jaffrey, Greenberg-Starr Professor of Pharmacology and a member of the Sandra and Edward Meyer Cancer Center at Weill Cornell Medicine.

DNA in nature exists mostly in a double-stranded, "twisted ladder" or "helical" form, and serves as a relatively stable store of genetic information. All of the other complex biological processes in cells are done by other types of molecules, especially proteins.

Last year, Dr Jaffrey and colleagues reported discovering one such molecule: a single-stranded DNA that folds in a way that allows it to mimic the activity of GFP.

The DNA molecule, which Dr Jaffrey dubbed "lettuce" for the colour of its fluorescent emissions, works by binding to another small organic molecule, a potentially fluorescent "fluorophore" similar to the one at the heart of GFP, and squeezing it in a way that activates its ability to fluoresce.

The researchers demonstrated the lettuce-fluorophore combination as a fluorescent tag for the rapid detection of SARS-CoV-2, the cause of COVID-19.

Dr Jaffrey and his team discovered lettuce by making many single-stranded DNAs and screening for those with the desired fluorophore-activating ability. But they didn't know what structure lettuce used to acquire this ability. To determine that structure, they turned -- in the new study -- to their long-time collaborator, NHLBI senior investigator Dr Adrian R Ferre-D'Amare.

In the research led by Dr Luiz Passalacqua, a research fellow at Dr Ferre-D'Amare's team, advanced structural imaging techniques were used, including cryo-electron microscopy, to resolve the structure of lettuce at atomic-scale resolution.

They found that it folds into a shape that has at its center a four-way junction of DNA, of a type never seen before, enclosing the fluorophore in a way that activates it. They also observed that lettuce's foldings are held together with bonds between nucleobases -- the building blocks of DNA that are often referred to as the "letters" in the four-letter DNA alphabet.

"What we have discovered is not DNA trying to be like a protein; it's a DNA that is doing what GFP does but in its own special way," said Dr Ferre-D'Amare.

The researchers said that the findings should speed the development of fluorescent DNA molecules such as lettuce for rapid-diagnostic tests as well as a host of other scientific applications in which a DNA-based fluorescent tag is desirable.

"Studies like this are going to be essential for the creation of new DNA-based tools," Dr Jaffrey said.