When we think of the structure of DNA, the image that most likely comes to mind is that of the iconic double helix. This shape was identified in 1953 as DNA's most common form, and while other structures have been spotted in lab samples, it wasn't certain whether these existed naturally or not. Now, Australian scientists have found one of these unusual forms, a twisted knot known as the i-motif, in living cells for the first time.
In a way, our bodies are built a little like computer code, but instead of ones and zeroes, the blueprint is made up of pairs of nucleotides represented by the letters G, C, A and T. These incredibly long strands of DNA contain all the information needed to grow everything from hair to hearts to toenails, and make sure it all functions correctly.
Those instructions don't just come from the DNA's contents, but its structure as well. The way it folds up inside cells changes how the code is "read," which could explain how different tissues and organs arise. Different structures, such as i-motif, have been observed in the lab, but until now it wasn't certain whether they could form naturally inside living cells.
"The i-motif is a four-stranded 'knot' of DNA," says Marcel Dinger, co-lead researcher on the study. "In the knot structure, C letters on the same strand of DNA bind to each other – so this is very different from a double helix, where 'letters' on opposite strands recognize each other, and where Cs bind to Gs."
To find i-motifs in the wild, researchers at the Garvan Institute of Medical Research developed a new tool. The active ingredient is a fragment of an antibody molecule that is specifically designed to recognize only i-motifs, and attach to them. Crucially, the tool ignored sections of DNA in its usual double helix form, as well as other structures. Once the antibody fragment had attached to the i-motif knots, it fluoresced green to show the researchers exactly where and when they were forming.
"What excited us most is that we could see the green spots – the i-motifs – appearing and disappearing over time, so we know that they are forming, dissolving and forming again," says Mahdi Zeraati, co-author of the study. "We think the coming and going of the i-motifs is a clue to what they do. It seems likely that they are there to help switch genes on or off, and to affect whether a gene is actively read or not."
The researchers say that the transient nature of the knots may help explain why they hadn't been detected earlier. The team found that the i-motifs form most often during the late G1 phase of a cell's life cycle, when the DNA is being read out. They've also pinpointed where they form – i-motifs have been spotted in "promoter" regions, which control the switching on and off of genes, as well as in telomeres, the protective caps on the ends of chromosomes that play a key role in the aging process.
"It's exciting to uncover a whole new form of DNA in cells – and these findings will set the stage for a whole new push to understand what this new DNA shape is really for, and whether it will impact on health and disease," says Dinger.
The research was published in the journal Nature Chemistry.