This is an artist’s impression of the i-motif DNA structure inside cells, along with the antibody-based tool used to detect it.
(Credit: Chris Hammang)

In 1953, James Watson and Francis Crick published a scientific paper revealing the groundbreaking discovery of the twisted-ladder DNA structure. By understanding the shape of DNA’s, science was able to unravel many mysteries of genetic code. 

Now, it appears that the double helix isn’t the only form in which DNA exist. Scientists have, for the first time, identified the existence of a new DNA structure, never before seen in living cells, that looks entirely different to the double-stranded DNA double helix. 

The discovery of the ‘twisted knot’ of DNA living inside human cells, confirms that our complex genetic code is crafted with more intricate symmetry than just the double helix structure everybody associates with DNA. The findings are reported in Nature Chemistry.

“When most of us think of DNA, we think of the double helix,” says antibody therapeutics researcher Daniel Christ from the Garvan Institute of Medical Research in Australia.

“This new research reminds us that totally different DNA structures exist – and could well be important for our cells.”

The new DNA component the team identified is called the intercalated motif (i-motif) structure, which was first discovered by researchers in the 1990s, but up until now had only ever been witnessed in vitro, not in living cells.

i-Motif Structure (Zeraati et al., Nat Chem, 2018)

Now, thanks to these new findings, we know that the i-motif occurs naturally in human cells, which means that the structure’s significance to cell biology demands new attention from researchers.

Until now, the lack of an antibody that is specific for i-motifs has severely hampered the understanding of their role. To detect the i-motifs inside cells, the researchers developed a fragment of an antibody molecule that could specifically recognise and attach to i-motifs with a very high affinity. 

Crucially, the antibody fragment didn’t detect DNA in helical form, nor did it recognise ‘G-quadruplex structures’ (a structurally similar four-stranded DNA arrangement).

With the new tool, researchers uncovered the location of i-motifs in a range of human cell lines. Using fluorescence techniques to pinpoint where the i-motifs were located, they identified numerous spots of green within the nucleus, which indicate the position of i-motifs.

“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 Dr. Mahdi Zeraati, first author of the study. 

The researchers showed that i-motifs mostly form at a particular point in the cell’s ‘life cycle’ — the late G1 phase, when DNA is being actively ‘read’. They also showed that i-motifs appear in some promoter regions — areas of DNA that control whether genes are switched on or off —and in telomeres, ‘end sections’ of chromosomes that are important in the ageing process.

“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,” Dr. Zeraati said. 

Now that we definitively know this new form of DNA exists in cells, it’ll give researchers a mandate to figure out just what these structures are doing inside our bodies.

As Zeraati explains, the answers could be really important – not just for the i-motif, but for A-DNA, Z-DNA, triplex DNA, and cruciform DNA too.

“We also think the transient nature of the i-motifs explains why they have been so very difficult to track down in cells until now,” professor Christ added. 

“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,” professor Marcel Dinger concluded, who co-led the research.