DNA’s virtual double helix does more than “just” store genetic information. Under certain conditions it can temporarily fold into unusual shapes. Researchers at Umeå University, Sweden, have now shown that such a structure, known as i-DNA, not only forms in living cells but also acts as a regulatory bottleneck linked to cancer.
You can think of i-DNA as a kind of “peek-a-boo structure” in the DNA molecule. Its formation is strictly controlled in time and must be resolved at exactly the right time. We think it plays an important role in gene regulation because these structures can appear and disappear in sync with changes in the state of the cell.”
Pallabi Sengupta, first author, postdoctoral researcher, Department of Medical Biochemistry and Biophysics, Umeå University
The study is now published in Nature Communications.
A highly unusual DNA structure
The familiar double helix can be imagined as a twisted ladder with a sugar-phosphate backbone as side rails and base pairs – adenine (A) paired with thymine (T) and cytosine (C) paired with guanine (G) – forming the rungs.
i-DNA, however, bears little resemblance to this scheme. Instead, it looks more like a warped, self-folding ladder tied in a knot. It consists of a single strand of DNA that folds back to form a four-stranded structure. At the molecular level, the structure is held not by typical AT and CG base pairs, but by cytosine pairs.
These rare, short-lived structures appear and disappear depending on the cellular environment. For decades, they were dismissed as too unstable to exist inside cells and regarded as laboratory artifacts. With new experimental techniques, researchers in Umeå can now demonstrate that i-DNA forms, but only briefly, just before DNA replication begins.
The core protein controls structure resolution
The study further shows that the PCBP1 protein acts as a critical regulator. It unwinds the i-DNA at the right time, allowing the DNA replication machinery to proceed. If the structures fail to open in time, they block replication, increasing the risk of DNA damage—a hallmark of increased vulnerability to cancer.
The researchers also discovered that i-DNA is not uniform: some structures unravel easily, while others are extremely resistant, depending on the underlying DNA sequence.
“The more cytosine base pairs that hold the knot together, the harder it is to untie. In some cases, hybrid structures can form, making the i-DNA even more stable,” explains Nasim Sabouri, professor at the Department of Medical Biochemistry and Biophysics at Umeå University, who led the study.
Notably, many i-DNA structures are found in regulatory regions of oncogenes—genes that drive cancer development—suggesting a direct link between i-DNA and disease.
To study these short-lived structures, the team combined biochemical assays, computational modeling and cell biology. They successfully visualized how PCBP1 progressively unwinds i-DNA and captured the structures in living cells at the exact moment in the cell cycle when they appear.
“By linking molecular mechanisms to actual effects on cells, we can show that this is biologically relevant and not a laboratory phenomenon,” says Ikenna Obi, a scientist at the Department of Medical Biochemistry and Biophysics at Umeå University.
New opportunities for drug development
The discovery reframes i-DNA from a molecular oddity to a potential weakness in cancer cells. Because cancer cells often experience high replication stress by trying to divide so fast that their DNA replication machinery is close to breaking down, any disruption in i-DNA handling can have serious consequences.
“If we can affect i-DNA or the protein that unwinds it, we may be able to push cancer cells beyond their tolerance limit. This opens up completely new avenues for drug development,” says Nasim Sabouri.
The study was conducted in collaboration with Natacha Gillet, a researcher at the National Center de la Recherche Scientifique (CNRS) in France.
