A twisted ‘knot’ of DNA, the i-motif has never before been directly seen inside living cells. Image credit: Zeraati et al, doi: 10.1038/s41557-018-0046-3.
A team of scientists from the Garvan Institute of Medical Research and the Universities of New South Wales and Sydney has identified a new DNA structure — called the intercalated motif (i-motif) — inside living human cells.
Deep inside the cells in our body lies our DNA. The information in the DNA code — all 6 billion A, C, G and T letters — provides precise instructions for how our bodies are built, and how they work.
The iconic ‘double helix’ shape of DNA has captured the public imagination since 1953, when James Watson and Francis Crick famously uncovered the structure of DNA.
However, it’s now known that short stretches of DNA can exist in other shapes, in the laboratory at least — and scientists suspect that these different shapes might play an important role in how and when the DNA code is ‘read.’
“When most of us think of DNA, we think of the double helix. This research reminds us that totally different DNA structures exist — and could well be important for our cells,” said co-lead author Dr. Daniel Christ, from the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research and St Vincent’s Clinical School at the University of New South Wales.
“The i-motif is a four-stranded ‘knot’ of DNA,” added co-lead author Dr. Marcel Dinger, also from the Garvan Institute of Medical Research and the University of New South Wales.
“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 [guanines].”
Although researchers have seen the i-motif before and have studied it in detail, it has only been witnessed in vitro — that is, under artificial conditions in the laboratory, and not inside cells. In fact, they have debated whether i-motif DNA structures would exist at all inside living things — a question that is resolved by the new findings.
To detect the i-motifs inside cells, Dr. Christ, Dr. Dinger and their colleagues developed a precise new tool — a fragment of an antibody molecule — that could specifically recognize and attach to i-motifs with a very high affinity.
Until now, the lack of an antibody that is specific for i-motifs has severely hampered the understanding of their role.
Crucially, the antibody fragment didn’t detect DNA in helical form, nor did it recognize ‘G-quadruplex structures’ (a structurally similar four-stranded DNA arrangement).
With the new tool, the team uncovered the location of ‘i-motifs’ in a range of human cell lines.
Using fluorescence techniques to pinpoint where the i-motifs were located, the study authors identified numerous spots of green within the nucleus, which indicate the position of i-motifs.
The scientists 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 aging 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,” said study first author Dr. Mahdi Zeraati, also from the Garvan Institute of Medical Research and the University of New South Wales.
“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,” Dr. 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,” Dr. Dinger said.
The team’s results appear in the journal Nature Chemistry.
Mahdi Zeraati et al. I-motif DNA structures are formed in the nuclei of human cells. Nature Chemistry, published online April 23, 2018; doi: 10.1038/s41557-018-0046-3