For the first time, scientists have detected a DNA structure inside living human cells that looks more like a four-stranded knot than the elegant double helix we know from biology textbooks.
The tangled shape, known as an i-motif, had been seen before in the lab, but nobody thought it could occur in human cells _ until now.
The new work shows not only that i-motifs do indeed exist in human cells, but that they may be quite common.
"Our imaging suggests that this is a normal thing that happens," said Marcel Dinger, a molecular biologist at the Garvan Institute for Medical Research in Sydney, Australia, and a senior author of the new work published Monday in Nature Chemistry.
"It is very likely that genomes in all the cells of our bodies are forming i-motifs at some point in time," he said.
Laurence Hurley, a professor of medical chemistry at the University of Arizona who was not involved with the study, said the new paper is important for chemical biology and molecular therapeutics.
He added that the new work lends credence to the idea that these unusual DNA shapes may play an essential role in human biology, perhaps by regulating gene expression.
The folded shape of the i-motif only occurs in a relatively small region of a genome _ sticking out like a bumpy knot in the smooth helical shape of the rest of a strand of DNA.
To be clear, not just any piece of DNA can fold itself into the four stranded i-motif shape. It requires a specific sequence of letters that include several cytosines, which are written as Cs in the genetic code.
Back in the mid-'90s scientists playing around in the laboratory discovered that under certain conditions a cytosine-rich region of a DNA strand could fold on top of itself, creating a four-stranded shape in which Cs paired with Cs instead of their usual partners, guanines or Gs.
However, in lab experiments it seemed that this DNA origami could only occur under acidic conditions that did not exist inside a cell.
"It was thought to be a weird idiosyncratic thing that the molecule can do, but not relevant for human biology," Dinger said.
More recent work has shown that in some cases an i-motif shape could form even in environments that weren't so acidic, said Randy Wadkins, a biochemist at the University of Mississippi in Oxford who was not involved with the new study.
In that case, i-motifs were observed when the DNA was in an extremely crowded environment, like it would be inside the nucleus of a cell.
Following a hunch, Dinger and his colleagues decided to see if they could find i-motifs inside living cells.
To do this, they worked with Daniel Christ, head of antibody therapeutics at the Garvan Institute. After lots of trial and error, Christ's lab was able to develop an antibody that could search out i-motifs in the genome and bind to them.
The antibodies were tagged with a marker that glows when a fluorescent light shines on it. By looking at a strand of DNA under a special microscope, the researchers were able to see how often an i-motif occurred in a genome by counting fluorescent dots.
I-motifs are what scientists call "dynamic" _ they can fold and unfold depending on the pH (or acidity) of their surroundings. In addition, the sequences that code for i-motifs are generally found not within a gene itself, but a little upstream, in a part of the genome known as the promoter region that determines whether or not a certain gene gets expressed.
These two facts suggest that i-motifs may be used as a type of switch that can regulate gene expression.
It is possible that certain cellular stressors can cause the pH inside the cell to change, which could cause an i-motif to form. This in turn could trigger an over-expression of a nearby gene or an under-expression.
"Think of it like a dial," Wadkins said. "But for now, we don't know whether that switch turns it up to 11 or turns it down to 0."
However, it is also possible that these i-motifs may do nothing at all.
"The caveat for all of this is that these antibodies may have just trapped these oddball structures when they were forming and they don't have any significance at all," he said. "It could be a fluctuating intermediary structure that formed for a second and has no biological significance."
Indeed, scientists have long known about other shapes that DNA can fold into in the lab, including those that resemble cruciforms and hair pins.
"DNA is a conformationally flexible molecule," Wadkins said. "But the question is, does this stuff have any biological relevance, because you don't want to spend your money and time going after something just because you did something funky in the lab."
For his part, Wadkins thinks it is likely that i-motifs do play a role in gene expression, but he said more work will be needed to say for certain.
And now that researchers know these strange four-stranded structures do frequently occur in human DNA, they are ready to find out.
"This opens up a whole new line of science," Dinger said.
