A new structure of DNA has been discovered in living cells for the first time by a team of Australian scientists, opening avenues for unprecedented research into the complex processes that manage the genome's vast library of information and instructions.
The four-stranded knots – called i-motifs – are a type of secondary shape that were first observed in laboratory samples of DNA in 1993. DNA strands are formed of two long chains of interconnected molecules, or nucleotides, that come in four flavors: adenine (A), guanine (G), thymine (T), and cytosine (C). I-motifs were noted to occur in sequences of the genome where there are many cytosines. Within these stretches, the cytosines deviate from the norm and form bonds with each other instead of linking up with a guanine on the opposite strand.
Yet because these shapes were only seen under artificial, high-pH conditions, i-motifs were initially dismissed as curious chemical rearrangements in response to acidity.
In recent years, however, scientists began to suspect that i-motifs not only occur naturally, but that they may play a role in regulating which genes get expressed. Of course, finding tiny DNA knots amongst the 6 billion-odd nucleotide base pairs in a human cell is no easy task.
The Garvan Institute of Medical Research group’s breakthrough, published in Nature Chemistry, came after they created a sort of molecular bloodhound: An antibody fragment that is perfectly shaped to attach to any i-motifs it encounters inside the nucleus of a cell. Once bound, the scientists could visually confirm the presence of any i-motifs because the antibody is fused to a fluorescent dye.
After exhaustively proving that their antibody would not create false-positives by binding to other shapes of DNA (the strands are known to take on several unorthodox configurations depending on what is going on inside the cell), the team was rewarded with the Eureka! moment-worthy sight of twinkling green spots appearing under the microscope.
"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," said first author Dr Mahdi Zeraati in a statement.
I-motifs appear to flash into existence at the telomeres – protective caps of non-coding DNA at the ends of each strand that have been implicated in longevity and disease – and when the cells were in the part of their lifecycle when they are gearing up to duplicate the genome and divide. According to co-author Daniel Christ, this transient nature helps explain why i-motifs were so hard to detect previously and confirms that their formation is anything but random.
The team concludes that the knots' presence likely influences whether or not a gene is read, aka translated into a protein. They note that future investigations will now be able to further explore the i-motif's role in normal cell functioning and determine its hand in the development of diseases such as cancer.
"There's so much of the genome that we don't understand, probably like 99 percent of it," Marcel Dinger, the other co-leader, told Live Science. Being able to detect i-motifs "makes possible to decode those parts of the genome and understand what they do."