Scientists have identified tens of thousands of mysterious “knots” in human DNA that may play a key role in controlling gene activity. The activity of 4-strand DNA in living cells has been revealed. Synthetic DNA with four extra letters has been created. DNA twists into strange shapes to fit into cells.
Scientists have identified tens of thousands of mysterious “knots” in human DNA that may play a key role in controlling gene activity. Knowing the precise locations of these knots, known as “i-motifs,” could lead to new treatments for diseases including cancer, according to the researchers behind the work.
DNA is made up of building blocks called nucleotides, each of which carries one of the following bases: adenine, guanine, thymine, or cytosine. These bases are the individual letters that make up the DNA code. DNA has a ladder-like structure, and typically the bases on one side of the ladder pair with a partner on the other side, joining in the middle to form the rungs of the ladder. Adenine pairs with thymine, and guanine pairs with cytosine.
However, sometimes cytosines can pair with each other rather than with guanine. This causes the DNA molecule to twist around itself, creating a four-stranded, protruding structure called an i-motif.
Researchers first discovered i-motifs in human cells in 2018. At the time, they suspected that these knots could be important regulators of the genome, helping to control which genes are turned on or off. Until now, however, little was known about exactly where these knotted structures were located or how many there were in the human genome.
In a new study published Aug. 29 in The EMBO Journal, the researchers mapped 50,000 i-motifs. These i-motifs are located throughout the genome, but they typically occur in regions of DNA that control gene activity, the study authors noted.
In the new study, scientists mapped 50,000 knot-like structures in DNA known as “i-motifs.” KEITH CHAMBERS/SCIENCE PHOTO LIBRARY
“Our results confirm that i-motifs are not just a laboratory curiosity, but a widespread phenomenon that likely plays a key role in genomic function,” Daniel Christ, a co-author of the study and director of the Centre for Targeted Therapies at the Garvan Institute of Medical Research in Australia, said in a statement.
Christ and colleagues found i-motifs in DNA extracted from human cells in the lab. They identified these nodes using antibodies designed to specifically recognize and form complexes with i-motifs. The team then purified these antibody-node complexes to sequence the DNA inside them.
“We found that i-motifs are associated with genes that are highly active during certain periods of the cell cycle,” said Christian David Peña Martinez, lead author of the study and a Garvan research fellow, in a statement. The cell cycle is the process by which cells replicate in the body.
“This suggests that they play a dynamic role in regulating gene activity,” Peña Martinez added.
The team also found i-motifs in the “promoter” regions of various cancer-related genes. Promoters are a type of genetic material that turns a given gene on and off, like a light switch. In cancer cells, these genes can become unregulated, leading to the increased cell division and growth characteristic of tumors.
This new discovery hints that i-motifs could one day be a target for cancer drugs, the team suggested. They found i-motifs in the MYC gene family, which is known to be dysregulated in about 70% of human cancers.
“This represents an exciting opportunity to target disease-related genes through the i-motif structure,” Peña Martinez said. Of course, more research is needed to translate this idea from theory to practice in cancer patients.
Activity of quadruple-stranded DNA in living cells revealed. Two thin strands twisted together into a helical spiral is the iconic shape of the DNA molecule. But sometimes DNA can form a rare quadruple helix, and this strange structure may play a role in diseases like cancer.
Not much is known about these four-stranded DNAs, known as G-quadruplexes — but now scientists have developed a new way to detect these strange molecules and observe how they behave in living cells. In a study published January 8, 2021, in the journal Nature Communications, the team described how certain proteins cause G-quadruplexes to unravel; their work could lead to new drugs that latch onto the four-stranded DNA and disrupt its activity. The drugs could intervene, for example, when strange DNA is fueling the growth of cancer.
“There is growing evidence that G-quadruplexes play important roles in a wide range of processes essential to life, as well as in a number of diseases,” study author Ben Lewis, from Imperial College London’s Department of Chemistry, said in a statement.
Overall, G-quadruplexes occur much more frequently in cancer cells than in healthy cells, according to the statement. Various studies have linked the presence of four-stranded DNA to the rapid division of cancer cells, a process that leads to tumor growth; so scientists have hypothesized that targeting the strange DNA with drugs could slow or stop this rampant cell division. Some studies already support this idea.
G-quadruplexes. Imperial College London
“But the missing link was imaging this structure directly in living cells,” Lewis said. In other words, scientists needed a better way to watch these DNA molecules in action. The new study begins to fill that gap.
G-quadruplexes can form either when a single double-stranded DNA molecule folds in on itself or when multiple strands of DNA join together at a single nucleic acid known as guanine — one of the building blocks of DNA, according to Discover Magazine. To detect this unusual DNA in cells, the team used a chemical called DAOTA-M2, which emits fluorescent light when it binds to G-quadruplexes. Instead of simply measuring the brightness of the light, which varies depending on the concentration of DNA molecules, the team also tracked how long the light shines.
Tracking how long the light lingered helped the team see how different molecules interacted with the four-stranded DNA in living cells. When a molecule latched onto a DNA strand, it displaced the glowing DAOTA-M2, causing the light to fade faster than if the chemical had remained in place. Using these techniques, the team identified two proteins called helicases that unwind the four-stranded DNA strands and initiate the process of breaking them down.
They also identified other molecules that bind to DNA; future studies of these molecular interactions could help scientists develop drugs that bind to DNA.
“Many researchers have been interested in the potential of G-quadruplex-binding molecules as potential drugs for diseases such as cancer,” said Ramon Vilar, a professor of medicinal inorganic chemistry at Imperial, in a statement. “Our method will help us advance our understanding of these potential new drugs.”
The researchers created synthetic DNA using four extra molecules, so the resulting product had a code made up of eight letters rather than four. With more letters, this DNA had a much greater capacity to store information. The scientists called the new DNA “hachimoji” — meaning “eight letters” in Japanese — expanding on previous work by different groups that had created similar DNA using six letters.
A study published February 20, 2019, in the journal Science supports the latter idea: Scientists recently formed a new type of DNA with an elegant double-helix structure and found that it has properties that could support life.
Natural DNA consists of four molecules called nitrogenous bases, which link together to form the code for life on Earth: A links with T; G links with C. Hachimoji’s DNA includes these four natural bases, plus four more synthetic nucleotide bases: P, B, Z, and S.
The research team, which included several different teams across the United States, created hundreds of these Hachimoji double helices with different combinations of natural and synthetic base pairs. They then conducted a series of experiments to see if the different double helices had the properties needed to support life.
Natural DNA has a distinctive property that no other genetic molecule seems to have: it is stable and predictable. This means that researchers can calculate exactly how it will behave in certain temperatures and environments, including when it will begin to degrade.
But it turns out that the researchers were able to do the same thing with Hachimoji’s DNA – they were able to develop a set of rules that could predict the stability of DNA when exposed to different temperatures.
Researchers have developed a new type of DNA in the lab that has eight letters instead of the natural four. Millie Georgiadis, Indiana University School of Medicine
But it’s not enough to create DNA that stores information. It also needs to be able to pass that information on to its sister RNA molecule, so that RNA can then instruct proteins to do all the things in the body.
With this in mind, the researchers developed synthetic enzymes—proteins that facilitate the reaction—that successfully copied Hachimoji’s DNA into Hachimoji’s RNA. What’s more, they found that the RNA molecule was able to fold into a sort of L-shape, which is necessary for the information to be transferred.
In addition, DNA strands must be able to twist into the same three-dimensional structure – the famous double helix.
The team created three crystal structures of Hachimoji’s DNA, each with a different eight-base-pair sequence, and found that each did indeed form a classic double helix.
However, for Hachimoji’s DNA to support life, there is a fifth requirement, Benner said. That is, it must be self-sustaining, or able to survive on its own. The researchers did not explore this step, however, to avoid turning the molecule into a biohazard that could one day infiltrate the genomes of organisms on Earth.
While this eight-letter DNA strand could provide insight into alternatives to life in space, it also has applications on our planet. An eight-letter genetic alphabet would store more information and bind to specific targets more specifically, Benner said. For example, Hachimoji DNA could be used to bind to liver cancer cells or anthrax toxins, or used to speed up chemical reactions.
“When the number of letters increases from six to eight, the diversity of DNA sequences increases significantly,” Ichiro Hirao, a synthetic molecular biologist at the A*STAR Institute of Bioengineering and Nanotechnology in Singapore, who was also not involved in the study, wrote in an email. (Hirao’s group, however, was involved in a previous study that created six-letter DNA strands.)
Of course, “this is just the first demonstration” of the eight-letter DNA double helix, and for practical use we need to improve the fidelity and efficiency of replication and transcription in RNA, Hirao said in an email. He suggests they will eventually be able to scale up the number of letters to even more.
In 2021, scientists captured high-definition video showing DNA taking on strange shapes to squeeze inside cells.
In 1952, Rosalind Franklin took the first indirect photograph of DNA by studying how X-rays bounced off these fundamental molecules. But it wasn’t until 2012 that scientists took a direct photograph of DNA using an electron microscope. Now, a team of researchers in the UK has captured a high-definition video of DNA in motion using a combination of advanced microscopy and modelling.
Human cells contain about 6.6 feet (2 meters) of DNA. Given that human cells are on the order of micrometers, DNA must be really good at “supercoiling,” or bending and folding itself to pack tightly inside a cell. But until recently, technology wasn’t good enough for scientists to clearly see what the structure of DNA looks like when it’s supercoiled, the authors write in the study.
To answer this question, the authors of the new study turned to “mini-circles of DNA” isolated and engineered from bacteria. These circular DNA structures are also found in human cells, and their function is largely unknown. The researchers used these circular structures because scientists can twist them in ways that would not work with long strands, the most common form of DNA, according to the statement.
DNA. University of Leeds
To see the movements in detail, the researchers used a combination of supercomputer simulations and atomic force microscopy, which involves sliding a sharp tip across the surface of a molecule and measuring the forces pushing against the tip to outline the structure.
“Seeing is believing, but with something as small as DNA, seeing the helical structure of the entire DNA molecule has been extremely challenging,” lead study author Alice Pine, a lecturer in polymers and soft matter at the University of Sheffield in the U.K., who recorded the new footage, said in a statement. “The videos we’ve developed allow us to watch DNA twist at a level of detail that has never been seen before.”
The microscope images were so detailed that they could see the double helix structure of DNA. After the researchers combined these images with simulations, they were able to see the position of each individual atom in the DNA as it moved, according to the statement.
Interestingly, the DNA in its relaxed form barely moved. But when twisted — as it typically does when pressed into a cell — the DNA transformed into a variety of other shapes, according to the paper. These different shapes affected how the DNA molecule interacted and bonded with other DNA molecules around it, the authors wrote in the paper.
Lynn Zechidrich, a professor at Baylor College of Medicine in Houston, Texas, who provided the mini-rings for the study, previously discovered how to use the ring structures as vectors for gene therapy, inserting small genetic messages into the rings.
The scientists who conducted the study “developed a technique that shows in great detail how wrinkled, bubbly, twisted, denatured and oddly shaped they are,” Zechidrich, who was not directly involved in the research, said in a statement. “We need to understand how supercoiling, which is so important for DNA activity in cells, affects DNA, in the hopes that we can someday mimic or control it.”
