Tag Archives: nucleotides

For the first time, researchers create “semi-synthetic” life form with man-made DNA

Researchers have created the first stable semi-synthetic life, a strain of E. coli bacteria with two extra artificial nucleotides in its genetic code.

Nucleotide chain at the “Miraikan” / The National Museum of Emerging Science and Innovation.
Image credits Miki Yoshihito / Flickr.

You, me, your pets, potatoes, coffee, basically all living things you can think of have one thing in common: the DNA that tells their cells what to do is encoded using only four bases. If you compare DNA to an instruction manual, nucleotides (or bases) would be the letters that make up words. In fact, we even represent them as letters — G, T, C, and A.

Pimp my DNA

You might have noticed that there’s only 4 of them. Which isn’t a lot. That’s why scientists have been toying around with the idea of adding extra letters to DNA for some time now.

It all started in 2014, when a team from the Scripps Research Institute in California successfully added synthetic nucelotides to a living organism’s DNA for the first time, creating so called semi-synthetic life. Their initial cultures were really bad at not dying, however. The team has spent two years refining the process, and has recently reported the creation of stable semi-synthetic organisms.

Their modified E. coli bacteria’s genetic code has two additional bases, X and Y, peppered throughout their DNA. The strain does not reject the X and Y bases and retains them in the genome for life. This achievement has incredible potential, as researchers can now tell cells what to do directly instead of rummaging around DNA strands for bits of code and being limited to natural processes.

“With the virtually unrestricted ability to maintain increased information, the optimised semi-synthetic organism now provides a suitable platform [to create] organisms with wholly unnatural attributes and traits not found elsewhere in nature,” the paper reads.

“This semi-synthetic organism constitutes a stable form of semi-synthetic life, and lays the foundation for efforts to impart life with new forms and functions.”

Bases for life

The team’s initial cultures weren’t viable as organisms. The main problems were that the cultures were weak and sickly compared to natural strains of E. coli, and that they couldn’t reliably replicate X and Y bases during division so their DNA often fractured during the process.

“If the semisynthetic organism is going to really be an organism, it has to be able to stably maintain [genetic] information,” said TSRI Professor and team leader Floyd Romsberg.

The team started by tweaking the nucelotide transport process, which inserts synthetic bases in the right spots of the bacterial genome. Their first transporter molecule was toxic to the bacteria, so it was altered until the cells showed no adverse reaction. Next, they changed the chemistry of the Y base so it was more easily recognized by the enzymes that power DNA replication during division. The last step was to use CRISPR-Cas9 to nudge  E. coli into considering the artificial bases as a natural part of their genome.

CRISPR-Cas9 is widely used as a genome-editing tool today, but it is originally a bacterial defensive mechanism. When encountering a new threat, such as a virus, bacteria take fragments of its genome and grafts it into their own DNA. Though foreign in nature, these pieces of code are treated as belonging to the bacteria. If the invader returns, these bits are used to create enzymes to attack them. The team programmed the semi-synthetic E. coli to treat genetic sequences without X and Y as a threat, meaning that any cells which lost them during replication were attacked.

Using the new methods, they were able to engineer stable E. coli cells. The bacteria are healthier and more autonomous than before. They also kept their artificial bases for 60 division cycles, so the team considers they an likely keep their genome make-up indefinitely.

Genetic gibberish

 

Each natural nucleotide pair encodes a different instruction. But cells don’t understand X and Y bases.
Image via Pixabay.

Right now, the X and Y bases don’t actually do anything. The pair they form doesn’t mean anything from the cell’s point of view — it doesn’t encode any information for the bacteria to use. Basically, they just take up space in the genome. In fact, they’re so foreign the bacteria don’t even know how to make more — the team has to supply X and Y for each division cycle.

As a proof of concept however, it shows that artificial bases can be grafted into a living organism and made to stick. The team will have to insert a gene that is actually readable for the bacteria to start using it.

Because X and Y are nothing like what nature has used up to now, Romsberg advises against panic that the semi-synthetic bug will evolve and wipe us out.

“Evolution works by starting with something close, and then changing what it can do in small steps,” Romesberg told Ian Sample at The Guardian.

“Our X and Y are unlike natural DNA, so nature has nothing close to start with. We have shown many times that when you do not provide X and Y, the cells die, every time.”

Having the ability to program cells to produce exotic proteins is the cornerstone in producing a huge range of new drugs. Alternatively, the E. coli can be used to produce novel materials, store information, and much more.

The full paper “A semi-synthetic organism with an expanded genetic alphabet” has been published in the journal PNAS.

Biomarker explains why some people catch colds more often than others

Researchers from the Carnegie Mellon University have identified a biological marker in the immune system that (starting from about age 22), predicts the probability of getting a common cold.

telomereThey found that telomeres play a big part in this likelihood. Telomeres are regions of repetitive nucleotide sequences at each end of a chromatid, which protect the end of the chromosome from deterioration or from fusion with neighboring chromosomes. Telomeres are alsoa biomarker of aging, with telomeres shortening as you advance in age. As a cell’s telomeres shorten, it loses its ability to function normally. Basically, shorter telomeres make you more susceptible to a number of diseases, such as cancer or cardiovascular disease – especially in older people. However, as it turns out, it plays a big role in younger adults, and has a tight connection with the common cold as well.

“Our work suggests the possibility that telomere length is a relatively consistent marker across the life span and that it can start predicting disease susceptibility in young adulthood,” said Sheldon Cohen who conducted the study, the Robert E. Doherty Professor of Psychology in CMU’s Dietrich College of Humanities and Social Sciences. “We knew that people in their late 50s and older with shorter telomeres are at a greater risk for illness and mortality. We also knew that factors other than aging, such as chronic stress and poor health behaviors, are associated with shorter telomeres in older people. Consequently, we expected that younger people would vary in their telomere length as well and wanted to see what this would mean for their health.”

He and his team measured the telomere length of white blood cells from 152 healthy volunteers aged 18-55 – inviduals who had been previously exposed to a rhinovirus, which causes a common cold, and quarantined for five days to see if they developed the cold.

The results clearly showed that that particpiants with shorter telomeres were much more likely to become infected with the virus. There was no connection to telomere length and this occurence in people 21 or younger, but after 22 years, telomere length started to predict whether individuals would develop an infection. As participant age increased, telomere length became an even stronger predictor; one telomere especially, of a specific white blood cell (a CD8CD28- T-cytolytic cell) was a superior predictor of infection and cold symptoms than other white blood cell types.

sheldon cohen“These cells are important in eliminating infected cells and those with shorter telomeres in the CD8CD28- cell population may be at greater risk for infection because they have fewer functional cells available to respond to the [cold] virus,” Cohen said. “The superior ability of CD8CD28- T-cytolytic cells to predict infection gives us an idea of which cells to focus on in future work on how telomere length influences the immune system’s response to infection and other immune-related challenges.”

Cohen then added:

“The increased importance of telomere length with age is likely because the younger participants had fewer very short telomeres, or that their young immune systems were able to compensate for the loss of effective cells.”

It has to be emphasized however that these are just the preliminary results, and much more research has to be conducted to clarify the implications of such an association.

The research was published in the Journal of the American Medical Association (JAMA)

These are actually designs assembled with lego bricks, but based on the same principle, scientists have devised a new method for DNA self-assembly. (c) Kurt V. Gothelf/Yonggang Ke et al

DNA ‘Lego’ bricks used to build 3D nano-objects

These are actually designs assembled with lego bricks, but based on the same principle, scientists have devised a new method for DNA self-assembly. (c)  Kurt V. Gothelf/Yonggang Ke et al

These are actually designs assembled with lego bricks, but based on the same principle, scientists have devised a new method for DNA self-assembly. (c) Kurt V. Gothelf/Yonggang Ke et al

In a breakthrough for nanotechnology, researchers at the Harvard’s Wyss Institute have found the right mix of chemistry and molecular programming to trick DNA strands to fit together perfectly, just like Lego bricks, and thus form various objects and shapes, all based on the scientists’ software design. Thus, a myriad of objects made out of DNA were created in the Harvard labs, from a space shuttle, to letters of the alphabet, to honeycombs. The scientists believe these resulting tiny DNA-based structures could serve a great purpose in medical research and treatment, as well as electronic devices.

The scientists’ method relies on synthetic strands of DNA that take in just 32 nucleotides, or molecular bits of genetic code. These can bind to as many as four neighboring strands or bricks. Thus, two bricks connect to one another at a 90-degree angle to form a 3D shape, just like a pair of two-stud Lego bricks. Each individual brick is coded in such a way that they self-assemble in a desired 3-D shape. What’s fantastic is that this method allows for intricate shapes to built on an extremely tiny scale opening up a slew of applications. For instance, a cube built up from 1,000 such bricks (10 by 10 by 10) measures just 25 nanometers in width – thousands of times smaller than the width of a human hair!

“Once we know how to compile the correct code of complex shapes and add it to the synthetic DNA strands, everything else is simple and natural,” said Yonggang Ke, a chemist at Harvard University. “Those DNA strands are like smart Lego bricks that know exactly where to go by themselves.”

The research is based on previous work from the same Wyss lab when the scientists used DNA to build 2D shapes. The 3-D assembly was made possible by using the exact right combinations of nucleotides (adenosine, thymine, cytosine and guanine) in the synthesized strands, so that the DNA’s base pair molecules bind to one another in a desired fashion. The process takes a while though. One shape resembling a cube took 72 hours for self-assembly.

Playing with DNA

So far, 102 different 3-D shapes were created using a 1,000-brick template.

These are computer-generated 3D models (left) and corresponding 2D projection microscopy images (right) of nanostructures self-assembled from synthetic DNA strands called DNA bricks. (c) Yonggang Ke, Wyss Institute, Harvard University

These are computer-generated 3D models (left) and corresponding 2D projection microscopy images (right) of nanostructures self-assembled from synthetic DNA strands called DNA bricks. (c) Yonggang Ke, Wyss Institute, Harvard University

This isn’t the first time 3-D molecular assembly from DNA has been made though. Previously, scientists used to rely on a method called the Origami method, which works by folding a single DNA strand into a desired shape. The technique is rather obtuse, however, and not nearly as effective as the “lego” method from Harvard. Origami requires custom “staple” DNA strands to fold the main, “scaffold” strand into a desired 3-D shape. In contrast, the lego method makes for a much easier assembly.

“This is a simple, versatile and robust method,” the study’s senior author, Peng Yin, said in a news release.

Still, considering the required applications both Origami and Lego methods can now be used by scientists, improving their toolbox. The scientists are confident that a range of new applications might be possible in molecular assembly, like complex nanostructures that could be used as smart drug delivery devices inside the human body.

“Personally, I am enthusiastic about the potential application of DNA nanotechnology to make intelligent drug-delivery vehicles and to arrange and wire molecular electronic components,” said  Kurt Gothelf, director of the Center for DNA Nanotechnology at Aarhus University in Denmark.

Findings were detailed in the journal Science.