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New Research Could Lead to DNA 3D Printer - 3DPrint.com
Technology is capable of amazing things, but it doesn’t mean those things are easy. It’s incredible that scientists can produce DNA in a lab, but the process is difficult, lengthy and requires toxic chemicals. Imagine, however, if they could simply print it, the way that you would 3D print anything else. That could be the future, after scientists at UC Berkeley and Lawrence Berkeley National Laboratory developed a new way to synthesize DNA. The method could lead to DNA printers, similar to ordinary 3D printers, that could produce DNA strands that are more accurate and 10 times longer than the strands produced with today’s methods – more quickly and easily, and without the use of toxic chemicals.
“If you’re a mechanical engineer, it’s really nice to have a 3D printer in your shop that can print out a part overnight so you can test it the next morning,” said UC Berkeley graduate student Dan Arlow. “If you’re a researcher or bioengineer and you have an instrument that streamlines DNA synthesis, a ‘DNA printer,’ you can test your ideas faster and try out more new ideas.
I think it will lead to a lot of innovation.”
The research was led by Arlow and PhD student Sebastian Palluk, a doctoral student at the Technische Universität Darmstadt in Germany and a visiting student at Berkeley Lab. It is published in a paper entitled “De novo DNA synthesis using polymerase-nucleotide conjugates,” which you can access here. The research was conducted at the Department of Energy’s Joint BioEnergy Institute (JBEI).
“I personally think Dan and Sebastian’s new method could revolutionize how we make DNA,” said Jay Keasling, a UC Berkeley professor of chemical and biomolecular engineering, senior faculty scientist at Berkeley Lab and Chief Executive Officer of JBEI.
Keasling and JBEI scientists specialize specialize in adding genes to microbes, typically yeast and bacteria, to sustainably produce useful products. Palluk came from Germany specifically to work with Arlow in Keasling’s lab.
L to R: Dan Arlow, Sebastian Palluk and Jay Keasling
“We believe that increased access to DNA constructs will speed up the development of new cures for diseases and simplify the production of new medicines,” Palluk said.
The synthesis of DNA is a growing business; companies are ordering custom-made genes so that they can produce chemicals, biologic drugs or industrial enzymes. Researchers purchase synthetic genes to engineer plants and animals or try out new CRISPR-based disease therapies. Some scientists have even researched storing information in DNA, but that would require much larger quantities of DNA than are currently synthesized. All of these applications require that synthesis produce the desired sequence of nucleotides or bases, the building blocks of DNA, in each of millions or billions of copies of DNA molecules.
Current DNA synthesis is limited to producing oligonucleotides about 200 bases long, because errors in the process lead to a low yield of correct sequences as the length increases. To assemble even a small gene, scientists have to stitch together segments of about 200 bases long. The turnaround time for a small gene of 1,500 bases long can be two weeks at a cost of $300, limiting the experiments that scientists can do.
Synthetic biologists like Arlow, Palluk and Keasling often insert a dozen different genes at once into a microbe to get it to produce a chemical, and each gene presents its own synthesis problems.
“As a student in Germany, I was part of an international synthetic biology competition, iGEM, where we tried to get E. coli bacteria to degrade plastic waste,” said Palluk. “But I soon realized that most of the research time was spent just getting all the DNA together, not doing the experiments to see if the engineered cells could break down the plastic. This really motivated me to look into the DNA synthesis process.”
The technology developed by Palluk, Arlow, Keasling and their team relies on a DNA-synthesizing enzyme found in cells of the immune system that has the natural ability to add nucleotides to an existing DNA molecule in water, where DNA is most stable. The technology results in increased precision, allowing synthesis of DNA strands several thousand bases long – a medium-sized gene.
“We have come up with a novel way to synthesize DNA that harnesses the machinery that nature itself uses to make DNA,” Palluk said. “This approach is promising because enzymes have evolved for millions of years to perform this exact chemistry.”
Cells create DNA by copying it with the help of several different polymerase enzymes that build on DNA already in the cell. But in the 1960s, scientists discovered a polymerase that doesn’t rely on an existing DNA template but instead randomly adds nucleotides to genes that make antibodies for the immune system. The enzyme, called terminal deoxynucleotidyl transferase (TdT), creates random variation in these genes, resulting in antibody proteins that are better able to attack new types of invaders.
TdT is fast and does not have side-reactions that could affect the resulting molecule. Scientists over the years have tried to use the enzyme to synthesize DNA sequences, but it was hard to control. The key is to find a way to get the enzyme to add one nucleotide and then stop, so that the sequence can be synthesized one base at a time.
Previous approaches tried to obtain that control by using modified nucleotides with a special blocking group that prevents multiple additions at once. After the DNA molecules have been extended by a blocked nucleotide, the blocking groups are removed to allow the next addition.
TdT, however, cannot accommodate a blocking group on the nucleotide being added. But Arlow came up with the idea to tether an unblocked nucleotide to TdT, so that after the nucleotide is added, the enzyme remains attached and prevents further additions. After the molecule has been extended, the tether is cut, releasing the enzyme and re-exposing the end for the next addition.
In the first trials, the researchers demonstrated that this technique is not only faster and simpler, but nearly as accurate as other techniques in each step of the synthesis.
“When we analyzed the products using NGS, we were able to determine that about 80 percent of the molecules had the desired 10-base sequence,” Arlow said.
“That means, on average, the yield of each step was around 98 percent, which is not too bad for a first go at this 50-plus-year-old problem. We want to get to 99.9 percent in order to make gene-length DNA.”
Once they can reach 99.9 percent fidelity, they can synthesize a 1,000-base-long molecule with a yield of more than 35 percent, which is currently impossible with existing techniques.
“By directly synthesizing longer DNA molecules, the need to stitch oligonucleotides together and the limitations arising from this tedious process could be reduced,” said Palluk. “Our dream is to directly synthesize gene-length sequences and get them to researchers within few days.”
“Our hope is that the technology will make it easier for bioengineers to more quickly figure out how to biomanufacture useful products, which could lead to more sustainable processes for producing the things that we all depend on in the world, including clothing, fuel and food, in a way that requires less petroleum,” said Arlow.
He added, “Our dream is to make a gene overnight. For companies trying to sustainably biomanufacture useful products, new pharmaceuticals, or tools for more environmentally friendly agriculture, and for JBEI and DOE, where we’re trying to produce fuels and chemicals from biomass, DNA synthesis is a key step. If you speed that up, it could drastically accelerate the whole process of discovery.”
Discuss this and other 3D printing topics at 3DPrintBoard.com or share your thoughts below.
[Source: UC Berkeley / Images: Marilyn Chung, Berkeley Lab]
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Tagged with: 3d printed dna • dna • dna printing • Joint BioEnergy Institute • Lawrence Berkeley National Laboratory • synthetic dna • uc berkeley • University of California at Berkeley
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3D printing of viable DNA molecules could resurrect the Jurassic era
It is well known that everything is better with lasers, and lasers seem to be able to make DNA 3D printing dangerously close to what we might call "accessible to the masses" , and it's all made possible by Cambrian Genomics, a biotech startup based in San Francisco.
Humans, it looks like we'll have cloned dinosaurs soon. You heard right. Now we can literally print viable strands of DNA. Of course, all this is not yet so close to real life, but these developments are clearly the first step into the real world of Jurassic Park. In a video published on Bloomberg, Cambrian Genomics co-founder Heinz Austin even claims that we will soon have cloned dinosaurs:
“This technology will allow us to actually bring back dinosaurs, bring back extinct animal species, and in addition, create new life forms that will help us survive in space and go to other planets”
Laboratory and synthesis of DNA molecules at 3D printing help
And apparently we will get not just dinosaurs, but dinosaurs capable of living in space.
Of course, for a couple more years we may not worry about our laboratory-grown space tyrannosaurs, with laser blasters on their backs and devouring people, but today it is already becoming just a matter of time. Anyone can create super space dinosaurs and they'll be great.
The cost of printing various genomes and their components, from left to right: protein, plasmid, bacterial genome, yeast genome, human genome.
Amazingly, it turns out that DNA printing is not a new technology at all. We have been doing this for many years now. This technology is used to create drugs, to study dangerous pathogens, and we can even program DNA to store huge amounts of data. The catch is not the ability to synthesize DNA, but the cost of the process. Printing the human genome using traditional methods would cost billions of dollars, and in doing so, we would get only one set of human chromosomes. This high price is due to the high failure rate in DNA cultivation. An incredibly large amount of DNA can be grown very quickly, but a large percentage of them will contain errors and defects that make them useless and therefore need to be sorted.
As you can probably guess, sorting billions of strands of DNA is a bit of a time consuming process.
But the new technology developed by Cambrian Genome speeds up this process many, many times over thanks to laser printers for DNA sorting, which makes this process much faster, and therefore more affordable. How accessible will it be? A DNA laser printer will produce more viable DNA at one time than all the machines in the world can produce in one year. Turning the DNA printing process into something that can be accessed by more than just some multi-billionaire or super villain who wants to breed a cosmic thug dinosaur would probably serve humanity well.
Growing synthetic DNA is not the easiest process, but, in fact, they are grown in a sense, like grass. Millions of strands are formed by mixing basic DNA compounds in a specific sequence. After the filaments are formed, they are detached from the structures on which they have grown and then attached to a one micron ball.
After one strand of DNA is attached to each bead, the strand itself is cloned in such a way that each bead has multiple copies of the strand that was attached to it first. The beads are then moved onto a small glass slide and a laser printer examines the DNA strands and selects those beads that contain the correct strands. Thus, full-fledged DNA molecules are sent to special cells, and all unwanted or defective DNA remains on the glass.
Genome lab 3D laser printer
This process starts with one million strands of DNA grown in the lab and ends up with a billion cloned, quality strands sorted at up to a hundred strands per second. As Heinz put it, this will make DNA a commodity.
"Anyone can be a genetic designer"
Of course, that's a little scary considering some of the consumer products that have managed to hit the market today, but it's surprising. We are already living in the future. We are no longer only printing cases for our smartphones, we are able to create life through 3D printing.
Yes, it will probably be 3D printed life that will turn into space dinosaurs that can eat us, but, you must admit, this is a truly exciting prospect.
If you want to learn more about the DNA laser printing process, watch this video and slideshow that explains the process in more detail: Back in 2014, Curiosity rover chief engineer at NASA's Jet Propulsion Laboratory, Adam Steltzner, proposed the idea of colonizing Mars with 3D printed humans. At the time, it seemed like a great and fantastic idea.
The essence of the idea was to use the encoded genetic code in the genome of bacteria to transfer information about a person to other planets. That is, to embed human genomes into the DNA of microorganisms, because, as you know, bacteria can perfectly fly to Mars. Accordingly, bacteria can be used as computer memory, like a flash drive that was sent to Mars.
The idea was fantastic, because it was not clear how to recode this information back. Adam Stenzler suggested using 3D printing, as they already knew how to recreate human tissues and organs.
American geneticist Craig Venter began work on the development of a "digital biological converter" that would be able to transfer a digital file at the speed of light and recreate the original version in a new location.
Three years later, a team of scientists, including Craig Venter, published an article in Nature Biotechnology presenting the results of their work. The article describes the development and use of a prototype digital biological converter (hereinafter referred to as Digital-to-Biological Converter, DBC), which produces components without human intervention. He can then combine those same components and automatically create high-precision synthetic DNA.
When testing, the scientists transferred a file with DNA information to the DBC. He, in turn, converted this information into oligonucleotides using tools developed by Synthetics Genomics (gene synthesis and the Gibson Assembly ™ method for recreating synthetic DNA with high fidelity).
Taking this DNA as a template, the DBC converter produced a series of biological materials - RNA, proteins and viral particles.
