Artificial Life Form Given "Synthetic DNA"

Scientists have created an artificial form of E. coli based on entirely synthetic DNA.

    Scientists in the UK have created an artificial life form called "Syn61", a form of bacteria that has a completely redesigned 4 million letter genome. This feat can help pave the way for designer bacteria capable of manufacturing new proteins, drugs, and other materials. The DNA was ordered in short sequences, then assembled into longer sequences in yeast cells via cellular machinery. These yeast cells produced segments of DNA measuring 500,000 letters long. After each of these segments were tested in partially synthetic bacteria, the 8 segments were combined to create Syn61.

      Jason Chin, the head of this project also took the liberty to correct errors in the synthesis of this bacteria, only 4 total letters. In addition to this, Dr. Chin along with colleague Julius Fredens, decided to remove some codon duplications in the bacteria genome. There are 64 possible codons that can be arranged from A G C and T, however they only code for 20 amino acids, meaning multiple codons can code for the same amino acid. Chin and his team believe that reducing the number of codons can increase the bacterias efficiency. Syn61 gets its name from the fact that only 61 of the 64 possible codons are used by the cell. The three left over codons can now be "reassigned" to non-naturally occurring amino acids, which could bring a different chemistry to the cell. The number of codons needed was also reduced to improve efficiency. One way of achieving this was to use less "stop codons" (UAA, UGA, UAG) which can also potentially increase the efficiency of Syn61. These efficiency improvement techniques will be quite useful once bacteria can be synthesized for the sole purpose of creating drugs and other useful biochemical materials. The team also took further measures to remove material in the cell that was no longer needed, such as tRNA of the deleted codons.

     Syn61 has shown to grow roughly 60% slower than E. coli, which could suggest that the removed duplicate codons may actually have some importance. Nonetheless Syn61 is alive and reproducing despite having every gene on its singular chromosome altered. Another interesting finding is that the altered genetic code provides resistance to a wide variety of viruses simply because Syn61 lacks the tools to translate or integrate viral DNA, which could pave the way in creating virus resistant industrial microbes, plants/crops, and even human cells. Dr. Chin says they have not yet attempted to modify the virus in this capacity to be virus specific, but it is "high on his to-do list."

    I found this article interesting because the creation of this microbe is a big step forward in synthetic biology. As more becomes known about this procedure we may be able to give ourselves immunity to certain viruses by receiving DNA specific to anti-viral materials. I also had not thought about the idea of "bacteria farming", in creating bacteria to produce a useful material.


https://www.bbc.com/news/science-environment-48297647?intlink_from_url=https://www.bbc.com/news/topics/c40rjmqdw54t/genetics&link_location=live-reporting-story

4 New DNA Letters Double Life's Alphabet

In an article from Scientific American, scientists have doubled the number of DNA bases into an eight-language that stores and transcribes information just as the natural four key bases- A, T, C and G. In a recent study, researchers revealed that the new synthetic bases can bind to each other and the double helices can hold its structure. The new synthetic pairs of bases are S and B, and P and Z. These new additional pairs share similar properties and sizes of the natural four bases but differs in terms of bonding patterns. The research demonstrated that the synthetic bases bound to their complementary partners and were able to keep up the structure of the double helices stable regardless of what orders the synthetic pairs were in. The letters of the synthetic DNA pair up as they form hydrogen bonds like the natural letters. In addition, the synthetic P and Z better binds to cancer cells than the natural four bases.

The synthetic DNA codes for a certain aptamer and can be transcribed to a RNA and can store information. According to the study, there has to be more research done before reaching a true eight-letter synthetic genetic system because it is still questionable if the synthetic DNA can be replicated by polymerases which is responsible for making DNA during cell division inside organisms.

I find this study very amusing because it demonstrated a huge breakthrough in genetics and created more diversity in the DNA bases. Using the new eight-letter language, scientists will be able to create more RNA from DNA sequences that can be used in medical diagnostics and genetic storage.

A DNA-based Vaccine for the Zika Virus

The infamous Zika Virus has been on the rise ever since the recent outbreak which began in 2015. Ever since, it has spread around the globe through Africa, Asia, South America, and North America. The Zika Virus is transmitted by mosquito bites. Further, the virus is sexuallytransmitted. The symptoms of the Zika Virus are headaches, fever, bloodshot eyes, rashes, muscle pain, and joint pain. In pregnant women, the child can be born with an abnormally small-sized head and will show the same symptoms previously listed. The infant can be tested for Zika using reverse-transcriptase polymerase chain reaction or serologic testing. Serologic testing is a method that looks to see if there are antibodies present in the blood.

Primarily, scientists studied animals that were naturally resistant to the virus. Then, they decided to work with animals that were susceptible to the virus. Scientists first injected these animals with the virus to ensure they were infected.  Next, the scientists gave the animals a synthetic, DNA-based vaccine that they developed. The vaccine has shown to produce antigen-specific antibodies and T cell responses that prevented the virus from infecting the organism. The virus was neutralized by the vaccine and caused no damage to the organism. Through this vaccine, the virus was unable to spread to the animal’s brain. This is what causes the abnormally small-sized head in infants infected with Zika. These animals were then injected with the virus again and still no change was observed. This result was seen in one hundred percent of the animals used in the study.

Currently, the DNA-based vaccine is being administered in two human clinical studies. It is so great to see what the power of genetic engineering can accomplish. The scientists were able to produce a synthetic strain of DNA to use in the vaccine produced. It is very interesting to me how they knew which base pairs to use and what DNA sequence would fight against the virus. Additionally, I am curious if they used a desired DNA sequence that codes for a specific protein needed to inhibit the virus from attacking the organism. Zika has, and still is, affecting so much of the population around the world. Scientists being successful with the vaccine on the human studies will help many individuals to be safe from the destructive disease. 

Synthetic biology: A yeast for all reasons

This article reports on work done by Dymond et al. to reengineer the genetic sequence of Saccharomyces cerevisiae, a baker’s yeast.  Previous work in the area of synthetic biology included the genetic reengineering of bacteria such as Escherichia coli and Mycoplasm.  In S. cerevisiae, Dymond and his team have been able to replace sections of two chromosomes with synthetic DNA: twenty regions from the naturally occurring yeast chromosome were removed and genes with bases longer than 500 were recoded to contain “watermarks”, sequences that are used for the easy differentiation between synthetic DNA and natural sequences.  The findings for this experiment indicate that synthetic DNA can be used with minimal risks: yeast cells did not suffer serious defects and the synthetic sequence was reproduced in living cells.  In addition to this, Dymond and his team introduced loxPsym sites into their synthetic DNA.  They found that, in the presence of an enzyme called Cre recombinase, loxPsym sites combine with each other to make new random structures.  These findings indicate that there is great potential to synthesize numerous yeast genomes with differing structures. The major setback to this research is that a lot amount of time, money, and labor is needed to continue it.  I think the work Dymond and his team are doing is very important to genetics and biology.  Using synthetic DNA to recode the genomes of different bacteria will accelerate experiments involving these organisms: their genome will be easier to understand and work with if it is recoded to be simpler.