Synthetic DNA & More

Steven Benner of the Foundation for Applied Molecular Evolution his team expanded the genetic alphabet with two new bases, called Z and P. The team provided structural evidence that multiple adjacent pairs of Z:P could form a normal geometric configuration. Benner then also created a library of genetic sequences with a random string of nucleotides that included the Z and P bases.

Adding just two new bases to the natural four opens up the possibility of creating brand new amino acids beyond the 20 standard amino acids that form the basis of the vast majority of proteins in living organisms. Since proteins are responsible for such a wide variety of human functions, from building and rebuilding muscle tissue to creating antibodies to fight off diseases, the hope of this expanded genetic alphabet is that developing entirely synthetic proteins could be used for new medical treatments.which can lead to the creation of new drugs and therapeutics (4.26).

Synthetic biologists have created two new artificial nucleotide bases that pair up with one another and, unlike, can incorporate into genetic sequences to form a properly structured double helix. The team has also used these artificial nucleotides to engineer genetic sequences that adhere specifically to to cancerous, cells.

A main task for the team to accomplish was to create enzymes that could copy a gene from a DNA molecule to an XNA molecule, and other enzymes that could copy that same gene back into DNA.Since then, the team has figured out how to fold strands of their synthetic XNA molecules to form enzymes. The XNA enzymes then displayed the ability to cut and paste individual pieces of XNA, which store and copy genetic information, while also building and breaking down certain molecules as needed (4.16, 4.17).

Because synthetic XNAzymes are much more stable than naturally occurring enzymes, the scientists believe that they could be particularly useful in developing new therapies for a range of diseases, including cancers and viral infections, which disrupt and exploit the nature of the human body. Dr. Phillip Hollinger, who is leading the team of researchers focused on XNA added: “Our XNAs are chemically extremely robust and, because they do not occur in nature, they are not recognized by the body’s natural degrading enzymes. This might make them an attractive candidate for long-lasting treatments that can disrupt disease-related RNAs” (4.19).

Researchers at the University of Illinois at Chicago and Northwestern University have engineered a single-unit ribosome that works nearly as well as the biological cellular component. The synthetic ribosome, called Ribo-T, was created in the laboratories of Alexander Mankin, director of the UIC College of Pharmacy’s Center for Biomolecular Sciences, and Northwestern’s Michael Jewett, assistant professor of chemical and biological engineering. The human-made ribosome could possibly be able to be manipulated in the laboratory to carry out functions that natural ribosomes cannot. When the cell makes a protein, mRNA (messenger RNA) is copied from DNA. A ribosome has two subunits made out of RNA and protein-- one big and one small subunit,. These two subunits unite on mRNA to form the functional unit that assembles the protein in a process called translation. Once a protein molecule is complete, the ribosomal subunits separate from each other. Ribo-T, however, is a synthetic ribosome with subunits that do not separate, and may be able to be modified to produce unique and functional polymers (large repeating units) for exploring ribosome functions or producing designer therapeutics (4.20, 4.21).

Exanded Genetic Alphabet:

Key to Medical Therapy

The scientists at Synthorx, however, have taken it up a notch, and have introduced two new bases, d5SICSTP (X) and dNaMTP(Y), into the E. coli bacteria’s DNA, where they have successfully paired with the four natural bases. Since E.coli is a bacteria that replicates very quickly, it is the perfect test material for synthetic biology experiments like this one. Researchers add the synthetic bases to natural E.coli genetic material and stimulate a reaction of the genetic material into a new protein. The next step is to get bacteria to adapt these synthetic nucleotides naturally and form proteins completely on their own.

DNA is made up of four base pairs of compounds called nucleotides: adenine (A) and thymine (T), and guanine (G) and cytosine (C). Combinations of just these four bases forms the genetic material of every living thing in nature, and serve a lot of different purposes, including coding for the production of amino acids.

Fighting Cancer

The research team mixed these genetic sequences with liver tumor cells to see which ones would adhere to the cancer cells. The sequences that stuck to the cancer cells were then mixed with normal liver cells to single out the ones that also bound to the normal cells. The team then took the remaining sequences and put them through the process again, and repeated the whole procedure multiple times. In the end, the team determined more than a dozen genetic molecules that specifically bound to the tumor cells. Those that were the strongest contained Z or P in the sequence. This suggests that “this system explored much of the sequence space available to this genetic system and that GACTZP libraries are richer reservoirs of functionality than standard libraries” (4.18)

XNA: Synthetic DNA

Synthetic Ribosomes

Synthetic Enzymes

Ribosomes are organelles found in every living organism. They are the protein factory of the cell. In each kingdom of life, these protein-synthesizers exist in two subunits, and have been for billions of years. Now, however, scientists have attached the two ribosomal subunits together. In so doing, they have opened the doors to both new discoveries on the biology of these machines and possibilities for synthetic biology applications. After all, “the ribosome is viewed as one of the most interesting and attractive machines for synthetic biology.” (4.20)

For example, ribosomes could be altered to produce proteins from synthetic amino acids that resist degradation. Proteins that are resistive could be useful for making drugs with longer-lasting activity. he engineered ribosome may enable the production of new drugs and next-generation biomaterials and lead to a better understanding of how ribosomes function (4.20).

Synthetic enzymes, which do not occur naturally, have been created using a synthetic form of DNA called XNA and were capable of triggering chemical reactions in the lab. Previously, it had been thought that DNA and RNA, which form the basis for all life on Earth, were the only way of storing genetic material; nonetheless, scientists have created synthetic enzymes from scratch, using genetic material created in the lab. These enzymes don’t contain DNA or RNA but they contain artificial XNA. These innovative enzymes could potentially be used to produce new medical treatments and find life on other planets. XNAzymes, as they are called, are capable of catalysing, or speeding up, simple reactions, like cutting and joining strands of RNA in a test tube. One of the XNAzymes can even join strands together, which represents one of the first steps towards creating a living system.

Each viable organism relies on the same genetic building blocks: the information that is found in DNA. But now, there is another class of genetic building material: "XNA" — a synthetic polymer that can carry the same information as DNA, but with a different arrangement of molecules. Philipp Holliger of the MRC Laboratory of Molecular Biology in Cambridge, UK and his team have focused on six XNAs (xeno-nucleic acids).

The X stands for Xeno, a greek root meaning “strange, or foreign”. The XNAs had different sugars, and in some of them the sugars are replaced with completely different molecules.They synthesized it using the same bases as DNA and RNA - adenine, thymine, guanine, cytosine and uracil, but the team swapped out the sugars onto which each of these bases are usually attached with other sugars and molecules that are not found in nature, hence the “Xeno-” prefix in XNA.