A New Genetic Language: Additional DNA Base Pairs Discovered

By: Anna Christou

Adenine, guanine, cytosine, and thymine—these four nitrogen-containing compounds, also known as A, G, C, and T, respectively, have been known, since the mid-twentieth century, to be the main components of DNA. DNA defines our characteristics, including how we look, behave, and grow, and the sequence of these base pairs is crucial to determining how DNA replicates and codes for protein. With the rise in genetic engineering, scientists have been able to manipulate these base pairs to change an organism’s genes, which has a variety of implications for research, creating vaccines, and developing drugs. Given the endless potential that studying four DNA base pairs affords us, it’s almost impossible to comprehend what we could do with eight base pairs. But recently, a group of researchers published a paper in Science, in which they revealed that they had synthesized four new DNA bases, naming the total of eight bases “hachimoji” (which means “eight letters” in Japanese). The synthesis of the four new bases—called S, B, P, and Z—radically changes our understanding of the genetic code and has the potential to transform genetic engineering.

DNA, which stands for deoxyribonucleic acid, is found in every cell and carries the information that determines the growth, development, and everyday functioning of an organism. DNA is a double-stranded molecule, and each strand consists of three components: nitrogen-containing bases (A, T, G, C), sugars, and a phosphate group. The bases of the two strands pair with each other through hydrogen-bonding and determine the identity of the genetic sequence. The main processes that DNA molecules undergo are replication, which allows cells to grow, and transcription, which helps DNA produce the different proteins that it codes for and which are necessary for a cell’s survival.

Replication occurs every time cells divide, since each daughter cell that results from the division must have the same genetic information as the parent cell. This ensures that the identity and normal functioning of each cell is maintained through every division. In transcription, an intermediate RNA molecule is created, which is then used to make proteins for use by the cell. RNA is very close in structure to DNA but the main function of RNA is to temporarily carry the information to make proteins.

The researchers synthesized two additional base pairs: S and B, as well as P and Z. Unlike the natural base pairs, these synthesized bases do not exist in nature. However, P, Z, S, and B have structures that are very similar to A, T, C, and G; they are also nitrogen-containing compounds that have small chemical differences to make them unique molecules. Like A, T, C, and G, they are able to undergo hydrogen-bonding, which is the link that holds bases and entire DNA strands together. The fact that the newly-synthesized base pairs have similar chemical structures and can hydrogen bond, just like the natural bases, indicates that they can behave very similarly.

After synthesis, the new base pairs had to be tested in order to determine whether they could undergo the same processes as natural DNA. The researchers added the synthetic base pairs into a double-stranded molecule that also included A, T, C, and G, and performed a variety of tests on this molecule to determine whether it maintained the characteristic features of natural DNA.

First, a crucial feature of DNA is that its base pairs are complementary and bind with each other through hydrogen bonding. This is necessary for preserving the identity of the genetic sequence and for ensuring that replication and transcription run smoothly. In this new molecule, the normal bonding between base pairs was preserved: A paired with T, and C paired with G, and notably, P paired with Z, and S paired with B. Also, the melting point—the temperature at which the bonds between base pairs break and the strands separate—of the molecule was very similar to that of natural DNA molecules. This important finding showed that the structure and stability of the synthetic base pairs is similar to that of natural DNA.

In addition, DNA is mutable: it can be changed both through natural and experimental mutations. Mutations provide an organism with genetic variation that allows it to adapt to different environments. Although mutations in DNA change the genetic sequence and potentially affect the functioning of a cell, DNA is easily changeable and the act of making mutations does not damage the structure and stability of DNA. As a matter of fact, researchers found that hachimoji that contained mutations were able to maintain the same structure; thus, like DNA, hachimoji is a mutable genetic information system. This feature of the hachimoji is crucial for its potential applications in genetic engineering: being a stable molecule that can withstand breaks and imperfections, it will likely be easily manipulated and inserted into cells.

The authors of the paper also tested whether transcription would occur, which is the process that copies a DNA sequence into an RNA molecule that can be used for protein synthesis. The synthetic DNA was able to undergo transcription, but only if specific RNA polymerases—enzymes that copy normal DNA into RNA in transcription—were present. The ability of this new DNA to make RNA opens up the possibility of developing new proteins, though limited by specific RNA polymerases. Also, the researchers did not test whether the RNA transcribed by the hachimoji would be able to be translated into protein. Nevertheless, the fact that the synthetic base pairs could be transcribed into DNA leads to endless pathways in genetic engineering, as RNA—a precursor to proteins—is often used in genetic engineering as a more direct method of inserting new proteins.

All in all, these researchers have established a new genetic system that can store and transfer genetic information with high stability and mutability. Thus far, this genetic system only exists in a precisely-controlled lab environment. Nevertheless, the authors of the paper emphasized that this finding has a wide variety of potential applications. With double the number of DNA bases as A, C, T, and G, hachimoji DNA has much more diversity and has the potential to make synthetic biology and genetic engineering more powerful. Currently, the number of codons, which make up proteins, is limited by the number of DNA bases at 64 possible codons. With an eight-letter alphabet, however, there are 4,096 codons—a change that dramatically increases the number of possible, unique proteins that can be created. Having more possible sequences and proteins, for example, would lift constraints on drugs that need to bind to protein-specific receptors and targets in order to work. Without a doubt, this discovery completely upends the standard approach to research; rather than work within the confines of four base pairs, scientists in a variety of fields can employ this revolutionary discovery in unprecedented ways.

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