Progression of DNA sequencing over the years

Nathnael Bekele

Although we can now use technology to quickly sequence entire genomes in a measure of a few weeks, DNA sequencing was originally a very time-consuming procedure. For example, it took 13 years to complete the Human Genome Project in 2003 and 3 billion dollars. The Human Genome Project was designed to sequence the first human reference genome (Fatima and Ebertz). Now, this would have taken “less than two weeks and at a cost of just around € 1,000” (Fatima and Ebertz)

The first breakthrough in DNA sequencing involved figuring out the structure of DNA. This was solved by James Watson, Francis Crick, and Rosalind Franklin in 1953 (Fatima and Ebertz). They found that DNA was found in a double helix structure made out of two standards interlinked with each other. DNA is made up of four chemical bases represented by the letters A, C, G, and T. “These bases combine in different three base combinations (such as ATG or TGG) to form amino acids which are the building blocks of proteins” (Sharman). Proteins are very important as they are used in the transportation of molecules and signals, enzymes, antibodies, and the making of structures (MedlinePlus). Knowing a DNA’s sequence can help understand the function of proteins it is used to form.

“In 1965, Robert Holley sequenced the first tRNA, for which he was awarded the Nobel Prize in 1986.” (Fatima and Ebertz). Transfer RNA (tRNA) is a smaller RNA molecule that is involved in protein synthesis (NHGRI). The tRNA is not as large as genomes or other RNA molecules so its sequencing was a step in understanding what sequencing methods are available.

“Fredrick Sanger kept working on an alternative DNA sequencing method and in 1977, developed the first DNA sequencing method that utilised radiolabelled partially digested fragments called “chain termination method”. This method went on to dominate the sequencing world for the next 30 years!” (Fatima and Ebertz)

The sanger method used “radiolabelled partial-digestion fragments” called terminators (Sharman) in order to find out the bases and the sequence of bases in a genome (Heather and Chain). This method basically used defective bases which would attach to the bases of the DNA and terminate the process of base pairing. Each base has its own radioactive label. So when the reaction has stopped, we are able to know the sequence of the genome by looking at the sequence of the different radioactive labels. This way Sanger was able to sequence the genome of “bacteriophage PhiX174 (virus that infects E. coli)” (Fatima and Ebertz).

An improvement to the Sanger method was shotgun sequencing. In the sanger method, all of the genome is studied at once. So, it takes a while for defective radiolabelled bases to pair with all the bases of the genome at hand. Shotgun sequencing first breaks apart the genome and then sequences each segment individually. This way many segments can be sequenced in parallel at the same time still using the Sanger method. This gives multiple sequences called reads (Sharman). “Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence” (Sharman). This speeds up the Sanger sequencing drastically.

Later on, this method was made even more efficient by using dyes instead of radiolabels for the terminators (Sharman). Originally the Sagner method read the resulting sequence by looking at the different radioactivities of the terminator bases. This is time-consuming as developing the images of these radioactive substances takes a while. However, by instead using different color dyes to label the bases, the sequence of the bases can easily be read.

Nowadays, there are more complex procedures that are used in order to sequence DNA. Furthermore, the process is automated almost entirely. Thus, scientists are able to sequence many genomes in a short amount of time. This is very helpful. As mentioned in previous blogs, comparing differences in gene expression and repression can be insightful in understanding the causes of diseases, and understanding how different proteins are formed.

Sources

Ebertz, Andreas, and Tamseel Fatima. “A Journey through the History of DNA Sequencing.” The DNA Universe BLOG, the-dna-universe.com/2020/11/02/a-journey-through-the-history-of-dna-sequencing/.

Heather, James M, and Benjamin Chain. “The Sequence of Sequencers: The History of Sequencing DNA.” Genomics, Academic Press, Jan. 2016, www.ncbi.nlm.nih.gov/pmc/articles/PMC4727787/.

Sharman, Sarah. “The Evolution of DNA Sequencing Technology.” HudsonAlpha Institute for Biotechnology, www.hudsonalpha.org/evolution-of-dna-sequencing-part-1/#:~:text=Around%201977%2C%20two%20groups%20independently,generation%20of%20DNA%20sequencing%20technology.

“Transfer RNA (Trna).” Genome.gov, www.genome.gov/genetics-glossary/Transfer-RNA#:~:text=Transfer%20RNA%20(abbreviated%20tRNA)%20is,that%20make%20up%20a%20protein.

“What Are Proteins and What Do They Do?: Medlineplus Genetics.” MedlinePlus, U.S. National Library of Medicine, medlineplus.gov/genetics/understanding/howgeneswork/protein/.