Reading the ACGT’s of DNA: What does sequencing mean?

by Ivy Rose Sebastian, Antonino Napoleone | April 8, 2022.

Did you know that the DNA in each of our cells contains six billion individual building blocks, all of which fit into a tiny space of just six microns?! If you were to stretch out this DNA, it would be about two meters long and, if you were to put together all the DNA from all your cells, it would be about twice the diameter of the solar system!
DNA or deoxyribonucleic acid is the fundamental building block of an organism and the total DNA content in an organism is called its genome. The genome provides the blueprint of instructions for the development and function of the organism. So naturally, if we could ‘read’ the genome, we should be able to get all the information about the organism, right? Then, how can we do so?

The ACGTs of DNA

DNA sequencing is the method that determines the exact order of the bases in a strand of DNA and allows us to ‘read’ it. DNA is made up of different combinations of four main nucleotide bases: adenine (A), thymine (T), cytosine (C), and guanine (G). These chemical building blocks only bind with their specific partners to form base pairs i.e. A with T and C with G and thereby, make up the DNA double helix which can store enormous amounts of genetic information within our tiny cells, forming the chromosome set (Figure 1). This complementary base-pairing is the underlying principle of DNA sequencing! So, how did the age of sequencing come about? What is its relevance in our society? Delve into this article to find out more about this innovative, state-of-the-art technology!

A long journey to DNA sequencing

The development of DNA sequencing from handwritten deductions to automated sequencing platforms resulted from continual collaborative efforts from the scientific community (Figure 2). After James Watson, Francis Crick and Rosalind Franklin discovered the structure of DNA in 1953, many attempts were made to sequence DNA. Robert Holley conducted the very first attempt to sequence nucleic acids in 1965, where he successfully sequenced the first transfer RNA (tRNA) from yeast, for which he later won the Nobel Prize.

Ray Wu, a Chinese American biologist based at Cornell University, published one of the first methods for sequencing DNA in 1970. Frederick Sanger and colleagues then implemented this technique and, over the 1970s, introduced the famous ‘Sanger method’, which made it possible to sequence long stretches of DNA in a short time. Sanger’s chain termination method dominated the sequencing world for the next 30 years!

Simultaneously, there was also another technique developed by Allan Maxam and Walter Gilbert at Harvard University, called the chain degradation method, but it soon fell out of favour as it was more complex and difficult to scale up.

Both techniques lacked automation and hence, were time-consuming and tedious. However, Sanger sequencing was more amenable to automation, paving the way for the first DNA sequencers. In 1986, the first automated DNA sequencer was devised by Leroy Hood and Michael Hunkapiller, who brought about two major improvements to the Sanger method: firstly, DNA fragments were fluorescently labelled (in contrast to using radioactive molecules), and secondly, data acquisition and analysis were done using computers (Figure 3) – an event that was simply startling for biologists at that time!

After the development of automated sequencers, the 2000s became a golden period for sequencing platforms. Since the 1990s, there has been rapid growth and development of sequencing methods and machines. Such innovations have improved efficiency and accuracy and radically lowered the costs of whole-genome sequencing, making it accessible and affordable.
Next-Generation Sequencing (NGS) is one such massive parallel sequencing technology that allows for a deeper acquisition of genomic information beyond the capacity of traditional DNA sequencing technologies.

Reading the Human Genome

The Human Genome Project, which was a huge collaborative effort that started in 1990, took 13 years and an astronomical amount of 3 billion US Dollars to be completed. However only 92% of the genome was completed, owing to the vast complexity of the genome, increasing costs, and tedious efforts. With current techniques, it could be done in less than 2 weeks and at a much lower cost of 1000 US Dollars. In the last week, nearly two decades later, a team of 100 scientists has finally published the sequence of the human genome in its entirety at a fraction of the costs that the initial project took using innovative sequencing methods (Figure 4).

Relevance of sequencing – to read or not to read?

Sequencing has wide-ranging applications; from improving disease diagnostics and personalised medicine to evolutionary biology and wildlife conservation! Here are a few applications that highlight the revolutionary impact of sequencing:

1. Medicine: Sequencing information can help researchers identify changes in genes, associations with diseases and phenotypes, and identify potential drug targets. This is especially true in the case of genetic diseases and cancer.
2. Virology: One of the most impactful and relevant applications of sequencing has been tracking and variant surveillance of the SARS-CoV-2 virus. This in turn aids in the rapid identification of new variants and helps to study their evolution (read further – The dynamics between immune protection and virus evolution).
3. Evolutionary Biology: NGS platforms can now be used to unveil insights into our evolutionary past. For example, for the first time in February 2021, scientists reported the sequencing of DNA from a mammoth, over a million years old. This is the oldest DNA to be sequenced to date!
4. Wildlife Conservation: Sequencing also plays a significant role in aiding conservation efforts. It allows scientists to research the underlying genetics and help monitor the reproductive health of endangered species.

Conclusions

As we can see, there are wide-ranging applications of sequencing technology and with time, there would be more innovations that would yield amazing new discoveries!

To quote Sanger,

“Scientific research is one of the most exciting and rewarding of occupations. It is like a voyage of discovery into unknown lands, seeking not for new territory but for new knowledge. It should appeal to those with a good sense of adventure.”

References:

• https://the-dna-universe.com/2020/11/02/a-journey-through-the-history-of-dna-sequencing/
• https://www.genome.gov/dna-day/15-ways/dna-sequencing
• https://www.genome.gov/es/node/17331
• https://bitesizebio.com/27892/decoding-the-genome-applications-of-dna-sequencing/
• Wheeler, D., Srinivasan, M., Egholm, M. et al. The complete genome of an individual by massively parallel DNA sequencing. Nature 452, 872–876 (2008). https://doi.org/10.1038/nature06884
• S. Nurk, et al. The complete sequence of a human genome. Science 376, 44–53 (2022).