DNA sequencing is the process of determining the sequence of nucleotide bases in a piece of DNA. While this may sound straightforward, the process is a complex with several steps and chemical analyses.
Researchers across multiple fields and industries utilize this method, offering a wide range of uses and applications. Researchers frequently use it in biochemistry, genomics, biological anthropology, evolutionary biology, medicine, virology, forensic science, and the growing ancestry testing industry.
A Brief History of DNA Sequencing
Although DNA was first isolated in 1869, its importance wasn’t discovered until decades later. The first DNA sequences were done over a hundred years later in the 1970s, using a laborious process called two-dimensional chromatography. This developed into the process known as Sanger sequencing.
Early DNA sequencing was first performed on viruses. The first complete DNA sequence was published in 1977 and belonged to bacteriophage φX174, a virus that attacks E. coli bacteria. Viruses have single-stranded DNA instead of the double-stranded DNA of both prokaryotes and eukaryotes, which made them much easier to sequence in the early days of DNA sequencing.
From there, DNA sequencing technology developed rapidly. In the 1990s, the National Institutes of Health (NIH) ran several sequencing projects for various species of bacteria with the goal of sequencing the human genome.
Researchers formally launched the Human Genome Project in 1990 and completed a gapless DNA sequence of the human genome 32 years later. The project officially published the complete human DNA sequence in January 2022.
DNA Sequencing Workflow
Sequencing DNA involves determining the order of the four nucleotide bases that make up the DNA molecule. This base order helps analysts identify the type of genetic information within a specific DNA segment.
To determine the order of base pairs, scientists first manipulate, amplify, and process the DNA segment. There are several ways to complete this:
Sanger Sequencing: The First Method
The oldest and simplest method is Sanger sequencing, which requires making multiple copies of the target DNA region.
In this process, scientists mix the DNA sample with both normal nucleotides and dye-labeled, chain-terminating dideoxy nucleotides in a tube. They then heat the mixture to denature the DNA and cool it to allow the primer to bind to the single-stranded template.
After this, DNA polymerase synthesizes new DNA. It continues adding free nucleotides to the chain until it happens to add a dideoxy nucleotide instead of a normal one.
At that point, no further nucleotides can be added, so the strand will end with the dideoxy nucleotide.
The next step is to run the DNA fragments through a gel matrix in a process called capillary gel electrophoresis. The smallest fragment, ending just one nucleotide after the primer, finishes this process first.
The next-smallest fragment, which contains two nucleotides, follows first, and the process continues up to the final fragment. A laser illuminates the dyes, and a detector records the signals to reconstruct the original DNA sequence one nucleotide at a time.
This process works, but it is extremely tedious and expensive compared to modern methods.
Next-Generation Sequencing: Faster, Scalable DNA Analysis
Modern methods are far more sophisticated than the Sanger technique developed over 40 years ago. These advanced methods are known as next-generation sequencing.
There are several next-generation sequencing methods that use different technologies, but they all have a few things in common.
Scientists run next-generation sequencing reactions in parallel using short nucleotide sequences, which they process simultaneously. As a result, they generate results much faster.
They also perform these reactions on a chip rather than in a tube or through gel electrophoresis. This approach allows them to sequence large quantities of DNA more quickly and cost-effectively than with Sanger method.
One of the most crucial parts of next-generation sequencing is the various algorithms that are used to assemble the DNA sequences. Since a large volume of data is generated from a single sequencing chip, computer programs like Phred and Phrap evaluate raw sequence data.
Trimming algorithms are then used to clean up the sequences and transform the raw data into usable material.
Nanopore technology, a next-generation sequencing method, threads single DNA strands through tiny pores in a membrane. Scientists read the DNA bases one at a time by measuring how each base alters the electrical flow of ions passing through the pore.
This method offers exceptional speed because researchers can reuse the same DNA molecule. They don’t need to replicate large batches of DNA before beginning their analysis.
Who Uses DNA Sequencing?
Medical Diagnostics
DNA sequencing is one of the best ways to identify the causes of rare genetic disorders. Only 4,000 of the more than 7,800 identified genetic disorders are linked to a specific gene.
Thus, looking at the entire genetic sequence of a person with a genetic disorder can provide information about which alleles cause a particular illness.
It’s also vital for treating cancer. Understanding the genetic basis of a tumor or cancer makes diagnostic decisions easier, plus it provides a better understanding of the potential treatment options a cancer patient may respond to.
Molecular Biology
Most biology laboratories now include DNA sequencing as an integral part of laboratory operations. Researchers use gene sequencing to study variations in the genetic makeup of model organisms and to verify the traits of cell lines and cloned tissue cultures.
DNA sequencing is the primary method of studying regulatory elements within cells and how variations in these regulatory sequences affect cells, tissues, and organisms. Being able to identify which genetic regions are responsible for gene expression is a valuable purpose of DNA sequencing in any molecular biology laboratory.
Forensic Science
DNA sequencing is the basis of modern forensic science. The ability to use low concentrations of DNA to obtain reliable genetic data through next-generation sequencing is extremely useful for crime scenes.
Experts can examine human remains using this approach to determine the cause of death. Poisoning damages DNA in affected organs—damage that standard autopsies can’t detect.
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