How to sequence DNA

Many biologists are using DNA sequencing to provide evidence to answer questions about creatures they study, but what does this mean? Well, sequencing is a method that allows us to read the chemical structure of DNA.

Before understanding how sequencing works, we must be familiar with its structure. DNA is a long chain-like smolecule given the full name 'DeoxyriboNucleic Acid'. The chain is made up of a series of four building blocks, called nucleotides (pronounced "new-cleo-tides"), referred to as 'A', 'C', 'G' and 'T'. Each nucleotide has a slightly different chemical structure, and the order of nucleotides in DNA gives a code. In reality, DNA is double stranded. The coding strand is used as the cells' instructions, while the non-coding strand provides stability, and acts as a back-up copy. The two strands are needed to copy DNA, in a natural process called replication. Scientists use this process to copy small sections of interesting DNA in huge amounts. The artificial process is then called 'amplification', and commonly used in DNA sequencing.

To first amplify DNA, we mix the DNA of the creature we are interested in (the template to be copied) with unused building blocks (free nucleotides) and tiny man-made DNA pieces called primers. Two different types of primers are used. Each type of primer joins an appropriate place of the creature's DNA it matches with. The two places in which the different primer types join give the outer boundaries of the region to be copied. Another thing the mix needs is a 'polymerase enzyme' (en-zime). This is a chemical machine used to join free nucleotides building blocks together. The primers which are bound to the creature's DNA give a start point for the enzyme to join new nucleotides onto, and the DNA chain then grows.

So how does sequencing work? Typically, sequencing is used to read a small piece of DNA between two limits already defined using the copying process above. It also works with a similar chemical mix, but only one type of primer is used. This primer provides the starting point for reading the DNA (=sequencing). As before, a new artificial DNA strand is made by joining building blocks together into a growing chain. Unlike amplification, special light reactive chemicals (called fluorescent dyes) are now included in the chemical mix for sequencing. There are four light reactive chemicals, each like one of the four-nucleotide building blocks (an A-like dye, C-like dye, etc). If a regular nucleotide building block is added to a growing DNA chain it can keep growing, but when a light reactive one is added, they stop the chain growing. This process generates lots of different length DNA chains, all stopped at different places because a light reactive chemical was added to the growing chain. Scientists then separate DNA chains of different lengths, and determine the last letter of each chain. One way to do this is to pass the DNA through a gel solid (which is like jelly/jello and not really very solid). The smallest chains pass through the gel the fastest and the type of light reactive chemical at the end of the chain identified. Next, a slightly longer chain passes through the gel and the type of chemical at its end detected. Next, even longer chains pass. Put in order by computer, the series of detected light reactive chemicals tells us the order that nucleotides occur along a strand of DNA, i.e. its DNA sequence.

Now we have a complete sequence for a piece of DNA (that may run to millions of nucleotides) we can compare them to other creatures to see where they are different and where they are the same. In much the same way as a palaeontologist compares the structures of bones of different animals, we can compare changes in nucleotides to see how things evolve.

Also see: http://seqcore.brcf.med.umich.edu/doc/educ/dnapr/sequencing.html

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