Let's explore how second generation sequencers work. So, this is a process that is also called sequencing by synthesis. So, along the way we're going to explore how DNA is copied. And we're going to use a cartoon representation of DNA. We're going to draw double stranded DNA as a pair of Lego towers that look like this, sort of touching each other. It's as though we took the double helix over here and we untwisted it to make a sort of flat ladder shape, and then used pairs of Lego's over here to represent the complimentary pairs of bases in the DNA. So, for example, here is a complimentary pair of Lego's, G and C. And likewise, they correspond to one rung of the double helix, like this orange and red that you see here. So, when a cell in your body divides to form two daughter cells, the genome in the cell gets copied. Every cell in your body, just about, has a copy of your genome, so when one of these cells divides, it needs to pass on a copy to each of the offspring cells. So, at the beginning we start out with double stranded DNA, and then it gets split into two single stranded molecules of DNA. It's as though we took this ladder and sort of chopped it right down the middle. So, the complementary base pairs are now separated and we have two separate strands. Each strand still has the genome sequence written on it and the two strands are complementary to each other, but not they are separated. And as you'll see, each of them acts as a kind of template. So, this template tells us that if we want to make this strand on the left here double stranded again then we want to start by putting a complementary base down here, opposite this G. So, we want to start by putting a C down here, complementary to the corresponding G. The name of the molecule, the enzyme that puts this piece in its place, that puts the complementary base in it's place, is called DNA polymerase. DNA polymerase is a little machine that, given one of these single stranded templates, like this one here on the left, and given a base, you know this base might be floating around somewhere just waiting to be incorporated. Given these two things, the polymerase will build the complementary strand, piece by piece, resulting in a double-stranded copy of the template strand. So, for example, the DNA polymerase might integrate this C nucleotide here, and then it will move on and integrate a T nucleotide here, because T is complementary to A. And then an A nucleotide here, and a T, and a G, and a G, and so on. So the result is, if we do this for both of the template strands, not just the one on the left but also the one on the right, then the result is we now have two double stranded copies of the original DNA. Second generation sequencers sequence DNA by eavesdropping on this process. So, in other words, if we could watch what the polymerase is doing, as it builds the complementary strand, then we can infer the sequence of the template molecule, and that's exactly what we want to be able to do. Now, of course, we want to do this not just for one template, but for many, many of millions, or perhaps even billions of templates all at once. And so how we do that is what we'll discuss in the following lecture.
