We're going to begin the explanation of exactly how the DNA molecules break and rejoined to allow for gene rearrangement. The mechanism is quite complicated. The first thing we're going to look at is the structure of the DNA signals, that is, the nucleotide sequences that make this whole thing possible. So, here is an old illustration of the three different genes. I warned you that each one of these sections has probably more complexity than I bothered to illustrate previously. So, let's take a portion of this, and show where you find these particular sequences, the recombination signal sequences. So, here is just a part of the lambda, the kappa, and the heavy chain. If you'll notice quickly, you're not going to see any funky stripe stuff around the constant regions. That's also true of the constant regions that we haven't shown on a heavy chain or the lambda light chain. So, you can see from this though that every variable region is going to have a downstream or three primes signal sequence. They're not all identical, but they're similar. All of the Js will have an upstream version of some kind. The D region that I'm going to join in-between them, will actually have things both up and down. Now, the interesting thing about this, is it looks like, if you look at the D region, that the recombination signal sequences take up more space, or they're longer than the actual D region itself. Well, while this may exaggerate to some degree, the relative sizes of the V signal sequences, it really doesn't on the D region. The D region that codes for amino acids, only codes for three of them, and is therefore only nine nucleotides long. As it turns out, each of the flanking sequences around it is longer than that. So, we'll get back to that. Here, we focus in on a portion of the kappa light chain gene. So, up here we can see the leader variable sequences, followed by the recombination signal sequence. We'll see here we have the gray region, which is going to be the heptamer, the lavender region, which will be a one turn base sequence, and the orange-red region which will be the AT-rich. So, and downstream below that, we have again another AT-rich, a two-turn sequence, and a heptamer followed by the yellow J region. So, when we're done, we're going to put together the V with the J. Let's look a little bit in more detail about what these really represent. All right, so what you will get in any recombination signal sequence is next to the region to be attached, you will have a seven base heptamer. That's what heptamer means, and we'll see that it's palindromic when we look at the specific nucleotides. So, here at the end of the V, the beginning of the J, are the two heptamers, and eventually they're going to actually contribute some nucleotides into the final product. Notice that the next thing that comes is either a one-turn or two-turn sequence. As it turns out, the way these things are set up, you must put a one-turn with a two-turn. That kind of prevents you from sticking two Vs together, or two Js together, because those two sequences are important in lining up this whole procedure, and making sure you're putting the right things together. The last sequence or the sequence in the middle, is an AT-rich nanomer which is also important in recognizing the multi-enzyme complex that puts these two guys together ultimately. So, when we're putting two sequences together, we have to put a one-turn with the two-turn. Although, if you look at the lambda, the two-turns follow the variables, and the one-turn proceeds the Js. But the principle is the same, whether you're looking at either light or the heavy chain gene. So, now let's go in and get a further closer look. Here we can see the nucleotide. If you recall, I said that this heptamer region of seven basis was palindromic, and if you look at this thing, it reads the same way front and back. So, I could read CACAGTG, or I could go the other way around, and go it goes CACATGTG on the backwards one. That's true on the other side as well, and you can see they're kind of flip sides of each other. The one-turn sequence has 12 basis, any old thing, that's why it's an X, and the two-turn has 23. So, what does that mean? What it means is if I start at one place on the DNA, and I count off 12 basis, I will find that I have made a full lap around the molecule, that is, I've made one turn. I have this illustrated on one of the supplementary videos, where I've got a 3D DNA model, and I can show you what happens when you count around it. Likewise, when you look at the two-turns sequence, I think you're probably not surprised to know that if you count 23 bases, you will make two laps around the DNA. This 23 base one, I'm doing in this sort of deep bluish purple, and I'm doing the 12 base one IN a lighter lavender so that you can tell them apart by color. The AT-rich regions are, again, pretty much the same. Notice its As on one side, and Ts on the other. This is an nanomer or nine basis, okay? So, running from the region to be pasted together, we have a palindrome, a turn sequence, and an AT. Then going the other way facing it, is another AT, a turn sequence, a palindrome. Those sequences will be read in order to essentially paste the respective Vs and Js together. Now, if we go back and take another look at the signals, we'll see again we have a bit more complication with the heavy. The first thing we're going to do is put together the D and the J. But notice there's no way on this one at least to say for example, put two Ds together, or likewise, we can't skip the D, and put the V and the H together because that would put two-turn signals together, and that's a no, no. So, we have these sequences. They're going to help the DNA attach to, and be moved around, and chemically rearranged by a enzyme complex called V(D)J recombinase. We're going to look at the exact mechanism of this in the next sequence.
