WEBVTT 00:00:08.336 --> 00:00:11.776 >> Sally: I think this year's iGEM competition is the best ever. 00:00:11.776 --> 00:00:14.126 The project we just heard about was amazing! 00:00:14.236 --> 00:00:17.766 >> Dude: And that bacterial flotation device was totally cool! 00:00:18.026 --> 00:00:20.746 It's the balloon-o-genesis module I've been looking for. 00:00:20.746 --> 00:00:23.256 I want to try it with my Bacterial Balloon idea. 00:00:23.636 --> 00:00:24.676 I know it'll work. 00:00:24.676 --> 00:00:27.456 >> Sally: I thought you were done with Bacterial Balloons! 00:00:27.456 --> 00:00:29.596 >> Dude: Sally, where's your curiosity? 00:00:29.706 --> 00:00:31.736 We'll need to put the flotation-thing-a-ma-gjiggy together 00:00:31.736 --> 00:00:35.786 with the Gas-o-Matic module and this time put some feedback program at the promoters 00:00:35.786 --> 00:00:40.376 to make the devices stop...this is SO going to work. 00:00:40.756 --> 00:00:43.866 >> Sally: We can try to build it when we get back to lab but some 00:00:43.866 --> 00:00:46.236 of it looks like very specialized DNA. 00:00:47.586 --> 00:00:50.196 First, we'll need a feedback loop that works for Buddy. 00:00:50.586 --> 00:00:54.416 Second, the flotation module is more than 6000 base pairs. 00:00:54.546 --> 00:00:58.416 Didn't that team say that it works better if these two sections are removed? 00:00:58.416 --> 00:01:02.766 Maybe we should directly synthesize the shorter flotation part with a Buddy feedback loop, 00:01:02.766 --> 00:01:06.366 then we can hook it up to the Gas-o-Matic module we already have in the lab. 00:01:06.496 --> 00:01:07.696 >> Dude: Now you're talking! 00:01:07.866 --> 00:01:12.506 But I think I forgot how to directly synthesize DNA...I mean we've done so many things 00:01:12.506 --> 00:01:15.006 in the lab and I remember a lot of them but... 00:01:15.096 --> 00:01:16.886 >> Sally: Dude, we don't synthesize it. 00:01:16.886 --> 00:01:18.726 We get a company to do that for us. 00:01:19.006 --> 00:01:19.216 >> Dude: Whew. 00:01:19.646 --> 00:01:22.396 So do I copy down this picture from the board and mail it to them? 00:01:22.476 --> 00:01:25.116 >> Sally: You could but they wouldn't know what to do with it. 00:01:25.306 --> 00:01:30.926 We'll need to send them the exact DNA sequence, and then they can string the Gs, As, Ts, 00:01:30.926 --> 00:01:32.786 and Cs together in the right order. 00:01:32.786 --> 00:01:36.045 Every DNA synthesis company does it a little differently 00:01:36.045 --> 00:01:38.216 but the chemistry is pretty standard. 00:01:38.216 --> 00:01:41.876 It involves protection and deprotection of a growing DNA chain 00:01:41.876 --> 00:01:45.826 with specialized bases called deoxynucleoside phosphoramidites. 00:01:45.886 --> 00:01:47.116 >> Dude: Gesundheit! 00:01:47.466 --> 00:01:48.286 Sorry. What's so special about them? 00:01:49.386 --> 00:01:53.666 >> Sally: Only one base links to a DNA chain at a time until you deprotect the end, 00:01:53.746 --> 00:01:56.765 which then allows you to add the next base in your sequence. 00:01:56.866 --> 00:01:58.096 >> Dude: That sounds like a pain. 00:01:58.256 --> 00:01:59.606 >> Sally: No, think about it. 00:01:59.606 --> 00:02:04.856 All you have to do is attach your first base, let's say a protected G, to some sort of polymer 00:02:04.856 --> 00:02:09.925 or bead, and then when you deprotect the G you can add a second base, how about an A? 00:02:10.056 --> 00:02:14.386 Then when you deprotect that A, you can add a third base, let's put a T there. 00:02:14.446 --> 00:02:14.856 >> Dude: Ha! 00:02:15.236 --> 00:02:16.816 even I know that won't work. 00:02:16.936 --> 00:02:18.666 What if that A doesn't hook up? 00:02:18.786 --> 00:02:21.666 Then you've got G-T instead of G-A-T. 00:02:21.876 --> 00:02:22.676 What good is that? 00:02:22.986 --> 00:02:26.656 >> Sally: Dude, you're smart, but so are the chemists who worked on this. 00:02:26.736 --> 00:02:30.416 There's one more step called "capping" so that any deprotected base 00:02:30.416 --> 00:02:34.296 that doesn't properly connect is shut down and can't be added to. 00:02:34.506 --> 00:02:38.016 Those shorter pieces of DNA can be taken out of the mix at the very end. 00:02:38.016 --> 00:02:40.316 >> Dude: But won't there be a lot of mistakes to get rid of? 00:02:40.696 --> 00:02:44.626 Even if capping works half the time, you'll be getting rid of half your sequence, 00:02:44.716 --> 00:02:47.336 then half of that half...you'll have nothing left. 00:02:47.866 --> 00:02:52.256 >> Sally: Luckily this construction process is more like 99% efficient. 00:02:52.256 --> 00:02:57.266 But even so, you can't build something as long as this 6000 base pair flotation device. 00:02:57.546 --> 00:03:02.716 Most companies build a bunch of shorter oligo nucleotides, maybe 60 base pairs long, 00:03:02.716 --> 00:03:05.116 and then use PCR to stitch them together. 00:03:05.116 --> 00:03:07.606 >> Dude: and you trust them to do all this right? 00:03:07.866 --> 00:03:12.066 >> Sally: They verify the final DNA by sequencing it before they send it to you. 00:03:12.196 --> 00:03:14.806 Sometimes there are problems at one stage or another 00:03:14.806 --> 00:03:19.226 but DNA synthesis is getting faster and less expensive every year. 00:03:19.486 --> 00:03:21.096 >> Dude: Sally this is great! 00:03:21.246 --> 00:03:25.576 With your credit card and my ideas, we can write some DNA that's completely new. 00:03:25.766 --> 00:03:26.886 Race you back to lab. 00:03:27.146 --> 00:03:29.326 I want to get this DNA ordered today.