1 00:00:08,336 --> 00:00:11,776 >> Sally: I think this year's iGEM competition is the best ever. 2 00:00:11,776 --> 00:00:14,126 The project we just heard about was amazing! 3 00:00:14,236 --> 00:00:17,766 >> Dude: And that bacterial flotation device was totally cool! 4 00:00:18,026 --> 00:00:20,746 It's the balloon-o-genesis module I've been looking for. 5 00:00:20,746 --> 00:00:23,256 I want to try it with my Bacterial Balloon idea. 6 00:00:23,636 --> 00:00:24,676 I know it'll work. 7 00:00:24,676 --> 00:00:27,456 >> Sally: I thought you were done with Bacterial Balloons! 8 00:00:27,456 --> 00:00:29,596 >> Dude: Sally, where's your curiosity? 9 00:00:29,706 --> 00:00:31,736 We'll need to put the flotation-thing-a-ma-gjiggy together 10 00:00:31,736 --> 00:00:35,786 with the Gas-o-Matic module and this time put some feedback program at the promoters 11 00:00:35,786 --> 00:00:40,376 to make the devices stop...this is SO going to work. 12 00:00:40,756 --> 00:00:43,866 >> Sally: We can try to build it when we get back to lab but some 13 00:00:43,866 --> 00:00:46,236 of it looks like very specialized DNA. 14 00:00:47,586 --> 00:00:50,196 First, we'll need a feedback loop that works for Buddy. 15 00:00:50,586 --> 00:00:54,416 Second, the flotation module is more than 6000 base pairs. 16 00:00:54,546 --> 00:00:58,416 Didn't that team say that it works better if these two sections are removed? 17 00:00:58,416 --> 00:01:02,766 Maybe we should directly synthesize the shorter flotation part with a Buddy feedback loop, 18 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. 19 00:01:06,496 --> 00:01:07,696 >> Dude: Now you're talking! 20 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 21 00:01:12,506 --> 00:01:15,006 in the lab and I remember a lot of them but... 22 00:01:15,096 --> 00:01:16,886 >> Sally: Dude, we don't synthesize it. 23 00:01:16,886 --> 00:01:18,726 We get a company to do that for us. 24 00:01:19,006 --> 00:01:19,216 >> Dude: Whew. 25 00:01:19,646 --> 00:01:22,396 So do I copy down this picture from the board and mail it to them? 26 00:01:22,476 --> 00:01:25,116 >> Sally: You could but they wouldn't know what to do with it. 27 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, 28 00:01:30,926 --> 00:01:32,786 and Cs together in the right order. 29 00:01:32,786 --> 00:01:36,046 Every DNA synthesis company does it a little differently 30 00:01:36,046 --> 00:01:38,216 but the chemistry is pretty standard. 31 00:01:38,216 --> 00:01:41,876 It involves protection and deprotection of a growing DNA chain 32 00:01:41,876 --> 00:01:45,826 with specialized bases called deoxynucleoside phosphoramidites. 33 00:01:45,886 --> 00:01:47,116 >> Dude: Gesundheit! 34 00:01:47,466 --> 00:01:48,286 Sorry. What's so special about them? 35 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, 36 00:01:53,746 --> 00:01:56,766 which then allows you to add the next base in your sequence. 37 00:01:56,866 --> 00:01:58,096 >> Dude: That sounds like a pain. 38 00:01:58,256 --> 00:01:59,606 >> Sally: No, think about it. 39 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 40 00:02:04,856 --> 00:02:09,926 or bead, and then when you deprotect the G you can add a second base, how about an A? 41 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. 42 00:02:14,446 --> 00:02:14,856 >> Dude: Ha! 43 00:02:15,236 --> 00:02:16,816 even I know that won't work. 44 00:02:16,936 --> 00:02:18,666 What if that A doesn't hook up? 45 00:02:18,786 --> 00:02:21,666 Then you've got G-T instead of G-A-T. 46 00:02:21,876 --> 00:02:22,676 What good is that? 47 00:02:22,986 --> 00:02:26,656 >> Sally: Dude, you're smart, but so are the chemists who worked on this. 48 00:02:26,736 --> 00:02:30,416 There's one more step called "capping" so that any deprotected base 49 00:02:30,416 --> 00:02:34,296 that doesn't properly connect is shut down and can't be added to. 50 00:02:34,506 --> 00:02:38,016 Those shorter pieces of DNA can be taken out of the mix at the very end. 51 00:02:38,016 --> 00:02:40,316 >> Dude: But won't there be a lot of mistakes to get rid of? 52 00:02:40,696 --> 00:02:44,626 Even if capping works half the time, you'll be getting rid of half your sequence, 53 00:02:44,716 --> 00:02:47,336 then half of that half...you'll have nothing left. 54 00:02:47,866 --> 00:02:52,256 >> Sally: Luckily this construction process is more like 99% efficient. 55 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. 56 00:02:57,546 --> 00:03:02,716 Most companies build a bunch of shorter oligo nucleotides, maybe 60 base pairs long, 57 00:03:02,716 --> 00:03:05,116 and then use PCR to stitch them together. 58 00:03:05,116 --> 00:03:07,606 >> Dude: and you trust them to do all this right? 59 00:03:07,866 --> 00:03:12,066 >> Sally: They verify the final DNA by sequencing it before they send it to you. 60 00:03:12,196 --> 00:03:14,806 Sometimes there are problems at one stage or another 61 00:03:14,806 --> 00:03:19,226 but DNA synthesis is getting faster and less expensive every year. 62 00:03:19,486 --> 00:03:21,096 >> Dude: Sally this is great! 63 00:03:21,246 --> 00:03:25,576 With your credit card and my ideas, we can write some DNA that's completely new. 64 00:03:25,766 --> 00:03:26,886 Race you back to lab. 65 00:03:27,146 --> 00:03:29,326 I want to get this DNA ordered today.