User:LFP6/Archive/Q&A With Brourd and Nando

Brourd: Sounds complicated, but continue :)  [4:31 PM]
LFP6: Basically it, I think  [5:31 PM]
LFP6: What else am i missing/  [5:31 PM]
LFP6: *?  [5:31 PM]
Brourd: What I am confused about is your use of the phrase "higher number = paired with something" which number are you referring to?  [4:32 PM]
LFP6: The SHAPE value\if you turn on numbers  [5:32 PM]
LFP6: Or  [5:32 PM]
LFP6: Based on the color scale  [5:32 PM]
Brourd: Okay. We'll start with the numbers.  [4:33 PM]
LFP6: Kaaay  [5:33 PM]
Brourd: Lower is usually referring to "paired"  [4:34 PM]
LFP6: (I would screenshot what I'm looking at, but I'm at a computer without lightshot :()  [5:34 PM]
LFP6: Oh  [5:34 PM]
LFP6: Woops, the scale i' looking at is positive in both directions!  [5:34 PM]
LFP6: *I'm  [5:34 PM]
Brourd: Must be a bad scale if it does that :P  [4:35 PM]
LFP6: So true tho  [5:35 PM]
Brourd: So, we'll start with the basics.  [4:36 PM]
Brourd: How does chemical mapping work?  [4:36 PM]
LFP6: Mapping is not a term that came up, at least not by that name  [5:37 PM]
Brourd: I could have swore that document had the useful information. [4:37 PM]
LFP6: lol [5:37 PM]
Brourd: gimme a sec [4:38 PM]
LFP6: Sure [5:37 PM]
Brourd: Hmmmmm [4:39 PM]
Brourd: http://eternawiki.org/wiki/index.php5/User:ElNando888/Blog/SHAPE%3F [4:39 PM]
Brourd: read this [4:39 PM]
Brourd: Soon, Nando will have been dating Eterna longer than [censored] [4:41 PM]
Brourd: He can fill in that joke :D [4:41 PM]
LFP6: Wow [5:41 PM]
LFP6: I did a search, and the word map never appears [5:41 PM]
Brourd: *mumble* *grumble* [4:41 PM]
LFP6: :) [5:41 PM]
Brourd: read that while I fine a page that has the word mapping. [4:42 PM]
LFP6: Do you mean how the SHAPE values are acquired? [5:42 PM]
Brourd: No. No. That's the complicated stuff. [4:42 PM]
LFP6: ... [5:42 PM]
Brourd: http://en.wikipedia.org/wiki/Chemical_imaging [4:43 PM]
Brourd: nah, that's wrong. [4:43 PM]
Brourd: anyway. Chemical mapping is just a term for the technique. [4:45 PM]
LFP6: Which technique? Sorry, not sure what you're referencing [5:46 PM]
Brourd: http://arxiv.org/ftp/arxiv/papers/1304/1304.1072.pdf [4:46 PM]
LFP6: wait [5:46 PM]
Brourd: Chemical mapping methods probe RNA structure by revealing and leveraging correlations of the nucleotide's structural accessibility or flexibility with its reactivity to various chemical probes. [4:47 PM]
Brourd: I like that definition. [4:47 PM]
LFP6: Isn't that talking about basically how we get the shape data? [5:46 PM]
Brourd: Chemical mapping refers to the experiments as a whole. [4:47 PM]
LFP6: Well, let me share what i think you're talking about and see how close I get [5:48 PM]
Brourd: Excellent [4:49 PM]
LFP6: So when the sequence is synthesized, it's exosed to soem chemical probes, which try and 'bond' (for lack of a better term, plus continuity) to the bases. [5:49 PM]
LFP6: So [5:49 PM]
LFP6: If it can 'bond', that means that the base probably isn't in an existing bond, or a weak one, so that base is able to move around [5:50 PM]
LFP6: And bond with the chemical [5:50 PM]
LFP6: if it is bonded, it's held in place, and the chemical has no way to reach it [5:51 PM]
LFP6: That what you were going for? [5:51 PM]
Brourd: Couldn't have said it better (well maybe a little) myself. [4:51 PM]
Brourd: The site of modification may depend on the protocol. [4:52 PM]
LFP6: modification of...? [5:52 PM]
Brourd: For example, the SHAPE chemical does not modify the nitrogenous base, but rather the 2' hydroxyl. [4:53 PM]
LFP6: what do you mean by modify then? [5:53 PM]
LFP6: And could you relink me to whatever it was that explains these numbers? :P [5:54 PM]
Brourd: Which one explained the numbers? [4:56 PM]
LFP6: IDK, you showed me something the other day [5:56 PM]
Brourd: Modify is just a fancy word for "the chemical alters the nucleotide in some way" [4:56 PM]
LFP6: That may have been specifically the difference between 5' and 3' [5:56 PM]
LFP6: What ways can it be changed? [5:57 PM]
Brourd: ah [4:57 PM]
LFP6: I'm not clear on what they mean [5:57 PM]
LFP6: Wow, we're carying on two conversations at once! [5:57 PM]
Brourd: Chemical bonding is one example. [4:57 PM]
LFP6: Right, and that's about where my lack of chemistry schooling kicks in (I don't get to that in a year or two) [5:58 PM]
LFP6: *for a [5:58 PM]
Brourd: Hydroxyl radicals may break the RNA backbone through. [4:58 PM]
Brourd: However, the goal is to cause reverse transcription to stop at the site of modification. [4:59 PM]
LFP6: When you say hydroxyl, do you mean a single instance of the compound? [5:59 PM]
Brourd: no, no. A hydroxyl radical is the neutral form of the hydroxide ion. [5:00 PM]
Brourd: HO without the minus. [5:00 PM]
LFP6: Sorry, my lack of knowledge is probably rather annoying. :S [6:00 PM]
Brourd: It's not necessary information to know :) [5:01 PM]
LFP6: The word I was looking for was molecule, btw. :P [6:01 PM]
TomoeUzumaki: LFP! [6:01 PM]
TomoeUzumaki: hey [6:01 PM]
Brourd: I'm not going to go into the specifics of molecules and ions ;) [5:02 PM]
Brourd: Anway... [5:02 PM]
Brourd: *anyway... [5:02 PM]
LFP6: Yo T [6:02 PM]
Brourd: Anyway :P [5:02 PM]
LFP6: Hehe [6:02 PM]
Brourd: Hey, tomoe. [5:02 PM]
TomoeUzumaki: y'all should check out my tumblr hahaha I redid it bc christmas break [6:02 PM]
LFP6: Oh? [6:02 PM]
TomoeUzumaki: yeah! [6:02 PM]
Brourd: Where were we? Ah, yes. The numbers. [5:03 PM]
Brourd: That's not important :P [5:04 PM]
LFP6: So... [6:05 PM]
TomoeUzumaki: ? [6:05 PM]
Brourd: Ignore most of the technical details for the directionality of the nucleotide. [5:06 PM]
LFP6: So, ignore half of what you say? :P [6:06 PM]
Brourd: Just know, the 2' hydroxyl is what the SHAPE probe modifies. [5:07 PM]
LFP6: Okey [6:07 PM]
Brourd: Even that is not necessary, just know it is not the base :P [5:07 PM]
Brourd: it modifies the sugar. [5:07 PM]
LFP6: is that where other nuceotides bond? [6:07 PM]
LFP6: Or it's just protected when bonded? [6:07 PM]
Brourd: Where were we [5:08 PM]
LFP6: Answering my question? :P [6:08 PM]
Brourd: Excellent [5:08 PM]
LFP6: other than that, numbers [6:08 PM]
Brourd: Ignore the numbers for directionality for now ;) [5:09 PM]
LFP6: Oh, never mind [6:09 PM]
LFP6: I thought we were talking about shape numbers before [6:09 PM]
Brourd: ah [5:09 PM]
Brourd: We'll get there. [5:09 PM]
LFP6: Thought back too far! [6:09 PM]
Brourd: First, let's talk about how many RNA molecules are synthesized. [5:10 PM]
LFP6: Kay [6:10 PM]
Brourd: You do understand that the data the Das lab gets back from sequencing is an average of thousands of data points, yes? [5:11 PM]
LFP6: Yes [6:11 PM]
Brourd: Awesome [5:12 PM]
LFP6: we don't have access to the raw, riht? [6:11 PM]
LFP6: I could see that being useful [6:12 PM]
Brourd: So, we do not have access to the "raw" numbers. [5:12 PM]
Brourd: That is, we do not have access to the counts for cDNA strands. [5:12 PM]
LFP6: Wish we could see the full dataset, and not just the average. Or if they would analyse for us to guess if there are competing structures [6:13 PM]
Brourd: ah [5:13 PM]
Brourd: each data point is a single cDNA strand. [5:14 PM]
Brourd: that cDNA strand tells you only one thing. [5:14 PM]
Brourd: that at that point in the RNA sequence, chemical modification occurred. [5:14 PM]
LFP6: How does it say that, exactly? [6:15 PM]
LFP6: does it try to modify again, or...? [6:15 PM]
Brourd: I am a cDNA strand X nucleotides in length. [5:15 PM]
LFP6: right [6:15 PM]
Brourd: The length where there are increased counts for the cDNA strands represent nucleotides that where exposed to chemical modification, and stopped the reverse transcription. [5:17 PM]
LFP6: What do you mean by length? [6:17 PM]
LFP6: Section of the RNA? [6:17 PM]
Brourd: Something like that. [5:17 PM]
Brourd: Let's draw a picture. [5:18 PM]
LFP6: So chemical modification = can't make DNA ther? [6:18 PM]
LFP6: *there [6:18 PM]
Brourd: Bingo. Reverse trascription stops at the site of chemical modification (or should) [5:19 PM]
LFP6: Why? Or is that a completely unneccesary question? [6:19 PM]
Brourd: Unnecessary, imo. All you need to know is that it does. You can always look that stuff up on your free time. [5:20 PM]
Brourd: http://prntscr.com/5ln58l [5:20 PM]
Brourd: So, a mock RNA [5:20 PM]
LFP6: All right [6:21 PM]
Brourd: the yellow numbers represent the total count of cDNA strands that are that length. [5:21 PM]
LFP6: Ok [6:21 PM]
Brourd: Nucleotides that are in loops will be more exposed to chemical modification. [5:21 PM]
Brourd: Therefore, the cDNA count will be higher. [5:21 PM]
Brourd: Because reverse transcription stopped early. [5:22 PM]
LFP6: Yeah, still confused about the 'length'... length is describing how long what is/ or what section of what? [6:22 PM]
LFP6: Otherwise, makes sense [6:22 PM]
Brourd: How long the cDNA strand is. [5:22 PM]
LFP6: So... Number of cDNA that is as long as...? [6:23 PM]
Nando: @LFP6: http://eternawiki.org/wiki/index.php5/1M7 [6:23 PM]
Nando: the picture says a lot [6:23 PM]
LFP6: mmm [6:24 PM]
Brourd: Ack, don't confuse him with biochemistry pictures. We aren't ready for that yet! [5:24 PM]
Nando: :D [6:24 PM]
Brourd: The explanation may help a bit. [5:26 PM]
LFP6: Anyhow [6:27 PM]
Brourd: btw, Nando. How goes your quest? [5:27 PM]
Brourd: Yes? [5:27 PM]
LFP6: What's next/ [6:27 PM]
Nando: my quest for sanity? pretty terrible :D [6:27 PM]
LFP6: *? [6:27 PM]
Brourd: Excellent. [5:28 PM]
Brourd: Hmmm, what's next. [5:28 PM]
Brourd: Summarize what chemical modification is (just the basics), and try your best to explain why it is important, and the result of reverse transcription. [5:28 PM]
LFP6: The chemical trys to bond to the sugar (or do something else, but this in our case) which it can if the base is unpaired. This stops the cDNA from being made, and we can tell see places where there are less of them, which means that there are pairs there [6:30 PM]
Brourd: hmmmm [5:31 PM]
LFP6: Oops... tell see... i' sounding like a certain Bionicle type (le-anything) [6:31 PM]
Nando: it doesn't stop the cDNA from being made, but it stops the RT enzyme before the end [6:31 PM]
Brourd: What would you rate that explanation for a kid learning this for the first time, Nando? [5:31 PM]
LFP6: Wait, there's an enzyme/ [6:31 PM]
Nando: not bad at all actually [6:31 PM]
LFP6: I keep missing shift so I get / instead of ? ... [6:31 PM]
Nando: it's called Reverse Transcriptase [6:32 PM]
LFP6: Which does what/ [6:32 PM]
Nando: it takes RNA, makes cDNA [6:32 PM]
LFP6: GAAH [6:32 PM]
LFP6: So... It stops the cDNA from being made... just not 'directly' :P [6:32 PM]
Nando: and it typically does it in reverse order, 3' to 5' [6:32 PM]
Nando: no [6:33 PM]
LFP6: ... [6:33 PM]
Nando: ok, without chemical modification, you would have: [6:33 PM]
Nando: 3'---[]---[]---[]---[]---[]---[]--5' [6:33 PM]
Nando: 20 dashes for 20 bases [6:33 PM]
Nando: ok? [6:33 PM]
LFP6: But you said it stopped the enzyme, which means that the cDNA aren't made...? [6:33 PM]
LFP6: Sure [6:33 PM]
Nando: you have 100 millions of these [6:33 PM]
LFP6: Mmhmm [6:33 PM]
Nando: now you put some SHAPE reactant in there [6:34 PM]
Nando: it's going to stick [6:34 PM]
LFP6: Sure [6:34 PM]
Nando: 3'---[]--*---[]---[]---[]---[]---5' [6:34 PM]
Nando: for instance [6:34 PM]
Nando: when the RT enzyme tries to make the cDNA, it will stop at the star [6:34 PM]
Nando: 3'---[]-- [6:34 PM]
Nando: that's the length we're talking about [6:35 PM]
Nando: alter it's all a matter of statistics [6:35 PM]
LFP6: FYI, the n' stuff was never explained... If I remember corerctly, the 3' is the lowest number in the EteRNA interface? [6:35 PM]
Nando: how many of length 1, length 2, etc [6:35 PM]
LFP6: Ah [6:35 PM]
Nando: 3' is the end, highest number [6:35 PM]
Nando: 5' is the start, 1 [6:35 PM]
LFP6: So, it doesn't want to end with a modified base [6:35 PM]
LFP6: Ah, thanks [6:35 PM]
Nando: RT goes in reverse order [6:36 PM]
LFP6: understood now [6:36 PM]
Brourd: This is why we pay Nando the big bucks. He uses pictures. [5:36 PM]
Nando: :D [6:36 PM]
Nando: making mistakes, but hey [6:36 PM]
Nando: it's actually a [6:36 PM]
Nando: 5'---[]-- [6:36 PM]
Nando: that you get as a result, but that's a detail, the important thing is the length [6:37 PM]
LFP6: but anyways, a cDNA will be happy ending with a (non?)-modified base, but the reverse is not true? [6:37 PM]
Nando: cDNA doesn't care how long it is or how it ends [6:37 PM]
Brourd: I don't think it can be happy at all :P [5:38 PM]
Nando: it's just that RT has no choice but to give up before the end, because of the blotted modified nucleotide [6:38 PM]
LFP6: brb [6:38 PM]
LFP6: back [6:42 PM]
Brourd: So, you were wondering why we do not get the raw cDNA counts, yes? [5:43 PM]
LFP6: Wait... So how does it get past it then to give more counts for the un-modified later in the strand?? [6:43 PM]
Brourd: Ah, excellent question. It doesn't. [5:44 PM]
LFP6: @B: well, I was going for theshape data of each particular RNA [6:44 PM]
LFP6: Wait [6:44 PM]
Brourd: There is a single hit for each RNA molecule. [5:44 PM]
LFP6: Then what was up with your screenshot? [6:44 PM]
Brourd: my screenshot would be an aggregate count of... [5:44 PM]
LFP6: And how can you tell if there's an un-modified later on if you can't count at that length? [6:44 PM]
Brourd: 60+ RNA molecules. [5:45 PM]
Brourd: So, as Nando says, it all comes down to statistics. [5:46 PM]
LFP6: That doesn't really answer the question... [6:45 PM]
Nando: yes, it does, actually [6:46 PM]
LFP6: but [6:46 PM]
LFP6: huh? [6:46 PM]
LFP6: How can it get a cound for a length it can't get to?\ [6:46 PM]
LFP6: *count [6:46 PM]
Brourd: Each RNA molecule is only modified once. [5:46 PM]
Nando: it's just that, statistics [6:46 PM]
LFP6: Ooooooooooooooh [6:46 PM]
Nando: because in the middle of the 100 millions samples, many were left untouched [6:46 PM]
Nando: many had hits just before the end [6:47 PM]
Nando: etc [6:47 PM]
LFP6: So only one base is changed on any one molecule?? [6:47 PM]
Brourd: That would be the ideal. [5:47 PM]
Nando: not always, but that's the goal of the experiment [6:47 PM]
Nando: achieve single hit statistics [6:47 PM]
LFP6: So that' a bigger reason why you have to have so many molecules synthesized then, not accuracy? [6:48 PM]
Nando: requires some solid experience in that domain [6:48 PM]
LFP6: Though, it does contribute to having accurate data. :P [6:48 PM]
Nando: large count of samples always help in statistics, that's clear [6:49 PM]
LFP6: But I mean [6:49 PM]
LFP6: If you only synthesized one molecule, you wouldn't be able to find the results of the whole sequence [6:49 PM]
Nando: I don't know of any technique that can say anythin with one sample [6:50 PM]
LFP6: And on that note, how is such variation in which base is modified assured? just random chance that happens to work favourably? [6:50 PM]
Nando: unless it's big enough for study by AFM [6:50 PM]
LFP6: @Nando: I know, but I'm saying if that one sample was known to be accurate [6:50 PM]
LFP6: Oh [6:51 PM]
Nando: no if, no single sample can represent an ensemble [6:51 PM]
LFP6: Right [6:51 PM]
LFP6: But I'm not talking about that. [6:51 PM]
Brourd: I believe he is asking about measurement error. [5:52 PM]
Nando: oh, Pandora's box [6:52 PM]
Nando: I'm outta here :P [6:52 PM]
Brourd: in this case, how much error exists in random, single hit statistics. [5:52 PM]
LFP6: no, no [6:52 PM]
Brourd: hahaha [5:52 PM]
LFP6: I'm saying that even if you didn't have to worry about that, you would still need multiple samples so that you could get a measurement for every base, as one sample only gives a result for one base [6:52 PM]
Nando: precisely LFP6 [6:53 PM]
LFP6: Okay. :P [6:53 PM]
LFP6: Because on the Wiki, it said nothing about that. :P [6:53 PM]
LFP6: it just talked about getting accurate data [6:53 PM]
Nando: feel free to improve it :D [6:53 PM]
LFP6: not that each sample only measures one base [6:53 PM]
Brourd: I think he is planning a complete overhaul. [5:54 PM]
LFP6: methinks I will, if I find the article! [6:53 PM]
LFP6: B, it's a UI overhaul, not content [6:54 PM]
LFP6: :) [6:54 PM]
LFP6: Er, much [6:54 PM]
LFP6: Content reorganization and possibly new content, perhaps, but... [6:54 PM]
LFP6: :) [6:54 PM]
TomoeUzumaki: hey, LFP, quick question [6:54 PM]
LFP6: Ya [6:54 PM]
LFP6: Shoot [6:54 PM]
TomoeUzumaki: any news? [6:54 PM]
Brourd: complete overhaul [5:55 PM]
LFP6: *Grumbles* My mother just got back, we're currently at my grandparents [6:55 PM]
TomoeUzumaki: aah [6:55 PM]
LFP6: I don't really want to ask, for fear of being a complete insensative idiot when she has more important things to worry about [6:55 PM]
Brourd: You should have me ask. [5:56 PM]
LFP6: if ya catch my drify [6:55 PM]
Brourd: I do not fear being seen as an insensitive idiot. [5:56 PM]
LFP6: Brourd, good luck finding where I am. :P [6:56 PM]
TomoeUzumaki: I totally get it [6:56 PM]
Brourd: Well, I would prefer a phone call. [5:56 PM]
LFP6: I mean, yes, IP, but that can't direct you to here. nor can you most likely get here fast enough. :P [6:56 PM]
LFP6: How will you get my number then? [6:56 PM]
LFP6: *Lips sealed* [6:56 PM]
Brourd: Luck and magic. [5:57 PM]
Brourd: Mostly NSA [5:57 PM]
LFP6: Ouch [6:57 PM]
Brourd: However, next on our list. The actual data. [5:57 PM]
Brourd: If you have not done so already, you should hug your mom. [5:58 PM]
LFP6: Truth there [6:58 PM]
Brourd: Anyway, the data is converted from cDNA counts, the true raw data, into digestable quantitative measurements. [5:59 PM]
Brourd: After *several* corrections. [5:59 PM]
LFP6: BSo... What is it an average of? [6:59 PM]
Brourd: of an ensemble of folds. [6:00 PM]
LFP6: If you're not actually looking it as on or off, but number of ons (or offs, depending how you count) [7:00 PM]
Brourd: The measurements are not technically an average in the traditional sense. Rather, the data for each indidivual location represents the statistical approximation of the reactivity for the residue there. [6:01 PM]
LFP6: Wow... Again, a Wiki fault... :( [7:02 PM]
Brourd: reactivity measurement 0 - the residue was not modified [6:02 PM]
LFP6: And Eli's doc, actually [7:02 PM]
LFP6: Giving me false ideas :P [7:02 PM]
LFP6: So... next [7:03 PM]
Brourd: reactivity measurement .5 - the residue was modified, but the cDNA count and final corrected measurement value are not comparable to those of the standard they use. [6:03 PM]
Brourd: reactivity measurement 1.0 - the residue was modified, and the final measurement is comparable to that of the average reactivity for the GAGUA pentaloop they use as a standard. [6:04 PM]
Brourd: It's really a comparison to an average :P [6:05 PM]
LFP6: Heh [7:04 PM]
Brourd: Although, don't get Nando started on that :D [6:06 PM]
LFP6: Of course [7:07 PM]
Nando: :P [7:07 PM]
Brourd: So what do you want to know next, LFP6? [6:08 PM]
Brourd: Or what do you feel you don't quite have an understanding of. [6:08 PM]
LFP6: What else do I need to know? [7:08 PM]
LFP6: I think I'm good up to here. 'cept for the numbers, which I am ok with ignoring until a time I care to look it up. :P [7:08 PM]
LFP6: As it is apperantly not all too important] [7:08 PM]
Brourd: Everything is important. There are just levels to importance. [6:09 PM]
LFP6: True [7:09 PM]
LFP6: And where it is applicable [7:09 PM]
LFP6: If not applicable, not important there! [7:09 PM]
Brourd: For example, just remember that RNA flows from 5' to 3'. [6:09 PM]
LFP6: yeah [7:09 PM]
Brourd: if RNA flowed [6:10 PM]
LFP6: is there a particular reason why there is a 'head'? just convention? [7:10 PM]
Brourd: Everything needs to have a name. [6:12 PM]
Brourd: It makes talking about it easier. [6:12 PM]
LFP6: Anyways, anything else you wish to teach me? [7:12 PM]
Brourd: So. Do you understand the basics of the Eterna interface? What yellow and blue mean? [6:13 PM]
Nando: there's a lot of symmetries in RNA, but the backbone is not one of them, it has a "normal" direction [7:13 PM]
Nando: so yeah, 5' (start) and 3' (end) [7:13 PM]
LFP6: Yes [7:13 PM]
LFP6: Nando, what does 'direction' indicate/ What is the thing starting and ending? Or again, just convention? [7:14 PM]
LFP6: er, what is moving between start and end [7:14 PM]
Nando: not just convention, many enzymes will decode or scan the strand in that direction [7:14 PM]
LFP6: Hm [7:15 PM]
Nando: some work in reverse, 3' to 5', and then they are denoted as Reverse something, Transcriptase for instance [7:15 PM]
LFP6: Interesting. Doesn't mean much to me, but I get the concept. :P [7:15 PM]
LFP6: Is it time to get into what I'll actually need to do for analysis B? [7:16 PM]
Nando: you know programming, LFP6? [7:17 PM]
LFP6: Somewhat [7:17 PM]
Nando: how does a CPU read instructions? [7:17 PM]
LFP6: From the RAM? :P [7:17 PM]
Nando: yes, but, from 0 to 1000000, or the reverse ? [7:18 PM]
LFP6: Dad: Depends on the processor [7:18 PM]
LFP6: $ such [7:18 PM]
LFP6: *& [7:18 PM]
Nando: RNA is often an information storage device, for coding proteins for instance [7:18 PM]
LFP6: Right [7:18 PM]
Nando: and it is read in a certain direction, not the other one [7:19 PM]
Nando: well, most of the time [7:19 PM]
LFP6: Ah [7:19 PM]
LFP6: So, direction read by almost anything being done with it [7:19 PM]
Nando: almost, but there are intriguing exceptions [7:20 PM]
Nando: which I won't talk about :D [7:20 PM]
LFP6: :D [7:20 PM]
LFP6: :] [7:20 PM]
Brourd: I think LFP6 is looking more for what defines 5' and 3' [6:20 PM]
Nando: where it comes from? [7:20 PM]
LFP6: well, at least at soe point yes [7:20 PM]
LFP6: That too! [7:20 PM]
TomoeUzumaki: aaah wait I know this [7:20 PM]
LFP6: 5 what and 3 what? [7:21 PM]
Brourd: C'mon tomoe, you can do this! [6:21 PM]
LFP6: Go go go! [7:21 PM]
Nando: gives the mike to Tomoe [7:21 PM]
LFP6: heh [7:21 PM]
Brourd: five apostrophe and three apostrophe :P [6:21 PM]
LFP6: Well... ;P [7:21 PM]
TomoeUzumaki: wait a second! [7:21 PM]
Brourd: I need to use italics more. [6:22 PM]
LFP6: yes [7:22 PM]
LFP6: i need to get a scriptable IRC client so i can use it without fussing and be able to use italics. :P [7:22 PM]
TomoeUzumaki: 5’ end is the carbon in the 5’ position of the sugar, to which the phosphate group is attached. The 3’ end is the 3’ position in the sugar to which the hydroxyl group (OH) is attached. [7:22 PM]
TomoeUzumaki: there we go [7:22 PM]
LFP6: You defined the term with the term [7:22 PM]
LFP6: What does the number 9and ') represent? [7:23 PM]
LFP6: What are we counting? [7:23 PM]
Brourd: That's science for you. [6:23 PM]
Nando: who wants a picture? [7:23 PM]
LFP6: Oops [7:23 PM]
LFP6: i'll take it [7:23 PM]
Nando: http://eternawiki.org/wiki/images/RNA_chemical_structure.gif [7:23 PM]
LFP6: Just shut up my keyboard! [7:23 PM]
LFP6: *Cringe* [7:24 PM]
Brourd: lol [6:24 PM]
LFP6: Wazzat/ [7:24 PM]
LFP6: *? [7:24 PM]
Nando: btw, O2' is simply the O-xygen hanging at the 2' position [7:24 PM]
LFP6: I don't recognize the symbols :S [7:24 PM]
Brourd: It's the chemical structure of a nucleotide. [6:25 PM]
TomoeUzumaki: the apostrophe is the "prime" [7:25 PM]
TomoeUzumaki: like shape --> [7:25 PM]
TomoeUzumaki: *SHAPE [7:25 PM]
Brourd: Alas, I now know how to read these [6:25 PM]
LFP6: foldit and EteRNA seriously need to do a project together so I can visualize this. :P [7:25 PM]
LFP6: hey! [7:25 PM]
TomoeUzumaki: selective 2' (prime) hydroxyl acylation analyzed by primer extension [7:25 PM]
LFP6: That's a way to do the 3D interface. :p [7:25 PM]
TomoeUzumaki: basically, the prime is the position [7:25 PM]
TomoeUzumaki: heh [7:25 PM]
TomoeUzumaki: but my man Vineet has that under control [7:25 PM]
LFP6: :) [7:26 PM]
Nando: the prime is simply there to distinguish the atoms in the whole nucleoside: no primes, it's on the base, prime, it's on the ribose [7:26 PM]
TomoeUzumaki: yep [7:26 PM]
LFP6: So... What is the ribose exactly? [7:26 PM]
TomoeUzumaki: the 5 carbon sugar [7:26 PM]
Nando: the pentagonal thing [7:26 PM]
TomoeUzumaki: that makes up the backbone [7:26 PM]
TomoeUzumaki: or that [7:26 PM]
LFP6: Well, yes [7:26 PM]
LFP6: But how can i relate this to the EteRNA interface? [7:26 PM]
TomoeUzumaki: eeee [7:27 PM]
TomoeUzumaki: well [7:27 PM]
LFP6: Oh [7:27 PM]
LFP6: Wait [7:27 PM]
LFP6: That's a 3D thing, isn't it? [7:27 PM]
TomoeUzumaki: yeah [7:27 PM]
LFP6: So... base hangs off the ribose? [7:27 PM]
TomoeUzumaki: tertiary structure stuff [7:27 PM]
TomoeUzumaki: yeah [7:27 PM]
LFP6: Oooooh [7:27 PM]
TomoeUzumaki: I can draw you a quick diagram [7:27 PM]
LFP6: I can connect to foldit [7:27 PM]
LFP6: The base is basically a sidechain [7:28 PM]
TomoeUzumaki: eeeh yeah kind of? [7:28 PM]
Nando: kind of, yes [7:28 PM]
LFP6: Similar; ribose:bb segment, base:sidechain [7:28 PM]
LFP6: right? [7:29 PM]
LFP6: Any reason that pic has two ribose and one base/ [7:29 PM]
LFP6: *? [7:29 PM]
Nando: hard to see a chain when you have only one link [7:29 PM]
LFP6: Ah [7:29 PM]
LFP6: And what is the role of the Phosphate? Glue between ribose? [7:30 PM]
Nando: exactly [7:30 PM]
LFP6: Hey, this makes sense! :D [7:30 PM]
Nando: yep :) [7:30 PM]
LFP6: ok, this thing needs to be logged so a good guide/wiki article can be made... Perhaps I'll post to my userpage blog thing [7:31 PM]
TomoeUzumaki: LFP, let me show you the 5-minute diagram I drew [7:31 PM]
TomoeUzumaki: gimme a sec [7:31 PM]
LFP6: maybe i'll make a 'stuff' section [7:31 PM]
Nando: cool [7:31 PM]
Brourd: Another stuff section on the wiki to follow? :P [6:32 PM]
LFP6: See, this is why I want a UI revamp. That way, things like blos actually have a framework/are integrated into the UI, and have ther own space [7:32 PM]
LFP6: *blogs [7:32 PM]
LFP6: *organizational space, collection area, whatever, just defaulted without having to specify [7:32 PM]
Nando: would be nice, yeah [7:32 PM]
LFP6: And is easy to see it's there [7:32 PM]
Brourd: Indeed [6:32 PM]
LFP6: Again, look at the LMB Wiki [7:32 PM]
LFP6: http://legomessageboards.wikia.com/wiki/LEGO_Message_Boards_Wiki [7:33 PM]
LFP6: Wikia is great with that [7:33 PM]
LFP6: ok, i need to head to dinner. [7:33 PM]
LFP6: I'll be back [7:33 PM]
TomoeUzumaki: http://prntscr.com/5lny1n [7:33 PM]
TomoeUzumaki: yep [7:33 PM]
TomoeUzumaki: that's the diagram hahaha [7:33 PM]
LFP6: Got ya [7:33 PM]