Hi, Jeehyung, OS: Windows 7 Professional (ver. 6.1 build: 7600), browser: Google Chrome (ver. 16.0.912.75 m).
I suspect it is the setup of my corporate McAfee SW or possibly blocking of computer ports - and the way the chat is implemented that could be part of the problem 
However, I can’t be the only one accessing EteRNA on a corporate laptop (in my leisure time) - thus I suspect that there are others that can’t access the camera as well
Q: Why do I need to alternate (zigzag) AU-pairs in strings?
A: Because it enhances the stability of the string. Here is a post about Why AU-pairs should alternate in strings.
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I think we need a bit of jargon help. There is the jargon that players use, and the jargon that is used in literature.
Ideally, we should help players understand both. Can we make something that succinctly defines all of these terms? Can we provide lots of visual examples?
Hi Quasispecies!
Yes, you are quite right. Especially as we now move on to reading science papers, some term explanantion will be needed.
We need to identify the key terms we need to know to be able to work together on this babel like project.
I think my Eterna dictionary is only a temporary solution. The best would be if we could somehow get the key terms build into the WIKI, as it has a more intuitive structure than reading a dictionary. Other posibilities than the WIKI?
I’m thinking what about having some sort of list where we all can add words we don’t understand but need to understand and then help each other with the explanation. And when a good explanation gets in, move it to the WIKI. We will need eterna crew to do some of the explanation too. And the biology students in here too.
Later when our discoveries get wider known, we will need to be able to make ourself understandable to the scientists.
Let me hear what the rest of you think. How can we solve this problem best possible?
Q: What is shape data and how do I read it?
A: Shape data is the chemical mapping of how the RNA bases are paired up after the RNA is synthesised. Yellow bases are the unpaired bases and blue base pairs are those that paired up. Click the yellow/blue picture of the design to see the shape data, when you are viewing the lab results. Shape data is a help when reading the results we get back from lab. For how to read the advanced shape data with continous colors, see this answer by Jee.
Q: Why do basepairs pair up?
A: The 3 basepairs AU, GU and GC each consists of one short base and one long base. The bases in a basepair is bound together by hydrogen bonds.
Hydrogen-bonds are typically weak attractions between two different molecules that holds those two molecules close together. (Definition Brightstorm.com) For a hydrogen bond to form, bases need to have a certain distance to each other.
The short bases consists of a single ringed base (green C and blue U) and are called pyrimidines.
The long bases are double ringed and are called purines (yellow A and red G)
I found the picture on this page.
To remember I chose to take the first letters in the short and long bases and connect them to something that I think I can remember. If it works, it works.
CUT - cut short
AG - A giant
Back to the pairing of bases. Picture that RNA folds up in helices like DNA. If you have two double ringed bases opposite each other, they will bump into each other and be too close to form proper hydrogen bonds. Two single rings would be too short to reach each other and thus not form bonds.
However a single ring and a double ring opposite each other have the perfect distance. It is the same in DNA, a short base opposite a longer base.
There is another reason that two long or short bases opposite each other won’t work, not thinking in the hydrogen bonds. The helix would be quite bumpy if basepairs of two short bases were next to a basepair of two long. It would screw with the biological machinery that have read and work along the line of basepairs in the helix of DNA.
Here is another regular question:
Why do G stabilizes loops?
If you haven’t read about why bases forms basepairs, you might want to see it as it holds the basis for understanding some of the following.
Answer: First here is what happens. A single G to the one side at the opening point in a loop, have a stabilising effect, if at the first spot in the loop across an A. This is called a G-A mismatch.
Drake explains mismatch like this:
When bases opposite to each other can not form a pair, it is called a mismatch. They result in unpaired bases, which form loops. The bigger the loop, the more energy it takes to hold together. Some mismatches are very efficient at splitting the strands from each other, encouraging loops to form. Loops starting with such mismatches take significantly less energy to hold.
Notice how the G-A mismatch lowers the energy in the loop. Less positive loops, means more stable loops.
Before
After
In a loop between two strings, you are allowed to place two G-A mismatches.
Now why do a G stabilize the loop? The G and A in a G-A mismatch are both are long bases. Those two are bad partners when in a helix, because they would bump into each other, being too close to each other to form proper bonds. But at the opening of a loop a mismatch can can work as stabilizer.
I asked Rhiju if G-A mismatch actually pair up - have hydrogen bonds between the G and A. He said, yes, they do.
It actually makes good sense. First they split the stack, making sure a loop opens up, then they have the perfect distance to each other, to actually form a pair with hydrogen bonds between them.
1-1 LOOPS
Something similar happens in 1-1 loops. G’s are long bases and two G’s opposite each other, can’t form a basepair in a string, as they would be bumb into each other and be to close to form hydrogen bonds. Instead they acts as splitters of a string, a mismatch.
I asked Rhiju if G-G in 1-1 loops forms hydrogen bond too and he says yes. Here two long bases (G’s) helps split the string up, which creates a loop and then they keeps it in place. In a 1-1 loop they are suddenly perfectly distanced to each other to pair up and form hydrogen bonds. And so they add great strenght to the 1-1 loop and strings around it.
Notice the big jump in energy between before and after stabilizing. Negative energy in loops is good.
In bigger loops, a G-G mismatch won’t work. In loops bigger than 1-1, you will need a G-A mismatch.
how does a G-G mismatch behave in lab? is it just like A-A as in the puzzles, where the tendency to form a loop is basically the same?
Sorry, Hogla, I am not sure how to answer this question.
Common question:
Q: Why are GU-pairs important in RNA?
A: GU-pairs have other electrical and chemical properties than the two regular Watson-Crick basepairs GC and AU.
Quasispecies said in chat sometime back:
The geometry of GU pairs is different than AU or GC, so GU pairs might help an RNA adopt a conformation that allows it to do something interesting.
Or as this abstract states it:
The G x U wobble base pair also has unique chemical, structural, dynamic and ligand-binding properties, which can only be partially mimicked by Watson-Crick base pairs or other mispairs. These features mark sites containing G x U pairs for recognition by proteins and other RNAs and allow the wobble pair to play essential functional roles in a remarkably wide range of biological processes.
Another usual question is:
Q: How long does it usually take for synthesis results to come back?
A: We are supposed to get results back from the first round before second round start, so we can use the results from first round to improve the second. And so on.
The puzzles are instant gratification, that is the game part of the game. The lab results are part of real world and thus prone to delay. That is the science part of the game. So be patient and don’t despair.
Q: My puzzle won’t finish submitting, what should I do?
A: I’ve had that happen a number of times. I just go back one page, open the puzzle again, deliberately flip a pair to cause a mismatch and then correct it. So far, that has worked everytime.
Answer by Wisdave
Q: How can I take screenshots?
A: You can use the ingame tool. This will give you a link to your picture, so you can share it in chat or in a message to another player.
You can also get a screenshot tool as a browser add on. Not all screenshot tools take pictures of all layers of the puzzles, like eg. the energy numbers. I use LightShot. It is for free and works with Firefox and Chrome.
If you know about other screenshot tools that work well with EteRNA, feel free to add them here.
Q: How can I hide the chat?
A: Click on “Players Online” in top of the chat box. This only gives a list of players and does not have any chatting going on. If you want it back again to follow the chat, just click “Chat”.
You have to be in a puzzle to disable the chat.
Answer by Brourd
Dr. Drax added this beautiful little detail on where GU’s are of use:
…tRNA, the chunks that translate from the three-NT sequences in mRNA to actual amino acids, often depend on GU bonds for their internal structure.
Q: Why is the free energy negative?
A: Our WIKI has a great explanation on why it is so.
Also see Ksteppe’s Understanding Free energy - using legos.
Q: How do I see the solution I made for a puzzle after I’ve cleared it?
A: When you re-enter the puzzle you cleared, the cleared solution will be loaded by default. However, if you try to re-solve the puzzle, then it would show that autosave instead of cleared solution. In that case, just reset the puzzle and reload to bring up the cleared solution again.
Answer by Jee
Q: Do you get more points for a new solution resolve?
A: Unfortunately no : [ you only get points for the first time solving it.
Answer by Jee