Elements to Incorporate in Lab Designs

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  • Updated 8 years ago
What sequences are we ignoring when designing lab submissions? What sorts of structural elements should appear in future lab candidates?

Post them here and I will copy them to a list of sequences and concepts to inspire future player designs and structural elements to investigate in future labs. If you want to use one or more of your lab submissions to try something "out of the box," consider taking a look at the first list. If you're designing a puzzle that you hope to see turned into a lab, check out the second.

This is (and will remain) a work in progress. I hope this thread can become a useful resource.
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Quasispecies

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Posted 8 years ago

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Brourd

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From the looks of it, your "structural elements to investigate in future labs" is quite thorough. Examples of elements I believe need to be tested at least once are larger bulges, larger, closed multiloops, and specialized shapes. In regards to specialized shapes, I am referring to shapes whose solutions are limited due to the EteRNA energy model. Examples include the string of bulges known as the zigzag, and various "fused loops."

A second thing we need to consider are larger designs, which could introduce new situations that will contribute to the rewriting of certain rules, such as increased numbers of multiloops, increased internal loops, longer stacks, and increased repetition.

For my final comment, I would like to mention a suggestion for "sequences and concepts to inspire future player designs." My suggestion is for the inclusion of twisted GU pairs

I don't know how well they would form, but I think it would be funny if they broke apart, creating the 2-2 loop that our tests have been unable to make.
If anything else comes up, I'll post it here, thanks Quasispecies
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Quasispecies

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Brourd - I like the twisted GU pairs idea. It happens in the sarcin loop of 23S rRNA. I was going to include it in the list.



When I've played with these pairs, EteRNA wants to turn them into a 2-2 loop if you don't place AU neighbors in the right orientation. Hopefully we can get some sort of relaxed energy restrictions added to the lab.
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Brourd

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Quasi in regards to that sequence, that is when the stacked pair has internal energy of 1.3, and it can be solved with GC pairs

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Quasispecies

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Thanks for pointing that out. I'll have to try that in a future lab. I think it's one of those situations where the line between a 2-bp stack and a 2-2 loop gets very blurry.

The design we were messing with last night is up now - "Lonepair Spire".
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Brourd

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I was wondering about this setup, and if it occurs in nature, or is simply a consequence of the EteRNA energy model
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Quasispecies

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Added to list.
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Eli Fisker

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Parallel lines

I have an idea about long parallel lines close together. I think the longer strings easier get caught up in each other in lab, as they are closer together than if they were sticking out from a multiloop. I would like to see how this fork shape does in lab.



In 3D the strings will propably bend a little. Maybe be a bit curly. What I want to know is if rules changes if strings are close together. Maybe this shape will be hard, as the bulges should be solved before we can actually see what happens. Strings on a multiloop may have better reasons to stay apart, though they doesn't always do. Maybe I should make a simpler version of the puzzle with just two and longer lines.
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Eli Fisker

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One more. We have tested adjacent stack in lab puzzles like The cross and The one bulged cross.

But we still haven't tested puzzles with bigger adjacent stacks.
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Quasispecies

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Eli - I will add your idea, though I'm sort of wondering how to do it.

Symmetric designs, like your fork, have repetitive substructures that can interfere with folding by creating alternative pairings. In the case of "The fork," there are three tetraloops preceeded by 5-bp stacks.

I'm not sure how to make sacks physically "collide" or "interfere" with one another, though. I imagine there are loop sequences that can reliably introduce turns and bends into an RNA. It might be possible to make a structure that can incorporate (or avoid) those sequences. How multiloops fold in 3 dimensions is an interesting question too. I really need to expand the section on coaxial stacking once I understand it better.

Let me know if you have any ideas.
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Brourd

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Here is another idea for concepts and sequences to test, having to do with pentaloops.





The small energy boost is due to the interactions between the nucleotides, and would be interesting to see the result when tested in the lab.
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stevetclark

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Here is my latest puzzle which has a 2-2 and a 4-4 loop.
http://eterna.cmu.edu/eterna_page.php...