I was a bit frustrated and unsatisfied with not being able to see the Free Energy of a formation in my Lab Designs until I actually clicked the mouse and created it. Too often, the results were not what I had planned or expected - so, to remedy this, I created the following table in Excel to set out the various energies of the various Quads in tabular format for easy sorting and viewing, and for use as a reference during Lab Design Activities.

For this table, I am defining a “Quad” as a set of four bases, or two adjacent base-pairs. This structure is the basis of the Stack; a "Quad is like a “rung” in a “Stack-Ladder.” A “Quad” is also the unit that has it’s Free Energy displayed (with the label “Stack”) in the Free Energy Window Display when you hover the mouse over the Stack. You’ll notice that this "Stack figure is not for the whole stack, but only for the “Quad” over which you are currently hovering. (This is not clear in the game for newer players, since the Stack is defined in the Tutorials as the whole “laddered” section between loops - so to keep meanings clear, I’m using “Quad” instead of “Stack” as it is labeled in the Free Energy Window, for the unit of two base-pairs consisting of four bases)

The Quads in the table are represented and displayed in 2x2 cells with the pairs in the vertical plane; that is, the pair is the set of two bases above and below one another. Each Quad consists of two of these vertically oriented pairs rendered side-by-side. The colors reflect the game base colors, and the Energy Number background colors reflect a rough, arbitrary division of Very Low, Low, Middle-Range, High, and Very High energy values.

It turns out that there are 36 unique Quad configurations. I created them in the spreadsheet at first in a sort of binary order, but after having them all laid out, I realized this table would be far more useful if sorted by Free Energy values.

Note that many of the permutaions are horizontal or vertical reflections of another Quad; some are 180-degree rotations. while still others are “half-twists” of another Quad. However, many very similar configurations have very different associated free-energy values. In particular note the energy differences between Quads 1 & 7 (30% energy difference), and between Quads 23 & 32 (54% energy difference), or again between Quads 33 & 36, where flipping one pair results in a change from -0.5 to +1.3! - easily the difference between stability and instability in a design

This table has also helped me to dispel at least one very popular misconception: that side by side AU pairs are stronger than an AU/UA pair. Not so, as this table reveals (Quads 29 & 30 vs. Quads 25 & 26); this is just not as apparent in the game readout. This table, it turns out, is full of little bits of helpful reference like that. And having it all laid out in Ascending Energy order is very convenient and helpful when designing for the Lab.

So, anyway here is the table; I hope this helps some of you all in constructing your Lab Designs; I have found that is has helped me quite a bit, both in increasing understanding, and as a reference in the Lab Design process. At the very least, it may be useful to familiarize yourself somewhat with this finite vocabulary of Quad variations and their associated Energy Values, or just for a quick glance every now and then for some particular question.

Best Regards,

-d9

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Apparently the scaling has blurred this .png a little - click on the table for a clearer, non-scaled version

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This is really cool, D9. How did you compute it?

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wow this is amzaing d9!!!

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I feel bad that you went through the trouble of going through everything and checking the values since you can find some of these parameters online:

http://www.bioinfo.rpi.edu/zukerm/cgi…

However, the visualization is soooooooo much better! I’m sure that the Zuker and Turner people will really appreciate this!

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Can you explain why, for example, #35 and #36 would have different energies? It looks to me like #35 is identical to #36 if I stand behind my monitor and look at it from behind. Do you get what I mean?

Edit: my biology is very rusty but I now remember something about the 5’ and 3’ ends. Maybe a better way for me to phrase the question, then, is: while inside eteRNA, how can we tell if we are in a #35 or #36 situation (besides creating the situation and then mousing over the quad)?

Good point Chris, if you look carefully, the nucleotides actually have directionality to them. The small arrows actually go 5’ to 3’.

wow. wouldnt have thought that directionality of these “quads” has such an effect on energy levels.

maybe the developers should add a 7th function that will swap quads around and not just pairs?

THANKS!!!

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Hi Chris,

First, this was no “trouble;” this was FUN!, Second, I had originally (naively) thought I was going to calculate all these values instead of merely doing a convenience transcription, but when I found the Zuker Pages at the Turner Labs site, I realized that the calculation was going to be prohibitively involved, and was way beyond the scope of what I was trying to produce for the game.

Anyway, thanks very much for your positive evaluation of the visualization - much appreciated.

-d9

I tested these values but got confused about the few mirrored ones (some mirrored combinations have the same kcal others don’t) and especially the “direction”: i.e. where the starting nucleotide is in relation to these quads as fixed point in space. Answer: starting point is to the top right, even though I can’t understand why that makes a difference yet.

Edit: as you can see these GU pairs have inverted kcal values (needed to add the manually after screenshot) than the ones in the OP based on where the 1st nucleotide is (or lets say counting order).

The quick answer to this is to go to http://en.wikipedia.org/wiki/DNA and search for the word “asymmetric.” Things just aren’t as symmetric as they look in the models!

Edit: Haha, I just noticed that the reason I was alerted to your question by email is because *i asked it myself on this very thread about 9 months ago*. I love the internet.

I realize this is a dead thread, but could we change the shapes of the bases in some way to indicate this asymmetry, or draw light strings in the target shape to indicate changes in the actual folding? Thanks!

I realize this is a dead thread, but could we change the shapes of the bases in some way to indicate this asymmetry, or draw light strings in the target shape to indicate changes in the actual folding? Thanks!

good ideas. Also I would like to be able to see the natural shape free energy without switching to natural mode - though this might be confusing. Maybe advanced settings could be expanded to include more goodies like your ideas, I would like that

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Nice, this helps a lot

Thanks so much for the alternative view point!

it works…

tnx for this, it took me a second to understand that the letters and nucleotide orientation were different:P this helps point out the bad G,U alternating and the good A,U alternating thing

Very handy!

I found this page a few weeks ago, but it took me quite a while to find it again.  It seems that this page is invisible to search for some reason.

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