Saturday, July 9, 2011

Beaded DNA Experiments: Major and Minor Grooves

When we last looked at my variations on Gwen's beaded DNA earrings pattern, I had changed the base pairs in the pattern to more accurately reflect the structure of a B-DNA double helix. I had also started to change the backbones of the structure as well:
Why would I go to the trouble of changing the DNA backbones? I was attempting, (albeit incorrectly, as I shall explain), to introduce major and minor grooves into the beaded DNA. 
Image by Richard Wheeler, used with permission

As seen and labeled in the image above, B-DNA has two grooves formed by the spaces in between each backbone. This detail is quite significant in molecular biology, when you consider that the proteins that read the genetic material in the DNA have two different grooves from which to pick from. Incidentally, since the major groove is wider than the minor groove by over 2:1, it is more-often used than the minor groove.

I originally thought that I had reflected this property of B-DNA by changing the backbones in the 14-base pair structure above. To check, I beaded a longer DNA structure of 29 base pairs. The sequence in this structure is that of the recognition sequence of the homing endonuclease PI-MtuI from Mycobacterium tuberculosis.
Unfortunately, this structure does not show the major and minor grooves that I was aiming for. The change in the backbones also made it more unstable than the original. 
I revisited my notes from my previous doctoral coursework, and reminded myself that it is not really the backbone that gives DNA its major and minor grooves: it's that the base pairs are offset from the backbones. You can think of it as a ladder where the rungs do not go through the center of the sides, but are instead sitting on the top or the bottom of the sides, like how railroad ties sit below their tracks and not through them.

After a couple of attempts, I managed to achieve this effect with the DNA pattern. 
To do this variation, I picked up an 8°, 11°, and 8° instead of the bugle bead called for at about 3:30 minutes in the original pattern, also changing the colors of the surrounding 11°s to match the base pairs. The colors between all four base pairs are not balanced, but that's by design, since the pyrimidines, T and C, are smaller than the purines, A and G. I used three seed beads of the same color between the base pairs for the backbone. To make the base pairs pucker up above the backbone, I skip the center 11° when passing through the beadwork again at about 4:00 and 4:20. The rest of the double helix is woven essentially the same as the original pattern. 

A 12-base pair structure woven with this method seemed to show both the major and minor grooves that I was going for:
(Thanks to lovelyfailed for this color palette, "Soapbox Parade")
Indeed, the offset base pairs can be observed by looking straight down the double helix.
But just to make sure that it worked on a larger structure, I wove the 29-base pair sequence from PI-MtuI once more, and I was pleased to find that it showed the same effect: 
I don't know about you, but I find this variation... Quite groovy! It's quite the likeness of the real thing:
I'm certainly not done with this pattern, but I'm very pleased with how this variation turned out. It's still a little large for earrings, but I bet that it would make a nice cuff! I think that a cuff-sized sequence would be about 55-60 base pairs long... Now I just have to find the right sequence!

Do you have a favorite DNA sequence?

12 comments:

  1. I'm digging watching the science geek correct the math geek's DNA beadwork! :)

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  2. I wouldn't call it a correction as much as a renovation, but either way I'm glad you're enjoying these variations! Sometimes I think I get a little too carried away with myself...

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  3. That is so cool. FeatheredGems, I'm enjoying it too! Wowza! I had assumed the grooviness came from how much extra ruffling the outer beads created, but it's fascinating to see precisely why I was wrong. I love the way the kinks in the rungs create the two kinds of grooves. I guess it makes sense that there was some kind of break in symmetry causing that. Thanks for this great post.

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  4. Thanks Gwen! I must admit that it makes more sense to me now than it did when I took Physical Biochemistry a number of years ago... Something about actually building up the double helix from an asymmetrical ladder made it click. It's also possible to induce so much asymmetry, by, say, adding another skipped 11° bead in the base pairs, to collapse the minor groove completely!

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  5. This is wonderful! I am no beader but I'm a biochemist and silversmith. Love how you did the minor/major grooves. :)

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  6. Thanks SilverBlueberry! It's a treat to meet another biochemist jeweler :)

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  7. Last night I finally realized why the crease down the middle makes the two sizes of grooves, like mountain folds and valley folds. Of course the side with the valley fold will form a smaller groove. I am going to make a pair for a bio professor today, and I'm excited to use some of your refinements.

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  8. Ooo cool! I can't wait to see pictures!

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  9. hello! im really interested in making one of these! do you have a pattern i can follow? if i manage to make a decent looking one, i could make more and they would make a great gift to my life science friends! :D if you could, could you please email the pattern to: melissa_soh@msn.com ? thanks in advance! :D

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  10. Thanks! Gwen made a youtube video showing how to weave this design, and you can see it on her blog here: http://gwenbeads.blogspot.com/2011/04/how-to-bead-weave-dna-double-helix.html

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