Thursday, July 21, 2011

Beaded DNA: Gene Regulation Necklace

Continuing with the theme of beaded DNA based off of Gwen's pattern, I figured that it was high time to use this design in a wearable item of jewelry. While I still think that my latest variation would be make a great cuff, I tend to wear more necklaces than bracelets, so I searched for the perfect sequence for a DNA necklace. Here's the final result:
The sequence of this necklace comes from the regulatory region of the lac operon of E. coli, specifically, the 106 base pairs between the start of the CRP binding site, and the start codon of lacZ. Regulation of the lac operon was the first mechanism of gene regulation to be discovered, and it remains the primary example of gene regulation taught in Genetics 101 classes today. 

The lac operon contains the genes necessary for an E. coli cell to digest the lactose sugar, but E. coli prefers to munch on the simpler glucose sugar. Therefore, the genes in the lac operon are only active, or expressed, when there is no glucose around, but plenty of lactose to eat instead. The cell knows to express the lac operon through a system of proteins that monitor the presence and absence of glucose and lactose, and according to these sugar levels, certain proteins will either bind or not bind to regions of the DNA sequence depicted in this necklace. Only when the lactose levels are high, but glucose levels low, will these proteins be in the correct combination to encourage lac operon expression. 
I used silver plated seed beads for the cytosines, capri blue for the guanines, green for the thymines, and purple for the adenines. For any of you who also had to memorize the ideal sequences of the -35 and -10 elements in a genetics class, the lac operon's -35 element of TTTACA is in the center of the above picture. Can you see the string of three green and purple base pairs? The -10 element sits just off-center of the necklace. 
Other than its importance in gene regulation, I chose this sequence for this necklace because it's an example of noncoding DNA, or a DNA sequence that does not serve as a blueprint for a protein. These types of sequences make up over 98% of the 3 billion base pairs of the human genome, and were once called "junk DNA" because they were thought to be of little consequence. Regulatory regions such as this one are just one example of the significance of noncoding DNA.
Plus, it makes a significantly cool necklace :)

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?

Saturday, July 2, 2011

Margie and Me Color Challenge: SoBe Style

The theme of today's Margie and Me Color Challenge reveal is "SoBe Style," a summery theme representing the Art Deco style of architecture that defined Miami in the '20s. I just love all the light pastels in this palette, combined with a touch of red and dark teal. 

For this challenge I decided to make earring charms to go with a pair of California Convertible earspirals that I bought from Harry Mason Designer Jewelry last year. I've always been a fan of their earspirals, and I like how their convertible earwires can be swapped with custom dangles for many different pairs of earrings on one pair of earwires. Very convenient if you're the type of person like me who enjoys making beadwoven earring charms, but not the actual earwires.

(Again, just to reiterate: the charms are mine, but the earspirals are not my design nor were they made by me.)

I started with a pair of teal Sakura Charm earrings that ended up a bit darker than the overall original palette, but I think that it works really well with this design:
Then I made a lighter pair using aquamarine crystals, in the Sakura Charm variation that I've been playing with for the past couple of weeks. This resulted in a much lighter effect:
Finally, I used a lighter shade of crystals in this helix-themed twist on a simple cube beaded bead. I think that helices are starting to be a theme around here... Anyway, I think that this pair strikes an ideal balance between all the colors in this palette. 
To get your own pair of earspirals, check out Harry Mason Designer Jewelry at their website, or at their store at Pier 39 in San Francisco. If you're in another part of California, check out your local Harvest Festival this fall to meet the artist in person!

Thanks as always to Marcie for putting on this fun color challenge. Check out all of the other participants pieces at Marcie's blog!

What's your favorite summer color palette?
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