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 :)

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?

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. 

Photo via National Geographic

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?

Old Flowers, New Flowers

The theme for the latest round of the Artbeads.com blogger program was "What's Old is New Again!" The idea is to take a vintage or antique item and combine it with modern elements to create an entirely new design. As I previously mentioned, I chose a cloisonné necklace that I received from my grandmother for this project, and decided to make little flowers out of Swarovski pendants and Japanese seed beads to match the flowers on the cloisonné beads. Here's the final result:

And the original necklace for comparison:

The project theme was announced at about the same time that Swarovski announced their new spring innovations, and I thought that the new chrysolite opal color would best match the green flowers. Unfortunately, this color was not yet in stock at Artbeads.com, and it isn't available in the top-drilled bicone shape anyway, so I settled on the peridot hue instead.

I also paired it with aquamarine...

... and rose, for all three flower colors on the cloisonné beads.

The flower design is a variation on the Sakura Charm pattern, which is available at beAd Infinitum.

The new necklace is shorter than the original, and I think that the crystals lend a much brighter air to it as well.

What's your favorite way to reimagine vintage jewelry?

Full disclosure: The swarovski crystals used in this necklace were received as a gift from Artbeads.com. No payment was made for the review of these products.

Beaded DNA Experiments: Base Pairing

A few months ago Gwen Fisher published a video using Doceri software on how to weave a pair of DNA double helix earrings using seed beads and thread. As a molecular biologist by training, I was completely enamored with this design and immediately set out to play with it (all the while kicking myself for not coming up with the idea first!), but I've only now gotten around to writing the first of what will be several posts on my variations on this pattern. If you haven't already seen her free video on how to make your own pair of DNA earrings, check out Gwen's blog for all the important details. 

I first tried this design on a short random sequence of eight base pairs:

I managed to get the design to work the first time, using significant tension in the second and third rounds of the design to get it to twist. The helix actually started to twist while I was beading the second round.

After trying out this pattern, I immediately wanted to modify it to make it look closer to the structure of real DNA The biggest difference between this design and a DNA double helix is that the bases, consisting of A, G, T, and C, are on the "rungs" of the DNA ladder, not on the sides. 

Image by Richard Wheeler, used with permission

The image above shows the chemical structure of B-DNA, the most common form of DNA. The bases are the flat ring structures containing the blue nitrogen atoms. The thymine and cytosine, or T and C bases, are called pyrimidines and have only one ring. The adenosine and guanine, or A and G bases, are purines, contain two joined rings, and are therefore somewhat bigger than the pyrimidines.

Each side of the DNA ladder, what we call the "backbones" of each of the two DNA strands that make up the double helix, is made up of a repeating sequence of sugars and phosphates. You can see in the image above that there is one sugar (the non-flat ring next to each base, containing no nitrogen or phosphorus) and one phosphate (made up of yellow phosphorus and red oxygen atoms) for each base. Therefore, the important genetic material in DNA is confined to the inner part of the structure. 

One other important feature of DNA is that, except in rare cases, A will always pair with T, and G will always pair with C. This is why DNA sequence databases such as the public National Center for Biotechnology Information will list the sequence of only one of the two strands; if our sequence is:

AGCCATATGAC

..we can match each base in the sequence with its partner to get the sequence of the other strand:

AGCCATATGAC

TCGGTATACTG

I tried to incorporate this aspect of DNA to modify Gwen's design to use color-coded twisted 6 mm bugle beads for the base pairs. I also changed the colors of the DNA backbone to solid blue for the 15° and 11° seed beads, and capri blue for the 8° seed bead, to try and mimic the repeating sugar-phosphate structure.

From a beadweaver's point of view, the structure works up and holds its twist just as well as the original. But the molecular biologist in me really wanted to see all four types of those bases. 

So I switched to 8° seed beads in place of bugle beads for the bases; two seed beads for the purines, and one for the pyrimidines, and also color-coded the 11° seed beads on either side to match its associated base (I also changed the backbone a little bit, but that's a topic for another post):

I like this arrangement much better. It results in a somewhat thicker helix, but it's much more biologically accurate. It would probably work better in a pendant or a cuff than in earrings. 

Gwen also tackled this arrangement by using 8° seed beads and a 3 mm firepolished crystal for each base pair, resulting in a slightly larger helix.

I'm still not done creating further variations on this design, but those are topics for future blog posts. Next time I'll talk about DNA's major and minor grooves...

Have you ever tried incorporating ideas from your day job into your beadwork? How did it work?

Origami Interlude: Kusudama

A little while ago I picked up Tomoko Fusé's Kusudama Origami because this book is chuck-full of the type of modular origami designs that I so enjoy. This book also explores the more traditional types of kusudama origami, where individual units of folded paper are strung or glued together into a (usually) round structure. I find modular origami more satisfying when a structure can be completed without glue or string, but the designs in this book are so pretty that I had to give this style a try. I started with a single double-flower version of her primula design:

Which quickly started to multiply..

I used 15 by 15 cm TANT paper for these flowers. This paper comes in a rainbow pack and in packs of different hues, and the red pack contains 12 different shades of red and bright orange. I only needed about half of the pack for the whole structure.

The finished "Bouquet of Primula" contains 16 individual flowers. I was hoping that I could use only 12 to achieve dodecahedral symmetry, but alas, more flowers were needed to fill out the whole ball. It measures about 9 inches in diameter.

I'm anxious to adapt this style of flower ball to beads, where dodecahedral symmetry might be more feasible. In the meantime, I'm enjoying my paper version. 

Have you tried a new style of craft lately? How did it turn out?

Floral WIP and Travel Notice

It's been a while since I've posted anything new; moving and traveling has eaten up most of my time over the past month. I did however manage to get started on my project for the next round of the Artbeads.com blogger program. The theme is "What's Old is New Again," and the idea is to take an old or vintage element and incorporate it into a new piece. I chose this blue floral cloisonné necklace that I received from my grandmother a few years ago, after she had it in her collection for many years.

I like the little pink, blue, and green flowers on each bead:

My original idea for this project involved Swarovski bicone pendants in beaded beads, but after Gwen figured out how to incorporate them into the Sakura Charm pattern, I just had to try this as well. While Gwen's final result is a 7-fold variation, I wanted to stay with the original 5-fold flower of the pattern to match the flowers on the cloisonné beads. It took me five attempts to arrive at something I was satisfied with. You can see my attempts in this photo, starting at the left and continuing clockwise to arrive at the charm in the center:

I found that to get a 5-fold flower to work with bicone pendants, I had to work with progressively smaller seed beads to get them to fit without being wobbly. The back of the charm also ended up somewhat different than the original; the weave and bead counts are slightly different, and the bail is rotated to straddle one of the bicones, instead of sitting between two of the petal beads.

I tried to match the colors to that of the flowers in the cloisonné beads. Do you think it's a good match?


Finally, I'll be traveling internationally for the next three weeks to spend some time with my husband as he participates in the San Francisco Symphony 2011 European Tour, so any jewelry orders placed from now until June 9 from either my Etsy or Artfire shops will ship on June 10. I will have some e-mail access on my trip, so I will still send out tutorial orders, but these orders might experience a delivery delay of up to 48 hours.

In the meantime, the Sakura Charm pattern, as well as the Circle Starburst and Balloon Box patterns, are available at beAd Infinitum 24/7.

Bon voyage!