Beaded DNA: Chirality

I did some more experimenting with Gwen's beaded DNA pattern, this time delving into differences in DNA handedness, otherwise known as chirality. Like a hand or a foot, a double helix can have either a right-handed or a left-handed structure. You might have noticed in my previous posts that I was favoring the right-handed form for my beaded structures, even though the original design is flexible enough to be twisted into either conformation.

Image by Richard Wheeler, used with permission

The above image shows three forms of DNA; A-DNA, B-DNA, and Z-DNA. The B-DNA in the middle is by far the most common form that exists in biology, and it has a right-handed chirality. The A-DNA on the left is also right-handed, and it exists when DNA is dehydrated enough to form a crystal structure (usually only in the lab). The Z-DNA on the right is the only structure of the three that exists in the left-handed conformation, and it looks quite different compared to B-DNA.

Z-DNA is a little thinner, and the backbone of each strand of the double helix (in red and orange above, and in hematite below) isn't a smooth, ribbon-like path. Rather, Z-DNA has a jagged backbone that zigzags with each pair of bases up and down the double helix. Its major and minor grooves are also less pronounced than in B-DNA. Z-DNA forms rarely in biology, and is generally found in DNA with a specific sequence; in this case, alternating pyrimidine-purine sequences, such as CGCGCGCGCG.

With some tinkering, I was able to create a Z-DNA version of my beaded PI-MtuI sequence. The original B-DNA version is on the right, and the new Z-DNA version is on the left:

To create this version, I first worked up the design using my own variations on Gwen's pattern, but when it came time to peyote stitch up and down the backbones of each strand (at about the 7 minute mark in the pattern), I added two 11° seed beads where I would have added one 8° seed bead. Then I zipped up and down the backbones once more, adding a 15° seed bead at the same place as the 11° seed beads, alternating its placement on either side of the 11° beads so that the backbones zig zag:

The resulting structure is more flexible than the B-DNA version, and not as aesthetically pleasing either, but it remarkably mimics the appearance of Z-DNA. You can even see how the major and minor grooves are less pronounced, and how there are fewer base pairs per turn in this version:

Other forms of DNA exist in biology as well, such as the Y-shaped junctions formed during DNA replication, and the very cool Holliday junctions created during meiosis and in some kinds of DNA repair. However, those structures will have to be topics for another blog post.