The Dynamic DNA Model User Guide
Inside the Color-Coded, Flexible Ladder with Epigenetic Switches
For more information about our model or teaching system go to our website, dnaandbeyond.org.
Also, contact us through our CEO, James Huhta, M.D., a world renowned perinatal cardiologist. He can be reached at 727-434-4492. Our Artistic Director, Dr. Tom Woodward, author of the teaching system, is at . His phone contact is 727-642-8574
Welcome to our first-born product of DNA and Beyond—the “Dynamic DNA Model”! This 38-inch colorful, sturdy, flexible plastic ladder of DNA has 21 rungs. Each rung is made up of a pair of DNA letters (nucleic acids) held together by magnets. These 21 rungs, known to biologists as “nucleic acid pairs,” are not only chemical letters, they actually spell out seven DNA words, with each word having three letters. Such DNA words are called “codons.” With our sequence of 21 letters, we are displaying seven codon-words of DNA, which is just a bit shorter than the smallest gene ever discovered! See the briefing-box at the end of this User Guide. There we share more information on the newly discovered “midget genes.”
Let’s Do the Twist: Our model of a super-short gene is designed to be flexible enough to allow one holding it to give a “twist” at the end of the solid handle. This provides a picture the twisting-ladder or “double helix” structure of the DNA molecule. The inset picture is taken of a happy owner, a college graduate in Denmark, who posed with his new twisting-gene model.
When placed flat on a table or counter, we can also show DNA’s ability to open and close (how DNA unzips, and then zips back together) in its daily function. This takes place through the embedded magnets at the tips of each pair of letters. Thus, the middle of each rung of the ladder “breaks open” when tugged. DNA’s opening enables the gene to be copied into a string of RNA while unzipped. DNA also unzips when it’s time for replication. One DNA is thereby turned into two duplicates of the original!
How long are normal or typical-length genes? Actually, the length of a gene can vary quite widely. Many typical average-length proteins (built by a gene’s embedded code) are 500 amino acids long or longer. Since each amino acid is specified by a 3-letter codon in the DNA, the gene sequence for such a protein would have 1500 letters, the equivalent of taking seventy of our models and joining them end to end. This would go three quarters the length of a football field. The longest known gene, “titin,” or “TTN,” is found in our muscle cells. Its length is truly staggering: well over 100,000 DNA letters! That would make the total gene length at this scale (the scale of our model) the equivalent of placing about 5,000 of our models end to end. It would stretch out for a length of more than three miles!
Color System: Our model teaches the seven basic building blocks of DNA using a seven-color code system. The Norwegian biology teacher pictured here with her brother is looking forward to using this color code in her high school class. Here’s how the code works...
Four Nucleic Acid Colors: Each rung is made up of two color-coded nucleic acid half-rungs: either Crimson with Green, or Azure with Tangerine. (Biochemists use the abbreviation of “A” for adenine, “T” for thymine, “C” for cytosine, and “G” for guanine.) Note: the colors and color-names here were chosen to remind anyone studying DNA of the A/T and C/G complimentary pairing. One possible help: think of “Crimson/Green” as Christmas colors, and think of “Azure/Tangerine” as the team colors of the University of Florida and other universities, including Illinois, Auburn, Virginia, Wheaton, Syracuse, and Boise State! In Florida where the model is produced we call these the “Gator colors”!
Three Other Color-codes:Each half rung is equipped with white outside sections signifying the deoxyribose sugar. (Sugar cubes and processed sugar are white, so that inspired the choice.) Between rungs are pairs of ball-shaped connectors with nooks; these are the “phosphate” molecules. For the “P” of phosphate, we use the color purple. The last member of the team is a pair of methyl tags, which we color magenta.Methane, a basic hydrocarbon, is CH4; the methyl molecule has a central carbon with three hydrogens—making it look like a Mickey Mouse with three ears. Methyl tags can be added or removed. This is the on/off switching mechanism of the epigenetic control system. They are attached to switch the gene off, and plucked away to turn the gene on.
Quick Review: Manipulating the Model
Each A/T or C/G rung, with its two half dowels, is held together as one rung by the action of magnets. Yet the rungs can break open, so the action of those same embedded magnets allow the half-rungs to break open when tugged on. This works best by far on a flat surface, and the handle which splits in two can be pulled apart first, followed by the rest of the ladder.
To twist the model, you have a few options. The ladder-chain has robust flexibility, so it can be laid out flat on a display table and twisted into a spiral. It also can be held vertically, or suspended horizontally in mid-air, and then twisted into the famous double-helix.
Epigenetic bonus…
As mentioned above, each model has a pair of tiny methyl molecules, a “carbon-head-with-three-hydrogen-ears.” The methyl tags have two options. They can be plugged into the two tiny holes on a pair of adjacent (and cater-corner) “C” letters, to show how a gene sequence can be “methylated”—causing it to “rest” or be switched off. The other option is to reverse this action: the methyl tags can be removed from those two “C” half-rungs, making the gene sequence “demethylated,” which has the effect of “waking up” the gene. It is then activated and ready for action, especially being copied and thus transcribed into RNA!
Songs-to-Sing!
DNA and Beyond has developed and registered with BMI a set of three songs, which teach the structure and function of the three information-packed macromolecules: DNA, RNA, and proteins. We will be publishing digital media in the near future, to enable you to use these songs when you use our Dynamic DNA Model.*
The first of these to be shared with the public has its lyrics printed below. It is to be sung to the popular tune (universally sung by children in the English-speaking world) of the “Alphabet Song.” Here, we are teaching the basic four letters of DNA (A with T, C with G) complete in their pairings, along with the role of “D” (deoxyribose) and “P” (phosphate) as holding the letters in place. Methylating the DNA, which causes the gene to rest when pairs of methyl tags are attached to certain “C” letters, is taught in the song as well. Okay, here goes…
A-with-T and C-with-G,
Held in place by D and P,
When I rest, you will see,
Methyl tags plugged into Cs ß Option: pause and make a brief snoring sound
Now I know my A-T-C-Gs
Won’t you come and twist with me? *Registered with BMI; protected by US copyright.
What about RNA?
Our “RNA Conversion Kit” ($9.00) contains eleven brown plastic sleeves. These slide onto “Ts” and convert either our DNA ladder into the RNA pattern. In RNA’s four-letter alphabet, which is A-with-U-and C-with-G, U replaces T. So we use a sleeved Umber (brown) tubular cover over the T (tangerine) half rung. Our RNA kit includes a fun-to-sing RNA song! Starting in June of 2017, look for our link to a password-access online DNA/RNA workshop!
A tiny note on the tiny smORF genes: Newly found midget genes, which at the lower end have 11 to 50 DNA words (codons), correspond to a DNA ladder of 33 to 150 letters. So, these are the rough DNA equivalent of a “DNA Tweet” with only 140 characters. They were uncovered by genetics laboratories in the past decade, working in the US and other countries. Such tiny genes—overlooked in earlier genetic research--are making headlines in scientific literature.
Two names are used for these snippets of DNA with fewer than 100 amino acids. Such a gene is called a “smORF” or a “sORF”! The petite protein chains built from the DNA information in these micro-genes are “micropeptides”!
Headline News: we are ready to send ordering information for our new tRNA gene…almost ten feet in length. One side even curls into the tRNA “cloverleaf” pattern (see above)!