Let’s celebrate the end of Start Codon Month!
Everyone should know AUG, the universal and unique Start Codon. The end of AUG is the end of the beginning of the code for every polypeptide ever made by a ribosome.
Try RNA!
Hey, ever made a model of an RNA “stem-loop” or “hairpin?”
Have you even imagined 3-dimensionally modeling the molecular process of “translation” - complete with physical codon:anticodon basepairing? (You can do this now!)
About double-stranded RNA (dsRNA):
The working parts of a ribosome are all made of mostly double-stranded RNA, with different parts of several long strands basepaired to each other (and locked tight by numerous different scaffolding proteins).
And tRNA is just an RNA strand with four pairs of self-complementary regions, forming four RNA double-helices, which some fold over and hold hands with each other.
And dsRNA is the heart of translation: the pairing of codon and anticodon is (a very short-lived) dsRNA.
Lots more dsRNA structures and functions still await elucidation!
The Genomics Explosion has revealed their widespread existence in huge diversity, but only a few of their molecular roles have been found out. (Functional characterization in biochemistry takes time!)
But I digress…
What about modeling translation?
The new-improved PlayDNA! platform now offers a Gene Expression Simulation bundle, with all the parts for transcribing a 12bp DNA and translating the mRNA to assemble a tripeptide. (The coding sequence ends with a STOP codon.)
Amino acids are modeled with molecular formula cartoons on stickers that you mount on jumbo paperclips. You get a limited set of amino acids, selected to spell out 3-letter words (MSG, MRS, MID, MAP).
…and the really nifty thing is:
tRNA structures in this game are simplified - you build only an abbreviated stem-loop anticodon arm - but you do get to see a single-stranded RNA double helix here, and the anticodon forms another realistic double helix with its codon on the mRNA.
Puzzle-solvers are thus forced to confront the specific constraints imposed by limited flexibility, and sculpt a three-dimensional hypothesis about the relative orientations of three adjacent RNA structures.
Even if we’re not training structural biophysicists, it’s great to explicitly visualize and manipulate the fundamental keys to the Genetic Code, with mechanical cooperation and competition among small molecular parts. This is GENETICS!
GENETICS IS MECHANICS
(Students could make a poster with this message written in secret code. It starts with 5’-GGNGAN… see Blog post #2 (16 Jan 2026) if that doesn’t make sense to you yet.)
CHECK OUT THE GENE EXPRESSION SIMULATION SLIDE SHOWS (.PPTX, 41.4MB)
AND THE SHORT STOP-MOTION ANIMATION (MP4, 26.1MB)
FREE DOWNLOADS!
If you already have a full supply of PlayDNA! (DNA kits)
…then someone might tell your institution’s bean-counters that the kits can be replaced and greatly supplemented by a supply of this new bundle pack. Maybe you could get your hands on the surplus kits, and package them up as holiday gifts to science teachers you may know at other schools… or to homeschoolers. Or maybe your institution somehow distributes surplus kits to others who can use them.
If you already have both DNA and RNA parts
…then you can put together your own Gene Expression game. Amino acid sticker sheets can be downloaded free for printout from the Resources page of TeachDNA.netHERE and HERE, and also the accompanying, indispensible Genetic Code chart.
Anyway, spread the word! For anyone who wants a low-cost trial, PlayDNA! Small Packs are available from Carolina.com for $20 plus tax & shipping.
These aminos come as stickers in the bundle, and here’s coding sequences:
MSG
AUG UCC GCA UGA
MRS
AUG CGC UCA UAG
MAP
AUG GCU CCA UAG
MID
AUG AUC GAC UGA
and here’s more that you can make DIY:
MAY
AUG GCC UAC UGA
MTV
AUG ACC GUC UAG
MAR
AUG GCU CGC UAA
MVP
AUG GUA CCC UGA
MRI
AUG CGC AUC UAG
MDS
AUG GAC UCC UAG
(You invent more!)
Sorry about the long radio silence.
I’ve been busy solving 3-dimensional puzzles on a larger scale, involving lumber, ladders, concrete forming and pouring, invasive underground bamboo, big rocks, small boats, long ropes, plus the family health problems are always there. Let’s get back on a regular schedule! As always, feel free to get in touch, <mQg@teachDNA.net>
cheers,
Morgan