DNA Molecular Models

There are many DNA Double Helix Models available for teaching & demonstration. The most recognizable is our 17 Base Pair DNA Model of which 2 were combined to build the Big Bang Theory DNA Model. Surprisingly, a much less expensive DNA Double Helix Model has many more advantages for teaching university & even high school students about the chemical structure & elegance of this most important molecule.

Why Teach DNA Structure with a 12 Base Pair DNA Model?

Genetic secrets was once hidden in the 3 billion base pairs of our genome can now be extracted in hours. The Human Genome Project has lead the revolution in gene sequencing technology that now impacts personal medicine, vaccines, forensics, ancestry tracing & much more. The depth of understanding now required has gone beyond simple Mendelian genetics.

The Indigo 12 Base Pair DNA model was designed for this purpose. The success of using manipulatives to teaching math concepts to elementary students is well known. Our DNA model can be just as effective teaching genetics concepts to budding biochemists. This simple exercise has many advantages, not the least of which is that it is incomparably economical. The model’s parts are reusable & with amortization, the cost per student-lab works out to about $0.15. More importantly it is simply a great tool for understanding the inherent structure of the DNA double helix.

12 Base Pair Teaching DNA Model

Our best teaching model for understanding base pair complementarity & sequencing & the structure & function of the DNA double helix.


Atom Geometry Matters

The Orbit Molecular Model system is unique among model styles in having trigonal carbon & nitrogen atoms with two geometries. Other models only use the standard 120o trigonal geometry for carbon & nitrogen in the purine & pyrimidine ring structures and the tetrahedral shape carbon found in thymine. The Orbit system differs in having a second trigonal carbon & trigonal nitrogen geometry for the 5/6 atom polycyclic purine rings as seen in the AT & GC base pairs.

This requires careful attention to choosing the appropriate atom geometry to ensure correct assembly. Failure to do so guarantees malformed rings that won’t form proper nucleotides and in turn cannot build a double helix. The advantage of this to the learning process is clear. A molecular modelling program automatically adjusts the atom geometry to accommodate the structure. Physical atoms cannot. This may be the most obvious appreciation for understanding VSEPR geometry that biology students are exposed to.

What Else Can Unique Trigonal Atoms Do?

A typical Organic Chemistry Model Set uses flexible tubes to create double & triple bonds that bow between tetrahedral carbon or nitrogen sp3 atoms. The Indigo® Instruments 12 Base Pair DNA Double Helix Model takes advantage of the central hole in the trigonal atoms to portray double bonds.

Special parts called “X” pegs fit this central hole. These allow a second bond, to be fitted in parallel with the main single univalent bond. Trigonal carbon & nitrogen atoms connected this way form purine & pyrimidine rings that are nearly flat. They lie neatly on the support layers & do not need to be tied down. They are held in place by gravity & further constrained by the sugar phosphate backbone.

DNA Adenine Thymidine Nucleotide Base Pairs

This image shows AT, top, with its double bonds on the thymidine facing upwards. The model is flipped, bottom, to reveal the double bonds on the adenine. This design ensures that when the base pairs on mounted on the support stand, there is an asymmetry that forms the major/minor grooves.

Why “Handedness” Matters

The individual nucleobases each have the same “handedness”. Each is constructed so that its double bonds are attached to the same side of the ring structure. The importance of this is apparent when the complementary bases adenine-thymine & guanine-cytosine are connected with their hydrogen bonds. The bases in a pair consist of one that is flipped over before attaching it to its complement. This faces the double bonds upwards on one side and downwards on the other.  This positioning of the double bonds ensures the base orientation will produce the 2 antiparallel strands of the double helix.  It is also a quick visual cue for the lab demonstrator that the model is assembled correctly.

The relevance of building the model this way becomes apparent once all the base pairs have been mounted on their layers & the sugar phosphate backbone is attached. The asymmetry arising from the antiparallel nature of the double helix strands can be seen by the larger major groove & the smaller minor groove. If the bases had been coupled without this attention to handedness, the two grooves would be identical.

The Double Height 24 Base Pair Version of the DNA Model

24 Base Pair, 3 Turn DNA Model

24 Base Pair, 2 Turn DNA Model

Special thanks to retired (May 2016) teacher, Dr. Roscoe Stribling of St. Andrews Episcopal School in Mississippi who sent us this picture of 2 models combined to form a 2m tall structure with 2 turns consisting of 24 base pairs. This is also fortuitous since it technically codes for 8 amino acids which is enough to build the shortest known peptides found in nature that have a biological function.

The model is supported externally using two lab support stands & is on display at the school in a room dedicated to Marshall Nirenberg who graduated from St. Andrew’s & went on to win a Nobel prize for breaking the genetic code. For anyone interesting in building a free standing version of this, let us know.

DNA & RNA Molecular Model Related Blogs

Best DNA Double Helix Teaching Tool. A testimonial from Dr. Roscoe Stribling whose school bought TEN of the 12 base pair models.

DNA Model “Xmas” Tree. A sampling of places around the world using the Indigo®  “Big Bang Theory DNA Model” for display.

Indigo® Big Bang Theory DNA Model; Then & Now. The first 17 base pair model (BBT precursor) went to Bell Labs in 2000.

Stereo image pair of the Indigo® Big Bang Theory DNA Model. If you can’t see one for real, the next best thing.

World’s longest DNA sequence decoded, The Indigo® “BBT” model has 1.8×1016 different combinations; buy yours while supplies last.

RNA, Gene & Enzyme That Kickstarted Evolution. An older piece written by Dr. Neil Straus who designed our DNA models. This article also features a one of its kind RNA model.

Gorbind Khorana. Indian born Nobel prize winner who deciphered the DNA code for amino acids/proteins.

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