Education Corner

Learners of all ages benefit from the ability to learn using hands-on approaches. This is particularly true for 3D topics such as structural biology. Although interactive computer graphics exercises can be helpful for upper-level students, they are not appropriate for all ages and situations. Furthermore, 2D textbook diagrams often fail to convey one of the most intellectually satisfying features of macromolecular structures–how well everything fits together in 3D. Here, we present templates for a set of paper models that can be cut from paper or cardstock and can be used for demonstrations of the fundamentals of DNA structure, DNA replication, and RNA translation.  These models were originally designed for the University of Chicago’s South Side Science Festival, but can also be used for interactive laboratory and classroom demonstrations or decorations.  They can be cut out by hand or (more easily) by paper cutting machines such as those sold for home hobbyists by Cricut and Silhouette.

DNA models

For 3D DNA models (Figure 1), the backbone is scored with valley and mountain folds to produce a curvature of 36° per base pair, and a rise per base pair that is proportionate to the helix diameter.  The individual nucleotides are represented as four different shapes that can be “base paired” using simple tabs and slots.  The purines are proportionately larger than the pyrimidines.  To help guide the eye, A and T have square ends while G and C have rounded ends.  The bases are attached to a simple elongated rectangular backbone.  We tested several compromises between nucleotide size (larger is better for viewing and for assembly by small hands), helix length, and the limitations of standard 8.5 x 11-inch US paper size.  The templates shown make 6 base pairs–just over half of a complete turn of a double helix–but can be taped together for longer model duplexes if desired. 

For our table at the science festival, we brought a selection of precut, prefolded 6-nt strands cut from different colors of cardstock.  These had 4 different sequences that could be paired into two duplexes.  Children were encouraged to choose their favorite color for the first DNA strand, then find one that it could pair with.  Helping them assemble the model provided time to describe age- and interest-appropriate “fun facts” about DNA.  For example, the “gee whiz” of how, if all the DNA in one person were stretched out like a string, it would extend far beyond the moon (BBC Science Focus) or the more advanced concept of how stacking the bases into a double helix protects the genetic information from chemical damage. Once assembled, we attached a string around the center of the top base pair and gave the children their own colorful DNA model, ready to hang up at home.

These 3D models also make fun classroom decorations, especially if taped together to make longer helices.  For the science festival, it was best to minimize assembly steps, but over time the models tend to stretch and sag.  They can be rigidified by taping a coffee-stirring stick across the top base pair, reinforcing the tab-in-slot base pairing with tape, and using the “with buttresses” template option (see below). 

For more advanced demonstrations, we created individual nucleotide templates with tabs and slots that guide assembly of the helical backbone (Figure 2).  These can be used to demonstrate how DNA is replicated.  They can also be used to show how the double helix is distorted if a mismatch is made, and to explain that DNA polymerases and repair machinery can look for such distortions when “proofreading” newly synthesized DNA.  This physically demonstrates the sometimes under-appreciated concept that a regular geometry is created only by Watson:Crick pairing of nucleotides.

Models for explaining RNA translation

To expand on the DNA models, we also developed models for demonstrating translation. To do this, we expanded our 6-mer DNA models from above into a 21-mer DNA sequence that accurately translates to the amino acids “S-C-I-E-N-C-E”. To make this interactive, we generated a base paired DNA sequence (Figure 3, yellow) and transcribed another strand as the RNA (Figure 3, orange). Note that for an advanced classroom setting, we have included a model that could be folded into a double helix as with the 6-mer DNA models. For the ease of our demonstration at the Southside Science Festival, we taped down the top strand and used the other to demonstrate amino acid pairing and to reduce chances for damage or disruption.  We could then excitedly ask participants if they wanted to help us decode the DNA. In our models, we include the coding 21-mer DNA strand and two different complementary strands – one that can be folded for the proper pairing and one designed to match without pairing.

For our hands-on demonstration, we first informed participants that DNA gets transcribed into RNA. We replaced the complementary DNA strand with a different-colored nucleotide strand where T’s were changed to U’s. Then, to demonstrate how translation works, we made a cardstock tRNA model. For ease, we took the structure of a tRNA (PDB ID 4tna) and represented it as a surface view, using ChimeraX (Figure 3). We also connected a generic rectangle near the anti-codon region to have a place for adding a codon. This was advantageous because being able to switch codons meant we could cut fewer tRNA models. Another key feature of our cardstock-tRNA was a hole in the top of the tRNA to allow for attachment of “amino acids”. This hole was useful because we designed our amino acids so that they could be easily removed and attached to form a chain. This chain is not particularly robust, and in a classroom setting it would be best to tape the chains together as the “protein” is translated. For the purposes of our demonstration, it worked well. 

We found that this demonstration was a great parallel to the DNA models, and it would be an excellent addition to the paper models in the classroom. Of note, our initial tRNA models were cut from a 12x24 sheet of paper, which may not be widely accessible for printing or cutting, so we have included a modified template.

Additional options

Our simple DNA model does not differentiate between the major and minor grooves.  They are indicated in the modified template with buttresses (see templates and directions here).  However, this model includes an additional tab-into-slot assembly step for each nucleotide that may exceed the patience of younger children.  These nucleotide models could also be made more realistic (but more complicated) by using multiple tabs and slots to represent H-bond donors and acceptors. 

For younger participants, we also made large individual nucleotides that could be paired.  To make the tRNA model printable, we have attached a modified template. An easy alternative would be to use a rectangle or T-shape with space for anticodons and attachment of amino acids. Another alternative would be the use of Velcro or magnets, but we felt the paper models were sufficient.