3D printing is a revolutionary technology with many applications in education and science. Several biology faculty have personal experience using filament based FDM 3D printers and have used these to build functional parts like microscope mounts for helping students use their phones for recording observations when using microscopes as well as parts to fix research equipment. While FDM printers have been useful, they have limitations on resolution and printing complex structures. Resin based MSLA 3D printers offer significant improvements in printing fine details and complex geometries and open new opportunities for printing models of biological components and intricate functional parts for use in the lab. We requested support to purchase a resin based MSLA 3D printer, processing equipment, and consumables for a pilot program to further explore the potential of using 3D printing in teaching and research.
Our short term goals for this project were:
- Learn/develop a workflow for converting protein/nucleic acid structural data, MRI data, and microscopy data to appropriate file formats (.stl files) for slicing software.
- Explore/learn commercial/open-source slicing software, such as Chitubox or Lychee, for resin-based 3D printing. Optimize slicer and support settings for our resin printer and develop clear written methods for printer use and operation.
- Produce 3D models of biological molecules/structures for use in BIOL 244 (Genetics), BIOL325 (Developmental Biology) and BIOL489 (Medical Genetics).
- Produce functional parts for use in Biology teaching and research labs.
Example use: teaching molecular structure using 3d printed models
A central theme in biology is that form fits function. This relationship can be difficult to appreciate at the molecular level as students can find it challenging to visualize things beyond the visible scale. In BIOL 244 (Genetics), students learn to draw the nucleotide building blocks of DNA and begin piecing together these components into a single stranded polymer. With a little practice students can memorize and draw the basic nucleotide structures prior to discussing the functions of various components of the structure and how changes to these components impacts replication and reading of the genetic code. These drawings are useful, but students often have challenges in extrapolating their 2D drawings to the 3D structures they represent. To address this we 3D printed models of nucleotides that could be assembled into a DNA double helix.
- A DNA model kit containing structural files (.stl) for nucleotide components is available at Thingiverse (https://www.thingiverse.com/thing:714312)
- Structural files were loaded into the free version of Lychee Slicer, allowing components to be scaled, arranged on the build plate, generation of structural supports for printing, and output of a .ctb file capable of being printed on the Elegoo Mars3 Pro MSLA printer
- .ctb files were transferred to the printer and printed using Siraya Tech Fast resin
- Excess resin was washed off the printed structures with isopropyl alcohol in the Elegoo Mercury Wash Station
- Components were freed from the build platform and supports were removed
- Prints were cured for 10 minutes in the Elegoo Mercury Cure Station
- Nucleotide components were fit together to generate complete nucleotide structures and a DNA double helix
3D models were incorporated into lessons on DNA structure in my Spring 2023 BIOL 244 Genetics course and into a review activity in my Spring 2023 BIOL 489 Medical Genetics course. The 3D models helped highlight several important concepts, such as the antiparallel orientation of nucleic acid polymers in a DNA double helix, the base pair interactions joining complimentary strands, the stacking of nucleic acid bases, and especially the differences between the major and minor grooves of the DNA double helix. A common comment from my BIOL 489 students, who had not had the 3D models to examine when they took BIOL 244 , was that the DNA structural finally made sense. Building the models for class gave me several new insights into the structure of DNA that I was able to highlight in class.
Lessons learned and future directions
Assembling the DNA model was very enlightening and a valuable activity to incorporate in future lessons. However, there are several challenges to incorporating this into class. I generated a fairly large model that had the benefit of being easy to assemble and highlight structural components. Printing enough nucleotide components to generate a DNA double helix model through two full turns required several days of printing and processing and used a significant amount of printing resin. I experimented with scaling down the size of components to reduce printing time and costs. The model can be successfully scaled down, but assembly becomes more challenging at smaller scales. Finding the right balance between ease of assembly and printing time/costs to generate components for a class of 24 students will require more experimentation.
Another challenged encountered was the durability of the printed components. While the resolution and quality of the printed components were stunning, parts occasionally broke durning assembly and when being handled by students. There are many different resin options available and experimenting with ones formulated for structural components that need to stand up to stress is a clear next step.
Expanding the versatility of 3d printing for biology
While repositories for 3D structure files, such as Thingiverse, can be a valuable source for starting a journey in 3D printing, they are limited to structures others have generated and shared. The versatility of 3D printing can be expanded through the ability to model new structures using CAD software programs such as Fusion 360 or Tinkercad and we have used these to generate replacement parts for lab equipment and making custom hardware for experiments. Another avenue for expanding the versatility of 3D printing is to utilize 3D biological data files to generate printable models. Two exciting options are structure files generated from protein crystallography or NMR experiments and MRI imaging data. Here we explored 3D printing protein/DNA structural data. The Protein Data Bank (PDB) (https://www.rcsb.org/) contains thousands of structures experimentally determined through X-ray crystallography or NMR. One of the first challenges in utilizing this data is converting it from the .pdb format available from RCSB to a format readable by 3D printing slicing software, such as a .stl file format. We utilized the freely available ChimeraX software from UCSF (https://www.cgl.ucsf.edu/chimera/) to directly load and manipulate structural data files from PDB and save these models as .stl files that we could load into Lychee slicer, process for printing, and generate .ctb files that could be printed on an Elegoo Mars 3 pro 3d printer. To supplement our BIOL 244 (Genetics) coverage of DNA conformations I printed and presented the A-DNA, B-DNA, and Z-DNA conformations (PDB files 1ana, 1bna, 2dcg respectively). The 3D printed structures were a vast improvement in helping students see the differences between these conformations compared to 2D representations. Additionally, I printed the structure of bacteriophage RNA polymerase (PDB file 1msw). While this is a far more complex structure, after examining it one can see the interactions between the protein and the DNA templated and gain a better appreciation of the channels running through the protein where the double stranded DNA molecule enters and the exit channels for the synthesized RNA molecule and the DNA template and nontemplate strands.
The MSLA 3D printer acquired through the Academic Technology Mini-Grant has opened new avenues for incorporating 3D printing into the biology curriculum and research. The detailed resolution possible through this technology is stunning. While the overall setup and workflow to get this technology up and running was fast and smooth, this was greatly facilitated by having a strong background in 3D printing using FDM machines. MSLA 3D printing has a steep learning curve compared to FDM technology and those looking to get into this technology should be aware that it may take a significant time investment to properly prepare and slice files for printing. MSLA printing resin is a potentially hazardous chemical and requires proper handling and disposal. Dedicated space and PPE are important to consider before getting started with this technology. Our first experiences with MSLA printing highlight the excellent resolution possible, but we still need to explore 3D printing resins for projects requiring greater durability.