Students of all ages love molecule models. They allow users to see the three-dimensional structure and arrangement of molecules, which can help them accelerate their learning for important topics like covalent bonds. Students in biochemistry class use molecular models to demonstrate nucleobase pairing. They also learn how the famous double-stranded, helical structure looks.
Despite their usefulness they have one limitation. They cannot represent intermolecular interaction. Hydrogen bonds are an important type of attraction force. They form between a hydrogen (donor) atom in one molecule, and an acceptor site in the other molecule, which is usually a nitrogen atom or oxygen atom. These bonds are difficult to model using molecular models because they vary in strength depending on the distance and angle between the donor and acceptor.
Hydrogen bonds are the driving force behind base pairing in DNA andRNA. Students would benefit from a molecular modeling that can better represent them. BasePairPuzzle is a new molecular DNA model that accurately represents base pairing. It was created by Associate Professor Jiro from Sophia University and Mr. Shota Nagura from StudioMIDAS.
This article, published online January 26, 2023 in the The, details about this model and its uses. Journal of Chemical Education.
BasePairPuzzle looks like a simple representation of the nucleobases C, G, U. These 3D-printed parts can fit commercial, cylindrical, neodymium magnets, thanks to the strategically placed crannies. These magnets are designed to mimic the electrostatic and hydrogen bonds that exist naturally between nucleobase pairs.
BasePairPuzzle is a cleverly designed tool that allows students to experience the interaction of nucleobases with one another. Associate Professor Kondo says that by designing the shapes and sizes of the pieces to fit into the palms of the hands and the right amount magnetic force and the clicking sound when hydrogen bond formation occurs, one can easily experience the sensation of molecules interfacing with each other.
While the puzzle is great for understanding why the complementary A–T and C–G pairs are by far the most common, it has the added benefit of allowing for non-complementary pairs to form. Students will see that there is much more to nucleobase pairings than the ones that are complementary. This diversity is what creates the diverse DNA andRNA structures we know.
Associate Professor Kondo says that this is because the pieces attract to each other through magnetic forces. Once students are able understand this, any combination of the four bases will stick together. It is important to note that any combination of bases made by students, including triplets or quartets, can exist within RNA structures found in living organisms.
BasePairPuzzle pieces are also available in a cylindrical mount that can hold complementary base pairs. It replicates the double-stranded, helical DNA structure. This allows students to easily identify the difference between the major & minor grooves. BasePairPuzzle also serves to demonstrate how DNA mutations are performed in an intuitive, step-by-step manner.
Professor Kondo, Associate Professor, has given numerous lectures and classes using BasePairPuzzle in both high school and university. He has received lots positive feedback from students. In an effort to offer a hands-on experience in nucleobase pairing, the researchers made the files needed to 3D print BasePairPuzzle parts free of cost.
Jiro Koondo et. al., BasePairPuzzle. Molecular Models for Manipulating Hydrogen Bonds and Base Pairs In Nucleic Acids. Journal of Chemical Education (2023). DOI: 10.1021/acs.jchemed.2c00964
Students will benefit from a new 3D-printed molecular model that teaches them about nucleobase pairing (February 27, 2023).
Retrieved 27 February 2023
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