Making ordered DNA and protein structures from computer-printed transparency film cut-outs

Abstract

Instructions are given for building physical scale models of ordered structures of B-form DNA, protein α-helix, and parallel and antiparallel protein β-pleated sheets made from colored computer printouts designed for transparency film sheets. Cut-outs from these sheets are easily assembled. Conventional color coding for atoms are used for both types of biopolymers. Arrows facilitate following chain direction for the polypeptides. For DNA, the 5' to 3' direction is guided by a 5' phosphate group and a free hydroxyl group. Important chiral centers, for example, α-carbon, deoxyribose C1', are easily made. The main advantages of this version of DNA are the proportional major and minor grooves as in the actual molecule. More importantly, because of transparency of the film one can see successive base-pair stacking very clearly and also the sense of relative base-pair rotation. Because of the introduction of two central metal wire axes, the model of B-form DNA can be twisted to give a rather good representation of A-form and even a semblance of a left-handed helix. The models of secondary structure of protein allow a better insight into the axial alignment of side chains, the formation of hydrogen bond, the handedness of the α-helix, and the backbone connection between the β-strands. Students taught by these models understand 3D features of the biopolymers better than from textbook illustrations, computer graphic representations, and even common paper and plastic versions. © 2009 by The International Union of Biochemistry and Molecular Biology.