Kinesthetic Learning: A New 3D Printed Model to Teach Primer Design and PCR Concepts in the Biochemistry Laboratory

Students frequently struggle to visualize chemical reactions at the molecular scale, leading to challenges in understanding DNA structure, primer behavior, and thermodynamic principles underlying polymerase chain reaction (PCR). This limits their ability to apply theoretical concepts when performing laboratory experiments and troubleshooting them. To address these challenges, a kinesthetic learning activity using 3D-printed UV-resin nucleotides featuring phosphodiester and hydrogen bonds, DNA complementarity, and nucleotide labeling was developed. This activity was implemented in an upper-division biochemistry laboratory course at the University of Arizona (n = 59 students). Students followed a guided worksheet designed with a focus on primer design, with the blocks used to build sequences, predict melting and annealing temperatures, design mutagenic primers, and construct hairpin and dimer structures. Learning was evaluated using isomorphic pre- and post-assessments. Students demonstrated significant improvement in total score percentages (Wilcoxon sign test p < 0.00001 and Cohen's d = 1.73) and in visual reasoning questions, which require interpretation and visual translation of primer design concepts (Wilcoxon p < 0.00001 and Cohen's d = 1.70). Students showed the greatest improvements in identifying and evaluating primer hairpin and dimer formation, while mutagenic primer design remained relatively challenging. Overall, these results indicate that participation in this instructional activity supports students' understanding of PCR primer behavior by direct exploration of primer interactions and secondary structure formation. This innovative, reusable, and adaptable activity complements online primer design tools and supports deeper learning across molecular biology and biochemistry curricula.