Incorporation of NUPACK-Based Simulation into Classroom and Laboratory Teaching of Nucleic Acids Hybridization for Undergraduate Biochemistry

The COVID-19 pandemic has accelerated the shift from traditional in-person teaching to remote and online learning, necessitating a more adaptable educational platform to serve the diverse needs of students. Transforming hands-on "wet lab" activities into virtual "dry lab" exercises can promote a more accessible and flexible learning environment, offering innovative methods to improve online teaching outcomes, incorporate interactive components, and provide student support. Here we describe our effort of utilizing NUPACK, a free cloud-based web application, to develop new educational modules on nucleic acids for teaching biochemistry lectures and laboratories. These modules include fundamental topics such as melting temperature, hybridization equilibrium, free energy, secondary folding structures of nucleic acids, and the thermal stability of single-nucleotide polymorphisms. The NUPACK-based DNA computational lab not only provides a hands-on learning experience to enhance students' understanding of nucleic acid structures, hybridizations, and characteristics but also facilitated the transition to remote learning during the pandemic. Furthermore, these computation-assisted DNA experiments have been extended to engage local high school students at Rutgers UniversityCamden. This article summarizes the curriculum development and guidelines for the DNA computational lab, aiming to benefit the education of nucleic acids in biochemistry for a wider audience of educators and learners.