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

## TL;DR

This paper describes using NUPACK to create virtual labs for teaching nucleic acid concepts in biochemistry, especially during the pandemic.

## Contribution

The novel use of NUPACK for educational modules on nucleic acid hybridization and structure in undergraduate biochemistry.

## Key findings

- NUPACK-based labs enhanced student understanding of nucleic acid structures and hybridization.
- The virtual labs supported remote learning and were extended to high school students.
- The approach improved accessibility and flexibility in biochemistry education.

## Abstract

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.