Exploring Nucleic Acid Structure‐Function Relationships in Remote Biochemistry Instruction

Abstract

The covid-19 pandemic has forced universities around the world to transition to online, remote, or hybrid instruction. This challenge is exacerbated in the laboratory sciences as the limitations on in-person instruction force instructors to conduct curriculum triage and develop new creative avenues for providing meaningful experiential learning opportunities. However, some learning objectives such as nucleic acid structure function relationships can still be pursued with the rigor necessary to train future biochemists and biophysicists using web-based RNA and DNA structural analysis programs. The decades of research in nucleic acid structure prediction algorithms and modeling programs have laid an exceptional foundation for remote teaching and learning in the biosciences. We evaluate the various nucleic acid secondary and tertiary structure prediction programs and their capabilities for remote laboratory activities and research projects. We identify the particular strengths of each program and learning objectives each one can be used to pursue. We also present a series of guided and independent inquiry activities using these prediction programs exploring nucleic acid secondary and tertiary structure suitable for introductory or advanced biochemistry courses using asynchronous or synchronous modalities. Activities include an exploration of nucleic acid secondary structures and relative stabilities, identifying non-canonical interactions within RNA folds, predicting tertiary interactions, comparing predicted structures to published experimentally-determined secondary structures, and investigating how mutations in the nucleic acid sequence can affect secondary and tertiary structure. Tools to increase engagement and discussion in synchronous virtual laboratory sessions are also presented. These activities focus on the SARS-CoV-2 viral RNA structure but can be modified for any particular RNA or DNA. Available biophysical technology resources provide an avenue for continuing high-level instruction despite the challenges of classroom and laboratory de-densification.