Harnessing single‐stranded DNA binding protein to explore protein–protein and protein–DNA interactions

Abstract

Proteins must interact with a variety of other cellular components to properly perform their functions. We have developed a series of five experiments based on the robust bacterial single‐stranded DNA binding protein (SSB) to characterize both known and unknown protein–protein and protein–DNA interactions. Students work in groups to generate and process data from electrophoretic mobility shift assays (EMSA), yeast two‐hybrid, far Western, chromatin immunoprecipitation (ChIP), and fluorescence microscopy experiments, including choosing a novel condition for each. A gamification approach was used to encourage student participation and laboratory safety. Student learning was assessed using pre‐ and post‐surveys and course grade data. The results indicate a clear increase in both content knowledge and confidence in the topics presented. Ranking of course activities indicated that performing the hands‐on laboratory exercises was the most valuable course component, and over half of the students would choose to take another course with a similar gamification component. Each of the five laboratory experiments can be performed in combination with each other or integrated separately into a related course, and the gamification structure can be applied to any course.

Evaluating two steps in transcription using a fluorescence‐based electrophoretic mobility shift assay

“…10 The experiment described is unique within the current education literature. Only a handful of other laboratory experiments 11,12 or problem-solving exercises 13,14 describe EMSAs. This experiment provides an experimental framework for students to explore the mechanism of transcription by distinguishing between the binding of RNAP and its transcriptional activity.…”

Learning lab skills online: Lessons from implementing video‐based instruction for a remote biotechnology lab

“…The course focuses on advanced biochemistry techniques, is cross‐listed for both senior undergraduates and graduate students (400/500‐level), and enrolls 16 students per semester. The course itself has been previously described 2 …”

“…The course itself has been previously described. 2 Students in the course come from a wide variety of backgrounds and majors. They include students pursuing a bachelor of science, masters, or PhD degree from the colleges of engineering, sciences, agriculture & life science, and natural resources.…”

Integrating Bioinformatics Tools Into Inquiry-Based Molecular Biology Laboratory Education Modules

“…Reasons for additional rounds of Development include activities not working as intended, or assessments revealing that scaffolding of the material was insufficient to achieve the learning objectives. Through the 5D process, MBLEMs have been created and disseminated over the years ( Witherow and Carson, 2011 ; Srougi and Carson, 2013 ; Ott and Carson, 2014 ; Lentz et al, 2017 ; Chen and Goller, 2020 ; Goller and Ott, 2020 ; Samsa et al, 2020 ; Garcia et al, 2021 ), ranging in topics from protein-protein interactions, signal transduction to metagenomics. This model has proven effective as demonstrated by the successful achievement of student learning outcomes and technical skills acquisition in these courses as assessed from quantitative course data (i.e., lab reports, exams, lab notebooks, and projects) and through analysis of qualitative student survey data.…”