Using Software Programs, SDM-Assist and SnapGene, to Maximize Learning Benefits of Performing Site Directed Mutagenesis while Minimizing Logistical Challenges

 

Jason O’Donnell

Advances in Biology Laboratory Education, 2022, Volume 42

https://doi.org/10.37590/able.v42.art14

Abstract

Site Directed Mutagenesis (SDM) is a biological multi-step laboratory technique that introduces a point mutation in a gene, usually to mutate an individual amino acid. Implementing SDM in a Course Based Undergraduate Research Experience course comes with advantages and disadvantages. It is advantageous because it can easily accommodate research-backed educational guidelines including student ownership and decision-making while incorporating and connecting fundamental skills. For example, with SDM a student can decide the amino acid for mutagenesis. Initial steps require designing primers with one or more mismatches for the amino acid mutation as well as an additional mismatch to create/remove a restriction enzyme site in the plasmid, which can later be used to verify mutagenesis. The choice in amino acid influences which restriction enzymes sites will be available, thereby influence experimental results and create opportunities for a student to play a larger role in the process while using their ?own? data. A disadvantage in using SDM is that it can be technically challenging to guide large classrooms of students through this process to arrive at their own decisions in a scientifically sound manner. For example, some amino acids are more technically challenging to mutate than others. In this workshop participants will learn how to use two freely available software programs, SDM-assist and SnapGene, to develop a student activity to maximize student decision-making while minimizing the technical challenges associated with the initial steps of this type of work. Participants will learn how each student can easily use SDM-assist to generate mutagenic primers and use SnapGene to predict the results of the mutagenesis. Participants will learn how these two programs have been incorporated in an upper-level Biology CURE. Real examples of student data will be shown and discussed.

Keywords:  Site Directed Mutagenesis (SDM), SDM-assist, SnapGene, mutagenic primers, protein structure and function

Virtual ABLE (ViABLE) (2021)