PCR primer design: an inquiry‐based introduction to bioinformatics on the World Wide Web

Abstract

A project is described which details the selection of PCR primers for an unknown gene of the Herpes Simplex Virus (Type 1) using tools available on the World Wide Web. Within the context of designing PCR primers, students are introduced to some of the basic tools used in the field of bioinformatics and have the opportunity to further develop the concepts of nucleic acid sequence and structure, based on the analysis of selected nucleotide primers. © 2000 IUBMB. Published by Elsevier Science Ltd. All rights reserved.

Integrating PCR Theory and Bioinformatics into a Research-oriented Primer Design Exercise

“…There is literature to support the introduction of primer design in undergraduate labs and workshops (Kim, 2000;and Shachack et al, 2005); however, few measure student performance and learning gains during or after implementation of these new materials. Therefore, we purposefully aligned the learning goals with exercise questions to assess the effectiveness of our primer design materials in meeting the specific learning goals of the lab.…”

Using sequence analysis software to teach molecular biology basics

“…As an introduction to simple bioinformatics manipulations, students start out by designing primers for PCR amplification of the ICP34.5 gene [4]. Briefly, students can import the ICP34.5 gene into Jellyfish TM and, using annotated frames, select oligonucleotides that will encompass the entire coding sequence of the gene.…”