"Mini-array" transcriptional analysis of the Listeria monocytogenes lecithinase operon as a class project: A student investigative molecular biology laboratory experience*

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

Transcription is the critical first step in expressing a gene, during which an RNA polymerase (RNAP) synthesizes an RNA copy of one strand of the DNA that encodes a gene. Here we describe a laboratory experiment that uses a single assay to probe two important steps in transcription: (1) RNAP binding to DNA, and (2) the transcriptional activity of the polymerase. Students probe both these steps in a single experiment using a fluorescence-based electrophoretic mobility shift assay (EMSA) and commercially available Escherichia coli RNAP. As an inquiry-driven component, students add the transcriptional inhibitor rifampicin to reactions and draw conclusions about its mechanism of inhibition by determining whether it blocks polymerase binding to DNA or transcriptional activity. Depending on the curriculum and learning goals of individual courses, this experimental module could be easily expanded to include additional experimentation that mimics a research environment more closely. After completing the experiment students understand basic principles of transcription, mechanisms of inhibition, and the use of EMSAs to probe protein/DNA interactions.

A new way to introduce microarray technology in a lecture/laboratory setting by studying the evolution of this modern technology

DNA microarray is an ordered grid containing known sequences of DNA, which represent many of the genes in a particular organism. Each DNA sequence is unique to a specific gene. This technology enables the researcher to screen many genes from cells or tissue grown in different conditions. We developed an undergraduate lecture and laboratory exercise using an interdisciplinary approach to the study of microarray technology. What made this approach unique was studying the evolution of the technology leading up to the formation of the MicroArray Quality Control Project (MAQC). Students realized that this technique has potential of saving lives, making it absolutely necessary to validate all results. Students were then able to complete their own microarray project, evaluate their results and continue to analyze a gene from the study, by further utilizing basic bioinformatic tools as well as critiquing primary journal articles.

Investigation of the properties of wild type and mutant alkaline phosphatase variants: A laboratory project linking genotype and phenotype

An understanding of the link between genotype and phenotype is essential for biology students. A 3-wk laboratory project aimed at demonstrating this link and introducing early year students to some aspects of the research process is described. Students investigate the properties of wild type and mutant variants of alkaline phosphatase using the techniques of both biochemistry and molecular biology. Changes in enzyme activity are correlated with the changes in DNA sequence that introduce restriction enzyme sites. Mutants are also used to analyze the regulation of phoA gene expression. The application of different techniques to the same experimental system helps students to integrate information from different parts of the course.