20.109(F07):Module 1

Module 1
Instructors: Drew Endy, Natalie Kuldell, and Agi Stachowiak

TA: Laure-Anne Ventouras

In this experiment, we will consider the genome of a virus, namely the bacteriophage M13. M13 is a self-assembling nano-machine with a compact genome that has been optimized by evolution to commandeer its bacterial host. Approximately 1000 new viruses are generated from a single infection event. Imagine harnessing this production. What could we build and what natural processes could we better understand? One approach we’ll take is to modify the existing genome in a subtle but useful way, namely by adding a useful sequence-tag that modifies the bacteriophage coat. We’ll examine how this modification affects the coat protein’s expression and overall phage production. Another approach we’ll take is to start from scratch, undertaking a full throttle redesign of the bacteriophage genome. We’ll employ a commercial DNA synthesis company to compile the redesigned genomic program and then we’ll see if it encoded infective M13 and if the genome of the bacterial host affects bacteriophage production. Through these investigations we’ll ask: is nature’s M13 genome “perfect” or can we do better?



Module 1 Day 1: Start-up genome engineering Module 1 Day 2: Agarose gel electrophoresis Module 1 Day 3: DNA ligation and bacterial transformation Module 1 Day 4: Examine candidate clones Module 1 Day 5: M13.1 Module 1 Day 6: Western analysis Module 1 Day 7: Probe western Module 1 Day 8: Oral Presentations direct link to the requirements for the genome engineering portfolio direct link to working page for M13 refactoring

TA notes, mod 1