20.109(F07):Module 1

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20.109(F07): Laboratory Fundamentals of Biological Engineering

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Module 1

Instructors: [1], [2], and | Agi Stachowiak


TA: [3]

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?

M13-coated coli from M. Russel
Map of M13 genome from M. Blaber

| 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