20.109(F15):Module 1

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20.109(F15): Laboratory Fundamentals of Biological Engineering

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Module 1

Lecturer: Bevin Engelward
Instructors: Noreen Lyell, Leslie McClain and Maxine Jonas

TA: Andee Wallace
Lab manager: Hsinhwa Lee


In this experimental module, with a view to quantify DNA repair by homologous recombination, you will modify the gene for EGFP (Enhanced Green Fluorescent Protein) to truncate the protein it encodes. Cells expressing the full-length protein glow green when exposed to light of the appropriate wavelength. You will be designing and then creating an expression vector to delete the first 32 amino acids of EGFP. Cells transfected with your expression vector should not glow green, a prediction you will test. You will also test whether this N-terminally truncated EGFP can recombine with a C-terminally truncated version to regenerate full length EGFP in vivo. Finally, you will have the opportunity to suggest changes to the experimental protocol that will increase the frequency of green cells in which there has been an inter-plasmid recombination event. We will then choose a few variables to test on the final day of the experiment.

Recombocell image from Dominika Wiktor of the Engelward Lab
A schematic overview of the Module 1.

Lab links: day by day

M1D1: DNA engineering using PCR
M1D2: Clean and cut DNA
M1D3: Agarose gel electrophoresis
M1D4: Ligation & transformation
M1D5: Examine candidate clones and tissue culture
M1D6: Lipofection
M1D7: Data analysis


DNA engineering summary: Assignment description

DNA engineering mini-presentation: Assignment description


  1. DNA double-strand break repair: From mechanistic understanding to cancer treatment
    DNA Repair 2007
    Thomas Helleday, Justin Lo, Dik C. van Gent, Bevin P. Engelward
    Sample Animation Animations were made by Justin Lo (BE class of '08), a former UROP student in Professor Engelward's laboratory!
  2. Homologous recombination as a mechanism of carcinogenesis
    Biochim Biophys Acta 21 March 2001
    Bishop AJ and Schiestl RH
  3. Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death
    EMBO J 15 January 1998
    E Sonoda, M S Sasaki, J M Buerstedde, O Bezzubova, A Shinohara, H Ogawa, M Takata, Y Yamaguchi-Iwai, and S Takeda M
  4. NEBuffer Performance Chart with Restriction Enzymes
    Old buffer system: URL
    New buffer system: URL

Notes for teaching faculty

TA notes, M1 F15 notes for orientation day