Matt Gethers

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I'm currently a sophomore in course 20. When I'm behaving myself, I'm allowed to work in the Endy Lab at MIT. I will be documenting my UROP projects here. I will put my 20.109 work directly below.

20.109 Work

M13 Engineering Ideas

Extractions, separations, etc. include ensuring that each gene has its own promoter, RBS, terminator, and any other pertinent regulatory sequences. In addition to separating the genes, it would also be wise to develop or utilize/modify an existing system like Biobricks to build the genome so that convenient restriction sites exist between the genes so they can be easily removed or replaced. I used the following annotation to locate and design changes to the genome.
Gene Modification
XExtract from gene II.
IIExtract gene X.
V Add some base pairs between V and VII to allow for a restriction site.
VIISeparate from gene IX.
IIIChange the GTG to ATG Start?
VI Add some base pairs between III and VI and VI anda I to allow for restriction sites.
ISeparate from genes IV and XI.
XISeparate from genes I and IV.
IVSeparate from genes I and XI.
M13 ORI 1 & 2 Are two ORIs necessary? If so, can they be consolidated?
KanR Possible to remove bps 6600 - 7100 upstream of KanR? Does this DNA have functional significance?
DNA Ligation Sample Expected Number of Transformants Observed Number of Transformants
Control PlasmidMany1184
BKB with cocktail but no ligase00
BKB with ligase and cocktail06
BKB with insert and ligase and cocktail #1A few0-1
BKB with insert and ligase and cocktail #2A few5
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