User:Nzimm

Neil Zimmerman

Bio

• MIT Class of 2009
• Major: Biological Engineering
• Minors: Management and Music
• Varsity Soccer
• Wind Ensemble (Clarinet)

20.109

M13K07 Genome Engineering Plans:

Gene	Plans
I	Change # of protein copies expressed to experiment with different sized channels
II	Modify residues to allow deactivation of p2 under certain conditions so that replication of + strand can be regulated
III	Insert myc to allow detection with an antibody
IV	Change # of protein copies expressed to experiment with different sized channels
V	Add fluorescent tag to monitor levels of p5-ssDNA complex
VI	Modify residues to help p3 bind more effectively to the ToIA protein on the E. coli F pilus
VII	Minimize the bulk of the protein to allow more room for modifications on p9
VIII	Insert myc (as in III) or another tag to serve as a “hook” for attaching constructs to M13
IX	Add residues to N-terminus to present on the outside of the phage coat
X	Add sensitivity to different stimulus than that of p2 in order to regulate replication of + strand in another fashion
XI	Modify residues to allow proteins other than p8 to embed in the membrane and serve as the phage filament coat

M13K07 Genome Refactoring:

In refactoring the M13K07 genome between the HpaI site in gene II and the BamHI site in gene III, I separated all overlapping elements across the region by copying overlapping sequences and placing the elements adjacent to one another on the refactored sequence. As a result, the refactored region is 1,000 bp larger than the original sequence. I also added annotation for & refactored the open reading frames of genes 2, 5, 7, and 10, which are not annotated in the M1307 part in the registry. I intend to separate each element with two unique restriction sites, so that the elements can be isolated & manipulated more easily. Below is a table describing the overlaps that were refactored.

Overlapping elements	Action
rbs g7 & g5 ORF	copied overlapping sequence & placed rbs g7 adjacent to the 3' end of the g5 ORF
promoter g8 & rbs g9	copied overlapping sequence & placed rbs g9 adjacent to the 3' end of promoter g8
promoter g3 & g8 ORF	copied overlapping sqeuence & placed promoter g3 adjacent to the 3' end of g8 ORF
g10 ORF, g10 rbs, g10 promoter, g5 promoter, & g2 ORF	copied g2 ORF & placed adjacent to 5' end of other (non-overlapping) elements
	inserted the sequence encoding the myc protein into the BamHI site of g3

Current Courses

• 20.109
• 7.05
• 14.01
• 21M.301

Other

Email: nzimm (at) mit (dot) edu