User:Chaoj

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Student Registration/Questionnaire

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20.109 Spring 2007

Last Name

Chao

First Name

Jennifer

Preferred name

Jen

Course/Minor

Course 20, minor in Management

Year of Graduation

2009

Telephone #

610-952-3098

Email

chaoj at mit dot edu




Day 1: Start up Genome Engineering

protein function re-engineering ideas
I assembly p1 and p11 interact with p4 so within the bacterial inner membrane, modify p1 to make secretion of the phages more effective. (speed/size of channel)
II replication of DNA + strand modify p2 so it nicks in such a way to make p5 respond quicker, send out a signal to p5 so it can protect the + stranded DNA
III phage tail protein (5 copies) add a tag to monitor phage escaping from host and the new phages budding from the bacterial surface
IV assembly modify p4 so assembly speed is increased in the outer membrane and modify it so it has a better interaction with p1. This will cause the channels where the phages are secreted to be more effective
V binds ssDNA modify p5 so it can better protect the + stranded DNA which will lead to more rapid replication and amplification; less competition with the double stranded DNA
VI phage tail protein (5 copies) similar to p3, p6 is the accessory protein to p3. Modify it so it has better and more effective interaction with 3, no interference
VII phage head protein (5 copies) companion protein to p9, make sure or modify p7 so it can better the interaction with p9, better binding affinity.
VIII phage coat protein (2700 copies) Modify so the shape changes by altering the coat formulation, make the phage more streamlined, sleek so increases proliferation speed.
IX phage head protein (5 copies) Modify resulting in faster secretion of DNA
X DNA replication linked to p2, modify so p10 is not so dependent on 2 and the DNA can still replicate and modify so there is better accumulation of + stranded DNA
XI assembly modify similar to p1 to change channel properties to make secretion of phages more effective

Day 4: Genome Refactoring

I refactored the phage genome to remove overlaps and added in restriction enzyme sites, which EcoRV and HindIII cut, between each part, more specifically Gene 8 and the Gene 3 promoter. I changed a few bases, and consequently some codons, but retained the same amino acid sequence while weakening the rbs or promoter. Considerations: 1)Unstuffed by splicing all genes from smaller parts into composite parts; removed overlaps. 2) eliminated promoter of gene 3, by changing a few bases that would not change amino acid sequences but would decrease the strength of the rbs or promoter. 3) add restriction sites between each part BBa_M30058.

New Parts: restriction enzyme sites

restriction enzyme code
EcoRV ATC
HindIII A^AGCT_T
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