Phillip Samayoa: M13 Renovation

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Gene Re-engineering Thoughts
I Restrict p1 and p11 from binding to determine whether the absence of channels results in a stop in the phage cycle that is occuring within the e.coli
II Add transcription factors for p2 into the genome so that more +strands can accumulate and create a higher turnover of phage production. (see p10 engineering ideas)
III Because p3 is more exposed than p6, use this to create the other end of the link between multiple m13s. Do this by adding a residue that binds the constant region of the antibody which recognizes the p9 residue (see gene IX engineering thoughts)
IV regulate and/or increase expression of p4 in order to create larger or smaller membranes with greater amounts of p8 on the surface. This together with the linked phages and metal binding of p8 could create different sizes of wires
V Add GFP tag to p5 in order to keep track of rate of replication as well as to monitor where in the life cycle the phage is in.
VI Modify p6 on m13 and TolA in E.coli with CFP and YFP for FRET measurements to determine the frequency of phage invasion of its host
VII modify p7 to restrict expression of this portion of m13 so that there is no steric hindrance of p9's binding to its "linking" antibody
VIII Modify P8 to bind metals so that the phage can be constructed to be an electrical conducting biomaterial
IX Because residues expressed on the 'N' terminus of p9 are expressed on the outside of the coat, add a residues that are recognized by an antibody in order to form a bridge to the p6 on another phage, thereby assembling a chain of m13s.
X re-arrange the genome such that p10 and p2 are not overlapping. Do this by moving the p10 gene (C-terminus of p2) to after the end of p2 with a sequence of nucleotides in between that serve as a spacer.
XI (see p1)

Question 3

While I do not think BBa_M1307 is a "standard biological part," I do think that it belongs in the registry. This "part" seems to fit the description of a device much better than a standard part. This is because the single stranded genome that it packages is composed of various different parts that together form a functional, plasmid-propagating phage. I might argue that the Kan resistant gene itself would be a standard part that forms one necessary component of the overall encoded system. But the entire sequence does not embody the idea of a part in the sense that it cannot be seamlessly inserted into a larger device to serve a particular, clear-defined function.