User:Slokwong

Name: Sophie Wong
Major: Course 20
Email: slokwong AT mit DOT edu

Notes on M13 Renovation

M13 genome

1. Overlapping regions:
   • g2 and g10 (496-831)
   • g9 and g8 (1301-1304)
   • g7 and g9 (1206-1209)
   • g1 and g11 (3916-4242) – g11 is contained in g1, share STOP codon
   • g1, g4, and g11 (4220-4242)
2. Independent genes:
   • g3, g5, g6

Restriction enzymes used

• Pst1 digest

M13K07 :

Gene	Function	Re-engineering Idea
I	assembly	Modify so that p1 can interact with multiple p4. Then analyze how phage secretion changes. Changing p1/p4 interaction affects how effectively the channels work.
II	replication	Modify such that it nicks the DNA in a way that helps p5 sequester the + strands more effectively, thus controlling the formation of double stranded DNA and perhaps making p5 work more efficiently by reducing competition. Be careful in modifying because it is linked to p10.
III	phage tail protein (5 copies)	add myc or alternative tag to monitor the time progression of the phage escape from host
IV	assembly	increase its affinity for p1
V	binds ssDNA	modify such that it can sequester the + stranded DNA more effectively so that there is less competition with the formation of double stranded DNA
VI	phage tail protein (5 copies)	since it is the accessory protein to p3, it can be modified so that p3 can interact more effectively with the host
VII	phage head protein (5 copies)	see modification for p9 since it is the companion protein.
VIII	phage coat protein (2700 copies)	add myc or alternative tag to aid in targeting various types of hosts
IX	phage head protein (5 copies)	modify in such a way to make the phage secretion occur at a faster rate so that interaction time with host is reduced. Also, modify it so that it interaction with p5 is more effective. Since part of p9 overlaps with g8, be careful in modification.
X	replication	modify such that + strands are not only dependent on the presence of p10. This works together with our modification of p2.
XI	assembly	same modification as p1.