User:Augusto Tentori

Augusto Tentori

Department of Biological Engineering
450 memorial drive
Cambridge, MA

atentoriatmitdotedu

Neuroengineering and neuromedia group at MIT.

Genome Engineering

Gene	Location	Function	Notes	Ideas
I	3196-4242	Phage assembly	Overlap with gene IV and shares stop codon with XI	Modify to allow for assembly of different size phage
II	8268-831	Double-stranded DNA replication	Overlap with gene X	Use stronger promoter to enhace virus production
III	1579-2856	Structural proteins. 5 copies in tail.	BamHI site is in gene III	Engineer to increase binding. Modify to allow binding to other organisms or surfaces.
IV	4220-5500	Phage assembly	Overlap with gene I and XI	Modify to allow for assembly of different size phage
V	843-1106	Helix-destabilizing in single-stranded viral DNA synthesis		Alter to understand specific purpose and function.
VI	2856-3194	Small hydrophobic protein (probably part of capsid). 5 copies in tail		Engineer to increase binding. Modify to allow binding to other organisms or surfaces.
VII	1108-1209	Structural proteins. 5 copies in head	Overlap with gene IX start codon	Allow for easy insertion of sequences. Allow easy insertion of a GFP protein for example.
VIII	1301-1522	Structural proteins. Capsid coat.	Overlap with gene IX stop codon	Allow for easy insertion of sequences. Allow easy insertion of a GFP protein for example.
IX	1206-1304	Structural proteins. 5 copies in head	Overlap with gene VIII start codon and gene VII start codon	Allow for easy insertion of sequences. Allow easy insertion of a GFP protein for example.
X	496-831	DNA replication	Overlap with gene II	Engineer to allow easy modification of viral production quantities.
XI	3916-4242	Assembly	Overlap with IV, inside gene I, share stop with I	Modify to allow for assembly of different size phage

Nature often preserves functionally critical genomic elements, and evolutionary cousins can help us identify which genetic elements are disposable, which are interchangeable, and which are essential. Who are M13's closest evolutionary relatives and how do they differ from the phage you're working with?

F1 Fd and M13 are all filamentous ssDNA bacteriophages that belong to the virus family Inoviridae. F1 does not need/have gene 11. Phage F1 DNA differs from phage M13 by 52 nucleotides, and from phage Fd by 186 nucleotides. The overall charges of their protein coats sometimes differ, for example, Fd has a lot more positive amino acids.

Look up part BBa_M1307 and write a response to the following criticism: "BBa_M1307 is not a standard biological part and does not belong in the registry.

BBa_M1307 represents the genome of the M13 virus. If we define a part as something that performs a very specific function then indeed BBaM1307 should not be considered a standard part as it itself is made up of several parts. Some parts encode for an outer coat, others for binding to the bacteria, etc.

Gel Electrophoresis

Length kb	Distance mm	Log(length)
10	15	4
3	23	3.47712
2	28	3.30103
1.5	30	3.17609
1	35	3
0.5	42	2.69897

The equation for the line is log(length)= -.06247*distance+4.9139 When we plug in the distance traveled by our digested sample, the equation yields 8.211.18 base pairs, which is really close to the expected 8669bp.