Week 6

Outline Background Information Update: new paper out July 21 st Experimental Progress Current challenges Bad template Successful colony PCR (try 2) Synthesis To do

Outline Background Information Update: new paper out July 21 st Experimental Progress Current challenges Bad template Successful colony PCR (try 2) Synthesis To do

1.Create KaiA and KaiBC biobricks. 2.Transform E. coli with Kai Biobricks to reconstitute KaiC phosphorylation cycle with no reporter attached. 3.Distant: Transform E. coli with Kai Biobricks to reconstitute KaiC phosphorylation cycle with Biobrick’d luciferase reporter.

New Information From Kageyama et al. (7/21/06) KaiC forms a hexamer KaiA phosphorylates the KaiC hexameric subunits KaiB traps KaiA when KaiC maximally phosphorylated; promotes KaiC dephosphorylation KaiC subunit suffling KaiA FLAG-tagged, KaiB His6-tagged while maintaining rhymaticity

Outline Background Information Update: new paper out July 21 st Experimental Progress Current challenges Bad template Successful colony PCR (try 2) Synthesis To do

Received sequencing results, which confirmed our digests showing that the 3kb fragment we were working with was not KaiABC. Began a new extraction of KaiABC fragment from cyanobacteria. Received primers for sequencing KaiABC and extracting coding sequence. Sent out our KaiABC synthesis order to Geneart. Renovating Wiki!

1. Using PCR to create and extract the correct constructs. 2. Synchronizing the Kai cycle within one E. coli cell. 3. Pick inducible promoters for KaiA and KaiBC. 4. Performing Western blots to detect KaiC within E. coli.

We found that our template which we extracted two weeks ago is not the correct template. Although a restriction digest suggested we had the correct template, our sequencing primers did not bind and site-specific mutagenesis has repeatedly failed.

From square one, we have successfully extracted another 3kb fragment from cyanobacteria DNA. This week we will retry cloning it into a Topo Vector, site-specific mutagenesis, and sequence the new template.

KaiABC extraction #2 Lane 4 and Lane 9: Purified liquid cultures. ~3kb and ~400bp fragments Lane 5 and Lane 6: Plated PCC7942 Other lanes: purified or raw liquid culture (failed)

Outline Background Information Update: new paper out July 21 st Experimental Progress Current challenges Bad template Successful colony PCR (try 2) Synthesis To do

kaiC 1618 bp In standard vector Bba_ bp Bba_ bp EcoRI NotI XbaISpeI NotI PstI KpnIXhoI mutation kaiB 367 bp In standard vector kaiA 913 bp In standard vector

Chose between: GeneART Coda Codon Devices Blue Heron DNA 2.0 Quote: $1.10/bp, business days Second best offer: Coda, at $1/bp but requiring assembly (~3wks) Should arrive between Aug. 7-11

Outline Background Information Update: new paper out July 21 st Experimental Progress Current challenges Bad template Successful colony PCR (try 2) Synthesis To do

Sequence our new 3kb constructs. Extract KaiA and KaiBC coding sequences from KaiABC region. Select inducible promoters for experiments. Create experiment constructs. Perform KaiABC synchronization experiments, and measure results.