Dedicated systems/Dedicated translation

Testing a new RBS-ribosome pair
I'm going to construct a new mutant 16srRNA. I'm going to try two of the sequences published by Chin and Rackham Rackham. I'm picking two of the mutants that don't require me to mutate the distant bases that the authors also mutate.

Orthogonal ribosome construction
I'm going to make this via 'Round-the-horn site-directed mutagenesis. This seems like the quickest way to make the full 5 base mutation in one go.

Primer design
pCH1497-ASD1     5'-CacaCTTAccttaaagaagcgtactttgtagtgctcacacag attgtctgatagaaagtga-3' 4rRNA-f primer   5'-TTGTGGTAccttaaagaagcgtactttgtagtgctcacacag-3'  Tm = 61.8C 10rRNA-f primer  5'-TGGGATTAccttaaagaagcgtactttgtagtgctcacacag-3'  Tm = 61.9C 4/10rRNA-r primer 5'-TGATCCAACCGCAGGTTCCCCTAC-3' Tm = 62.8C

Experimental details

 * My plasmid is 10kB so Sean Moore suggested adding fresh polymerase in half-way through. I didn't actually manage to do that on the first attempt.
 * Sean also suggested dropping the melting temperature by a few degrees and also the extension temperature. I did 91C for melting and 69C for extension.
 * I used Pfu Ultra and Phusion as my polymerases.
 * According to the gel I ran of the PCR product (I ran 10&mu;l), phusion worked(?) but pfu ultra did not. Not sure yet why the phusion lanes are smeary.  I think I'll redo this and try to add in the fresh polymerase this time.
 * Not sure why the PCR product of 10rRNA looks slightly longer than 4rRNA. Maybe just because there is more DNA?
 * I did a 10&mu;l ligation rather than the 5 that Sean recommends.
 * Got ~50 colonies on each plate of BL21(DE3) with a wide range of sizes(?). I PCR'd 3 big and 3 small on each plate.  Only got the right band from the small colonies, not sure why.
 * Will start cultures of 4-6 and 10-4, 10-5 and 10-6.
 * Sequencing says that 4-6 worked, although it mutated an A to a G just upstream of the ASD. I'll test this anyway to see if it works.  I should also check to see if this mutation is due to an error in my reverse primer as it would have been in this region.
 * I got no sequence results for 10-6 and 10-5 seems to have had the ASD cut out. I'll try re-prepping 10-6 and see how that sequences.
 * From the second gel, start cultures of lanes 3, 6, 11 and 12.
 * Colonies 10-1 and 4-2 sequenced correctly. nice.
 * In addition, I'm keeping 10-5 from the first sequencing since it has the ASD deleted and 4-5 from the second sequencing as it has a slightly different ASD than expected.

alignment results

Reporter Devices
I designed six new reporter devices for dedicated translation and six new reporter devices for dedicated transcription and translation. I checked for -
 * random start codons
 * BB restriction sites
 * cryptic SD sequences
 * secondary structure

More later.