Team:Rice University/Notebook/24 June 2008

=Tuesday 24 June=
 * Selim Sheikh:
 * Designed set of sequencing primers (using Vector NTI Advance 10 http://www.invitrogen.com/site/us/en/home/LINNEA-Online-Guides/LINNEA-Communities/Vector-NTI-Community/Sequence-analysis-and-data-management-software-for-PCs.html) to be used in PCR of lambda DNA to amplify the region bounded by the restriction sites M.NgoMIV and AvrII:
 * product of length 4362
 * contains region of the molecule from 20040 to 24401
 * Tm = 78.4 C   TaOpt: 58.7 C    GC: 45.5
 * sense primer: GCCGGCGATGCCAGTGCATCAGCTGCTCAG <--primer name: stfU L
 * length: 30    Tm = 78.2 C     GC = 66.7
 * antisense primer: CCTAGGCAGGTCATTGGCAACAGTG <---primer name: stfU R
 * length: 25    Tm = 62.5 C     GC = 56.0
 * length: 25    Tm = 62.5 C     GC = 56.0


 * David Ouyang
 * We are currently having some difficulties extracting the DNA from the binder for this year. We have tried multiple transformations with positive controls (the + grew, the biobricks did not). Today we tried a PCR of the extracted DNA against a positive control.




 * S = Positive Control 1: A biobrick part we want to sequence
 * + = Template was a mix of S,1, and 2, to make sure that the dye or anything else from extraction does not inhibit PCR
 * 1 = Biobrick G2:1006. Lambda promoter + RFP. Expected length: 935
 * 2 = Biobrick h3:1002. tetR + CFP. Expected length 940


 * The PCR was done with MCS primers which might explain the additional length of the product. The DNA extracted from the binder is faint compared to the + and ladder.