Team:Duke/Parts

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Construction Background

Some flow this summer showed that pdCas9 with crRNA targeting this GFP1 sequence repressed nicely (as did GFP3 but not GFP2) so we picked this one to try making decoys for. The actual sequence is the 20bp of GFP1, the PAM, and then 10 more bp of spacer that come from the GFP orf. We added the spacer reasoning that dCas9 occupies space outside of just the 20bp matching crRNA, and after eyeballing the crystal structure 4008.pdb (which should be referenced & pictured) it looked like we needed about enough space for 1 additional turn of DNA outside of the 20bp. 10.5bp is ~1 turn, 3 bp is taken care of by PAM, so we added 10 to be safe.

During the summer we tested repression of GFP (pSB6A1-K608012) by pdCas9 with crRNA targeting the sequences below.

Sequence Ungated Mean
DH5alpha ZI 0.16
fluorescence relative to reporter-only 0.003661327231
Reporter43.7
fluorescence relative to reporter-only1
dCas942.73333333
fluorescence relative to reporter-only0.9778794813
GFP1 (ccatctaattcaacaagaat)13.4
fluorescence relative to reporter-only0.3066361556
GFP2 (agtagtgcaaataaatttaa)48.6
fluorescence relative to reporter-only1.112128146
GFP3 (gtagtgacaagtgttggcca)15.43333333
fluorescence relative to reporter-only0.3531655225

Crystal structure 4OO8 from the Doudna Lab. Cas9 is in blue, gRNA in red, and the DNA to which the complex binds is in yellow. Click for the PubMed article.

From our PCR-based construction scheme we isolated 1x and 6x decoys, and then expanded the 6x array to 12x. These parts were submitted to the registry as BBa_K1545000 BBa_K1545001 and BBa_K1545001


BBa_K1545000
BBa_K1545001
BBa_K1545002