Characterization Notebook

Goal: Develop a well-characterized library of parts for the MoClo Assembly Method

Subgoals:

J23100_AB, J23113_AB, J23115_AB, J23115_EB, J23116_AB, J23116_EB, J23117_AB, J23118_AB, J23119_AB
BCD1_BC, BCD2_BC, BCD8_BC, BCD12_BC, BCD13_BC, BCD16_BC: completed 6/27/13

Assemble level 1 circuits for characterization of Repressible Promoter
Run flow cytometry on the promoter characterization circuits
Assemble level 2 inverter as an example of the library’s use
Switch the backbone in some existing level 1 parts to study how different antibiotics affect the flow cytometry data: completed:6/21/13

May

Week of May 12, 2013

Learned about synthetic biology, MoClo, and developed plans for our summer projects, specifically histidine kinase and quorum sensing.
Learned about Clotho software suite and learned how to use Eugene, RavenCAD, and Pigeon from other members of the CIDAR lab.
Familiarized ourselves with protocols and lab etiquette
Stocked up on lab supplies (plates, broth, plasmids)

Week of May 19, 2013

Began to create new bicistronic design RBS’s (BCDs): used PCR on BCD2 template to make BCD1, followed with LV0 reaction
Began to restock low concentration and low volume plasmid for level 0 parts

Week of May 26, 2013

Sent BCD1 made last week for sequence verification
Assembled Lv1 circuits to test out new fluorescent proteins (CyPet, DsRed, mCitrine, mOrange) and for flow cytometry training
Ran flow cytometry with Traci for our training
Continued to restock low concentration and low volume parts

Week of June 2, 2013

Continued creating new BCD set from BCD2 template, ran PCR to make BCD8, BCD12, BCD13, BCD16, followed with LV0 Rxn, and sequence verification. All reactions yielded original BCD2, likely due to preparing buffer the night before. Retried the same LV0 experiment later in the week.
Met with Dr. Jake Beal from BBN Tools. He showed us how to use BBN’s Synthetic Biology Tools to analyze our future flow cytometry data.
Performed ligation PCR in order to generate the following constitutive promoters: J23110_AB, J23113_AB, J23115_AB, J23115_EB, J23116_AB, J23116_EB, J23117_AB, J23118_AB, J23119_AB
Met with Wellesley HCI team for a synthetic biology training session and to learn about each other’s projects. We also held Eugene tutorials and practiced making Eugene scripts for some famous experiments. We also had our first social event, bowling at Jillian’s!

Week of June 9, 2013

Tried to PCR apFAB46_AB, apFAB57_AB, apFAB61_AB, apFAB70_AB, apFAB71_AB promoters but unfortunately it failed
Tried PCR for R0079_EB, R0079_FB, C0012_CD, and C0062_CD but the transformations proved unsuccessful
Continued the second try on BCD Lv0 Parts, also failed: only produced BCD2 template. Probably too much DNA template in the PCR reaction. Retried entire protocol starting from PCR. BCD16_BC was successful
Archived frozen stocks and plasmids of BCD1_BC and BCD1lox_BC
Travelled to Wellesley to brainstorm some ideas for improving the visualization of the Eugene language
Attempted Level 1 reactions using J23100_AB, BCD1_BC, BCD2_BC, B0034_BC. B0034m1_BC, B0034m2_BC, E1010m_CD, B0015_DE, DVL1_AE; 80% of reactions failed. Discovered that BCD1_BC, BCD2_BC, B0034_BC, B0034m1_BC, and B0034m2_BC might be contaminated. Did Zymo transformation with RBS and BCDs that failed due to following an older protocol. Did Bioline transformation of RBS and BCDs

Week of June 16,2013

Continued third try on unsuccessful BCD Lv0 parts. This time we gel extracted the PCR products and used a higher quality ligase in the reaction mixture
Performed backbone switch for RFP transcriptional units from KAN to CAM and AMP

pJ004R_AE, pJ024R_AE, pJ034R_AE, pJ044R_AE, pJ054R_AE, pJ064R_AE, pJ074R_AE, pJ084R_AE, pJ094R_AE in both DVL0_GB and DVL2_AF

Attempted 6 Lvl 1 reactions: pJ004C40_AE, pJ004C79_AE, pJ00B1C40_AE, pJ00B1C79_AE, pJ00B2C40_AE, and pJ00B2C79_AE. Unfortunately the transformations did not result in colonies. It was later found that the terminator used B0015_DF was contaminated
Began PCR for B0015_DH, an essential terminator for our inverter constructs that has proven difficult to generate in the past
Did level 1 reactions to try and construct transcriptional units to impart resistance to spectinomycin, ampicillin, and kanamycin. These are referred to as pJ002maadA_EF, pJ002mbla_EF, and pJ002mkanR_EF, respectively

All level 1 reactions produced no insert when run on the gel. This was determined to be because the B0015_DF was actually B0033m_BC. A new PCR and streak out of B0015_DF from the -80 were started

Sequence confirmed J23110_AB, J23116_EB, J23117_AB, and J23118_AB and archived them. J23113_AB and J23115_AB were not sequence confirmed and will be restarted in the future
Transformed the BioBrick plasmids pSB1AT3 and pSB3T5 and miniprepped them. Both were then used as template in a PCR reaction to produce the tetA_CD level 0 part. The first level 0 reaction failed, but the second produced the appropriate band on a gel and was eventually sequence confirmed
Bioline transformation of RBS and BCDs from previous week was a success. Picked new colonies for overnight cultures and sent in samples for sequencing

Week of June 23, 2013

Sent BCD8, 12, and 13 for sequence verification. All were successful
Started workflow for Lv0s needed for pRepressible Library: C0012_CD, C0062_CD, C0071_CD, R0010_FB, R0079_FB by streaking out BioBrick cultures for the respective parts
Tested all Lvl 0, 1, and 2 destination vectors for possible biobrick backbone contamination. DVL0_DH was missing a SpeI site and DVL0_FB was missing 4 base pairs from its Lac Z insert
Did sequence analysis of BCD1_BC, BCD2_BC, B0034_BC, B0034m1_BC, B0034m2_BC. Sequences were correct; archived and stored new frozen stocks and plasmids

Week of June 30,2013

Added fusion sites to C0071, C0062, C0012, R0010, R0079 using PCR, followed with clean up, Lv0 Reaction, and sequence verification. R0010_FB, R0079_FB, and C0071_CD were successful. C0012_CD and C0062_CD were not. We think the DVL0_CD backbone is contaminated with empty biobrick backbone, causing an inefficient reaction and transformation. Tried to pick more colonies from plate to see if we could find some that contained the desired plasmid.
Struck out B0015_DF from the -20C and -80C frozen stocks to sequence since we think these samples are incorrect
B0015_DH was sequence confirmed but with only one SpeI site. It will function as a MoClo part but should not be used as a template in the future