Team:BYU Provo/Notebook/Metabolism/mayjune

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<h1 >BYU 2014 Notebook </h1>
<p style="color:#FFFFFF"> <a href="https://2014.igem.org/wiki/index.php?title=Team:BYU_Provo/Notebook/Metabolism/mayjune&action=edit"style="color:#FFFFFF"> Edit May June</a> </p>
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==Week of May 10th==

===May 6, 2014===

Nano-dropped the Promoter plasmids that were recently purified. Almost all of the plasmids were over 100ng/ul concentration. 

===May 8, 2014===
Set up PCR to amplify Bla gene. Used Q5 polymerase and Q5 protocol. 
*Q5 PCR
*24.5 ul ddH20
*10 ul Q5 Buffer
*10 ul Q5 Enhancer
*1 ul Bla forward primer BI374
*1 ul Bla reverse primer BI375
*1ul dNTP’s
*1ul Template psB1A3 (resuspended with 10ul ddH20 from iGEM 2013 kit plate 5, well 1G)
*0.5ul Q5

===May 9, 2014===

Ran a gel to check PCR products. Looks great! 
Did PCR-up of PCR product using Gen-Elute Kit:
#	Add 0.5mL column prep solution to column, spin at 12000 RPM 1 min. Discard eluate after 1 min. 
#	Transfer PCR reaction mix into the tube
#	 Add (5x’s volume) of binding solution to 1 volutm of PCR reaction and mix, 250ul
#	Add to column, centrifuge at max speed for 1 min
#	After 1 min discared eluate, but retain collection tube
#	Add 0.5 ml of diluted Wash Solution to the column, centrifuge at max speed for 1 minute
#	After 1 minute, discard the eluate, replace the column back in the collection tube. Centrifuge an additional 2 minutes to dry. 
#	Place the column in a clean tube. Add 50ul elution buffer, wait 1 min. Spin max speed 1 min. Remove column, voila!

Ran restriction digests on vectors and insert. Chose the IGEM plasmids containing a strong, and medium-strong promoter strength respectively)

===May 10, 2014===
RD Protocol (repeated for each of the three samples)
*14ul ddH20
*5ul NEB Buffer 4
*0.5 ul 100x BSA
*30 ul DNA sample---(1 each of BBa_J23102, BBa_J23118, and PCR amplified Bla gene)
*1.5 ul each of SpeI HF, and XbaI 

Incubated at 37C for 1.5hrs.

==Week of May 24th==
===May 20, 2014====
Set up colony PCR. Chose 8 colonies from the transformation and streaked colonies onto another plate. Colonies 1-7 were white colonies. We chose colony 8 as a red colony to act as a negative control. Made a master mix (10x) the Taq PCR Protocol
Taq PCR 
*19 ul ddH20
*2.5 ul Std. Reaction buffer
*0.5 ul 10 mM dNTPs
*0.5 ul each promer
*0.5 ul Taq DNA polymerase
*2 ul of boiled colony sample per tube. 
===May 21, 2014===
Ran a gel to verify PCR. Colonies 1, and 4-7 look good. Set up overnights.
===May 22, 2014===
Did plasmid preps on overnights from colonies 4-7. 
Nanodropped:

 206.1 ng/ul 260/280: 1.89
 215.4 ng/ul 260/280: 1.89
 400.2 ng/ul 260/280:1.85
 170.0 ng/ul 260/280: 1.84
Set up restriction digests on New Plasmid (pIG91+BlaGenepIG102), and promoter plasmids to build final construct with promoter and the bla gene together. 
RD 5-221M (pIG102 cut with EcoR1 and Xba)
*14ul ddH20
*5ul 10x NEB buffer cutsmart
*.5 ul BSA
*30 ul pIG 102
*1.5ul EcoR1 HF
*1.5 ul Xba
Incubate at 37 for 1.5 hrs
RD 5-222M, and RD 5-223M
Same protocol as above except:
Enzymes used are EcoR1 HF and Spe1 HF
Buffer 4 Used
Two reactions, one containing promoter plasmid J23104 (5-222M), and the other J23111 (5-223M)
 Ran Low Melt Gel at 90V for 46 min. 
Each of the Plasmids showed up, which was good for pIG102, where we want that to be our vector. Other RD only saw the plasmids and not the promoter part which we are trying to insert into pIG102….

==Week of May 17th==

===May 13, 2014===
Figured out that we didn’t want to use the promoter vectors that I digested. We tried using pIG91 from the freezer, but the RD gel did not show any DNA present.
Also did plasmid mini-preps according to the Sigma-Aldrich kit, for new pIG91. 

===May 15, 2014===
Assisted in setting up new RD of pIG91. 
Assisted Nano-dropping the recently purified pIG91 plasmisds, all concentrations were approximately 100ng/ul.
Assisted in setting up ligation of digested pIG91 (treated with CIP), with the digested Bla. Both were digested using SpeI HF and XbaI. This is so that we can then have our part in the iGEM registry plasmid to allow for quick and easy future cloning.