Team:Toronto/Notebook-w04-thu
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Week 4: June 9 2016
Thursday, 6/9
Members Present: Karim, Hamed, Alex, Cathy, Tam, Kat, Andrea, Bohdan, Celine
LAB:
Morning:
- Tried to autoclave SOC.
- Washed glassware and stored in lab. Put away communal glassware in 317.
- Threw out a lot of expired/useless reagents & samples from Yuki (-20)-
Afternoon:
- Autoclaved SOC, aliquoted 30 x 1mL. Now on the shelf.
- Obtained DH10B from Kevin, streaked out a plate (now in the broken shaker). Made 5ml and 100ml overnight cultures.
- Looked into recalibrating our UV spec.
Administrative:
- RIP Polaris, our -80C fridge (also all of our samples from 2014 & 2015). Susie has promised to try and find us sapce for one freezer box.
- Susie will try and find us an ethanol burner, but suggested that we should consider buying our own.
- CSM budget confirmed and approved
TO DO:
For the next day:
LAB TEAM:
Check on overnight cultures
Suggest splitting into two teams: Team A - TSS buffer. Team B - Grow cells to proper OD.
Obtain a space in a -80 to store the competent cells. Test on Monday
LAB MANAGERS:
Figure out how to get a label maker
Sign the MedStore General Purchasing Delegation of Signing Authority Form & Run it by Susie
Set up an IDT account at: http://go.idtdna.com/iGEM2016.html
Organize the drawers
Gmail correspondence:
Meetings/Notes:
i-TASSER assessment of the binding pocket size:
Au in generally atomic radius fluctuates around 1.78 A which means that the binding pocket size should fit Au ions significantly.
The modified sites for A113T and P118A show a smaller pocket size compared to the wt GolS significantly in terms of volume and dimension wise (4.6 A and 4.8 A < 5.8 A).
Based on the research article about modification of GolS to enhance binding affinity for Au ions, these 2 mutants shows higher binding affinity to both Au(III) and Au(I). There is a trend in terms of binding affinity that is: as the pocket size becomes smaller, however larger than the estimated atomic radius of the metal ion (Au(I): 1.58 A, Au(III) 0.75 A), the binding affinity for Au(I) and Au(III) enhances.
Applying this same principle, the GolS A113T and P118A has a larger volume and dimensions than the wt GolS. Based on the trend, it is clear that the double mutant GolS may not show similar specificity to Au ions like GolS A113T and GolS P118A
In the meantime, the pocket size for CupR is unfeasible to do calculations for pocket size.
Meeting with Naveen:
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Turns out that there aren't two sets of primers (ie. bridging oligos and primers)
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Kevin has sent UNS primer sequences to Naveen, who will forward them to us
References:
