Team:Stanford/Notebook/Lab Work/Week 6

From 2010.igem.org

(Difference between revisions)
(Laura's Notebook)
(Laura's Notebook)
Line 77: Line 77:
'''Suggestions from Christina:'''
'''Suggestions from Christina:'''
-
#diagnostic gels from yesterday's digestions (done by Francisco)
+
*diagnostic gels from yesterday's digestions (done by Francisco)
-
*run promoters (pBAD, pLUX) on 0.8%, RSID's (1 and 2) and sRNA's (1, 2, 1C, 2C) on 2%
+
run promoters (pBAD, pLUX) on 0.8%, RSID's (1 and 2) and sRNA's (1, 2, 1C, 2C) on 2%
-
*gel extract everything (on separate gels), depending on how complete digestions look- if PCR cleanup, SIP treat
+
gel extract everything (on separate gels), depending on how complete digestions look- if PCR cleanup, SIP treat
-
#PCR cleanup inserts (PCR assembled parts)
+
*PCR cleanup inserts (PCR assembled parts)
-
*use MiniElute columns
+
use MiniElute columns
-
*use 10 mM Tris instead of H2O (water here is acidic, and elution is pH-dependant)
+
use 10 mM Tris instead of H2O (water here is acidic, and elution is pH-dependant)
-
*let sit 1 minute before eluting
+
let sit 1 minute before eluting
-
*load 1 uL on diagnostic gel
+
load 1 uL on diagnostic gel
-
#check enzymes to see if getting low: order more if necessary
+
*check enzymes to see if getting low: order more if necessary
-
#colony PCR
+
*colony PCR
-
*primers: complementary to prefix and suffix or VF and VR? (VF and VR- further from ends to allow subsequent sequencing)
+
primers: complementary to prefix and suffix or VF and VR? (VF and VR- further from ends to allow subsequent sequencing)
**expected lengths with and without insert: ladder choice, gel %, extension time
**expected lengths with and without insert: ladder choice, gel %, extension time
-
*10 uL reactions, run 5 uL on gel
+
10 uL reactions, run 5 uL on gel
-
*setting up reactions:
+
setting up reactions:
**make, aliquot master mix (SuperMix + primers)
**make, aliquot master mix (SuperMix + primers)
**pick colony with innoculating needle: inoculate PCR reaction, then streak on small square or wedge on a plate (make sure plates are dry)
**pick colony with innoculating needle: inoculate PCR reaction, then streak on small square or wedge on a plate (make sure plates are dry)
**screen (PCR) 5 colonies to start, but streak out 10-15 extras just in case/for further screenings  
**screen (PCR) 5 colonies to start, but streak out 10-15 extras just in case/for further screenings  
-
*if no bands on gel, could be: not enough cells, not correct plasmid
+
if no bands on gel, could be: not enough cells, not correct plasmid
-
*if positive results, get sequenced
+
if positive results, get sequenced
== 8/5 Thursday ==
== 8/5 Thursday ==

Revision as of 21:50, 4 August 2010

Contents

8/2 Monday

Greg's Notebook

  • Inoculated freezer stocks of most of our parts with Alex
  • Began planning for promoter characterization project:
    • Going to do 3A ligations of the form: promoter + superfolded GFP + Kan plasmid
    • Process:
      • Digest parts with at least 2 ug DNA
      • PCR cleanup
      • Diagnostic gel (remember to save uncut DNA for control)
      • Ligate in PCR tubes
      • Heat inactivate at 65 C for 20 min
  • Performed first digestion (F2620 + sfGFP + pSB4k5)
Part # Part amount BSA NEB (#, amount) Enzymes (1 uL each) Water
F2620 10.8 3 2, 3 E + S 11.2
pSB4k5 20 3 3, 3 E + P 2
sfGFP 11.76 3 2, 3 X + P 10.24
  • Let digestions run for 1 hour at 37 C
  • Ran diagnostic gel:
    • sfGFP digested nicely, F2620 yielded 3 bands corresponding to insert, cut plasmid, and uncut plamid
    • pSB4k5 gave only one band and a smudge, so I decided to redigest with only .5 uL of each enzyme, leaving it to run overnight


8/3 Tuesday

Greg's Notebook

  • Ran diagnostic gel of overnight pSB4k5 digest
    • Still didn't work; there were 3 bands, the smallest of which was about the size of the plasmid backbone, and there was no band corresponding to the ccdB insert
  • Decided to re-redigest pSB4k5 using .5 uL of each enzyme for only 1 hour
    • After running on a diagnostic gel, discovered that this, too, failed in the same way as the previous digestions had. I decided to try other Kan plasmids
  • PCR'd Chris's transcription factor promoter (pTFc)
  • Ran nanodrop of pTFc and yesterday's sfGFP and F2620:
Part # 230 280 Concentration
pTFc A 1.36 1.79 196.1
pTFc B 2.08 1.86 159.7
sfGFP 1.89 1.87 52.9
F2620 1.82 1.82 35.5


8/4 Wednesday

Greg's Notebook

  • Performed restriction digest of pTFc, J23100, J23106, J23109, F2620, pSB2k3, pBAD*, pSB1k3
    • *There wasn't enough pBAD, so I used all that was left (~20uL). Even if this digest fails I still have the previously-digested stuff at a low-ish concentration

Laura's Notebook

NanoDrop data for Alex's miniprep samples:

260/280 260/230 ng/uL
I13500 1.82 1.31 221.7
J23106 1.85 1.42 187.6
J23109 1.88 1.47 210.5

Suggestions from Christina:

  • diagnostic gels from yesterday's digestions (done by Francisco)

run promoters (pBAD, pLUX) on 0.8%, RSID's (1 and 2) and sRNA's (1, 2, 1C, 2C) on 2% gel extract everything (on separate gels), depending on how complete digestions look- if PCR cleanup, SIP treat

  • PCR cleanup inserts (PCR assembled parts)

use MiniElute columns use 10 mM Tris instead of H2O (water here is acidic, and elution is pH-dependant) let sit 1 minute before eluting load 1 uL on diagnostic gel

  • check enzymes to see if getting low: order more if necessary
  • colony PCR

primers: complementary to prefix and suffix or VF and VR? (VF and VR- further from ends to allow subsequent sequencing)

    • expected lengths with and without insert: ladder choice, gel %, extension time

10 uL reactions, run 5 uL on gel setting up reactions:

    • make, aliquot master mix (SuperMix + primers)
    • pick colony with innoculating needle: inoculate PCR reaction, then streak on small square or wedge on a plate (make sure plates are dry)
    • screen (PCR) 5 colonies to start, but streak out 10-15 extras just in case/for further screenings

if no bands on gel, could be: not enough cells, not correct plasmid if positive results, get sequenced

8/5 Thursday

8/6 Friday