Week 7: Monday 23rd - Sunday 29th August



51. Experiment: Transformation with pJS555 & pSB1C3 (Theo and Hannah)

Received a new plasmid from Jim Slock, so have transformed some chemically competent cells with it to build up a stock and test it later/we think it will glow for longer than the previous one (says Mr. Lovely)).

Theo transformed TOP10 with pSB1C3 from registry.

52. Experiment: Check for promoter+rbs+p.p.luc - obtain from the colony from transformation on page 37. (Paul)

Colony PCR

Take sample from colony with loop and put in 20μl of water to obtain DNA template.

Then prepare on isoFreeze PCR chiller in lister order:

  • 10μl of 2xPhusion Master Mix
  • 1μl of VR
  • 1μl of VF2
  • 1μl of DNA template
  • 7μl of Nuclease-Free H20

Then PCR:

1. 98°C for 15 mins

2. 98°C for 10 secs

3. 65°C for 30 secs

4. 72°C for 1 min

5. repeat 2-4 35 times

6. 72°C for 10 mins

7. 4°C forever


Tube 1: 197.4ng/μl

Tube 2: 235.3ng/μl

Gel Electrophoresis

  • Tube 1: 194.7ng/μl
    • 4μl of DNA
    • 3μl of 6x Orange Loading Dye
    • 13μl Nuclease Free H20
  • Tube 2: 235.3ng/μl
    • 3μl of DNA
    • 3μl of 6x Orange Loading Dye
    • 14μl of Nuclease Free H20

53. Experiment: Extracting glycerol stocks of TOP10 with promoter+rbs+p.p.luc from registry. (Emily and Peter)

1. Take tube of glycerol stock from -80°C 2. Use loop/tooth pick (we used a loop) to streak on ampicillin resistance plate. Let it melt first, then streak.

NB NEVER let glycerol stocks thaw. They should be out and back in the -80°C freezer in 2-3mins max

3. Place in 30°C incubator overnight.

To be continued tomorrow.

54. Check for promoter+rbs+luc from p32 by luciferin injection. (Paul and Ben)

We used protocol described on p22.

3x Freezymes at -80°C, thawing at 37°C

55. Experiment: Gibson assembly of pBAD luxCDABEG in psB1C3

PCR Construct Forward Primer Tm Reverse Primer Temp Temp to use Template DNA Amplifies
Prefix.Pbad.Start of C 9.prefix.f .pBadstart 53 1.luxCstart.r .pBadend 66.25 56 Pbad pBAD
End of Pbad.C.D.Start of A 2.pBADend.f .luxCstart 51.76 4.luxAstart.r .luxDend 50.81 53 Phk555 CD
End of D.A.BStart of E 3.luxDend.f .luxAstart 54.32 6.luxEstart.r .luxBend 71.56 57 Phk555 AB
End of B.E.G.Suffix 5.luxBend.f .luxEstart 51.63 7.suffix.r ev.luxGend 56 54 Phk555 EG
End of G.Suffix.Plasmid.Prefix.Start of B 8.luxGend.f or.suffix 68.73 10.pBadstart.r .prefix 72 71 Plasmid Backbone (BBa_Jo4450) pSB1C3

Added (on ice!) in 5 individual (A-E) PCR tubes

2x Phusion Master Mix 25µl
Forward Primer 0.25µl
Reverse Primer 0.25µl
Template DNA 2µl
Distilled water 22.5

Programs on PCR machines

start cycle machine 1 machine 2 machine 3 end
98°C 98°C 56°C 53°C 71°C 72°C 72°C 10°C
30s 10s 15s 15s 15s 1.45min 7.5min ad infinitum
Denaturation Annealing Elongation

Results: Machine 1 had a power fail very close to the end of the program Machine 2 had a loose lid; the tubes popped open and there was no liquid left Machine 3 had entirely melted the top of the PCR tube

The experiment was repeated, but this time all reactions (A-E) were run in Machine 2 (see p.38 for program).

Nanodrop Measurements

A pBAD 455.6ng/µl
B CD 339.3ng/µl
C AB 937.4ng/µl
D EG 165.1ng/µl
E pSb1C3 430.8ng/µl
pA pBAD 173.5ng/µl
pC AB 159.7ng/µl
pE 974.6ng/µl

blanked with distilled water

Gel electrophoresis

Gel loading mixtures were made up according to:

A B C D E pA pC pE
6x orange LD (µl) 3 3 3 3 3 3 3 3
plasmid DNA (µl) 2 2 1 5 2 5 5 1
nuclease-free water (µl) 15 15 16 12 15 12 12 16

final volume 20µl

A 1% agarose E-gel was loaded as follows

Easyladder 2 A B C D E pA pC pE
10µl 20 20 20 20 20 20 20 20

Bands were observed at the following lengths:

A B C D E pA pC pE
1-2 3-5 2-3 2 2 1-2 2 1-2

Bands for pA, B, pC, D & pE were cut out the gel and DNA was extracted following the QIAquick Gel Extraction Kit protocol

Preparation of Gibson assembly 1.33x master mix

Taq ligase 40u/µl 50µl
5x isothermal buffer 100µl
T5 exonuclease 1u/µl 2µl
Phusion polymerase 2u/µl 6.25µl
Nuclease--free water 216.75

Gibson Assembly Reaction added to PCR tube:

15µl Gibson 1.33x master mix
1µl purified pA
1µl purified B
1µl purified pC
1µl purified D
1µl purified pE

Incubated for 1h at 50C Stored at 4C overnight

length nanodrop after gel
pBAD 1210b (A) 22.7ng/µl
CD 2388b (B) 2.7ng/µl
AB 2097b (C) 10.0ng/µl
EG 1863b (D) 20.9ng/µl
pSB1C3 2072b (E) 5.1ng/µl


56. Experiment: Transformation of TOP10, red strain and with Gibson assembly (pBAD, luxCDABEG, pSB1C3) (Will and Anja)

Followed protocol on p13+14. Transformed:

with Gibson reactions
TOP10 1, 2, 3
red (BW25113 Δhns::kan) 1, 2, 3
black (GM230 hns-205::Tn10 TetR) 1, 2, 3

Plated 150µl on LB agar plates with Chl. each (9pl.)

57. Experiment: Repeat gel electrophoresis from p.39+40 (Will and Anja)

Followed protocol on p.39+40 (pcr products had been kept in -20°C overnight).

Results: A, C, D, pA & pC were of appropriate size. B (again 3-5kb) and E, pE (slightly lower than expected, closer to D than C) were of inappropriate size.

It was decided to run new PCR reactions for B (CD) and E (pSB1C3) following the protocol on p.38.

Nanodrop measurements: (blanked with Di H20)

B (CD) 980.7ng/µl

E (pSB1C3) 127.5ng/µl

Gel Electrophoresis:

Gel loading mixtures made up as follows:

6x Orange LD (µl) 3 3
plasmid DNA (µl) 7 1
nuclease free H20 (µl) 10 16

A 1% Agarose (E-gel) was loaded as follows:

Easyladder 2 E B all other wells filled H20
10µl 20µl 20µl

58. Experiment: Making liquid culture of tetR repressed promoter, rbs + luc in TOP10 (from registry) (Peter and Emily)

Make LB broth with campicillin, adding 200µl ampicillin to 200ml LB to make 100µg/ml concentration final solution.

Plates prepared from glycerol stocks had grown well, but were transferred from 30°C to 37°C incubator for better growth - the temperature effect on luciferase won't matter. The coonies were very small. A single colony was chosen using a loop, placed in 3ml of LB&Amp and shaken. 3 tubes were used and placed in the 30°C incubator overnight.

59. Experiment: Gel Extraction (Anja)

Results from Gel electrophoresis on p.42.

E showed a band slightly above 2kb.

B again showed a band between 3-5kb.

Bands for A & pA, B, pC, D, pE were cut out from 'repeated' gel on p.41 and 'Enew' as well as a trace of seemingly correctly sized B ('B trace') were cut out from gel on p.42. DNA was extracted following the 'QIAquick Gel Extraction Kit (miniElute columns)' protocol.

The purified DNA was stored at 4°C overnight.


Nanodrop measurements:

A 38.8ng/µl
B 24.7ng/µl
B trace 32.5ng/µl
C 13.2ng/µl
D 24.0ng/µl
E 14.5ng/µl
E new 13.3ng/µl

60. Experiment: PCR of B trace with primers for amplification of B & gel electrophoresis (Will and Anja)

Followed protocol on p.38.

Nanodrop measurements: B trace PCR 492.2ng/µl

Gel Electrophoresis

Gel loading mix:

6x orange LD 3µl
plasmid DNA 2µl (B Trace PCR)
DI H20 15µl (nuclease-free)

Gel loading as follows:

Easyladder 2 3 trace PCR all other wells filled with
10µl 20µl 20µl H20

61. Experiment: Diagnostic gel of Gibson assembly reaction (Bill and Anja)

Gel electrophoresis

Gel loading mixtures:

pA B pC D pE G1 G2 G3
6x orange LD (µl) 3 3 3 3 3 3 3 3
5 2 5 5 1 12 12 12
12 15 12 12 16 5 5 5

Loaded gel:

Easyladder 2 pA B pC D pE G1 G2 G3
10µl 20 20 20 20 20 20 20 20

Result: In neither G1, G2 or G3 did any high molecular weight bands occur other than those for pA, B, pC, D and pE individually => Gibson assembly reaction did not work.

62. Experiment: Test Gibson Master Mix for functionality (Bill and Anja)

Gibson assembly reaction

Added to a PCR tube:

15µl Gibson 1.33x Master Mix
2.5µl pC (AB)
2.5µl D (EG)

Incubated for 1h at 50°C

Gel electrophoresis

pC D G1 G2
6x orange LD (µl) 3 3 3 3
plasmid DNA (µl) 5 5 17 17
nuclease-free H20 12 12 - -

(All other wells were filled with DI H20)

Gel loaded as follows:

Easyladder 2 pC D G1 G2
10µl 20µl 20µl 20µl 20µl
Results: ~3kb 2-3kb 1 over 5kb, 1 over 5kb,
1 around 5kb 1 around 3-5kb
After 10 more mins: ~2.3kb ~1.9kb 5kb, 2.5kb, 2.1kb 5kb, 2.5kb, 2.1kb

=> Gibson Master Mix is functional


63. Experiment: Gibson assembly of pBAD, luxCD AB EG and pSB1C3 as well as all individual 'neighbour parts' in pairs (Will and Anja)

Gibson Master Mix A (pBAD) B (CD) C (AB) D (EG) E (pSB1C3)
G1 (µl) 15 1 1 1 1 1
G2 (µl) 15 2.5 2.5
G3 (µl) 15 2.5 2.5
G4 (µl) 15 2.5 2.5
G5 (µl) 15 2.5 2.5
G6 (µl) 15 2.5 2.5
j1 (µl) 15 1 1 1 1 1
j2 (µl) 15 2.5 2.5
j3 (µl) 15 2.5 2.5
j4 (µl) 15 2.5 2.5
j5 (µl) 15 2.5 2.5
j6 (µl) 15 2.5 2.5

G1-G6: A->E (new) refer to gel extracted PCR fragments

j1-j6: A->E (pA, B, pC, D & pE) refer to PCR reactions (that have not been run on a gel and gel extracted)

Gibson assembly reactions were made up in PCR tubes according to the table above. The reaction mixtures were spun down (mixed by flicking tube), and incubated at 50°C.

Gel Electrophoresis

2 separate gels were run:

1. Gel loading mixtures:

pA B pC E j1 j2 j3 j4 j5 j6
6x Orange LD (µl) 3 3 3 3 3 3 3 3 3 3
Plasmid DNA (µl) 5 5 5 5 5 5 5 5 5 5
Nuclease-free H20 (µl) 12 12 12 12 12 12 12 12 12 12

Gel was loaded as follows:

Easyladder II pA B pC E j1 j2 j3 j4 j5 j6
10µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl

2. Gel loading mixtures:

A B C Enew G1 G2 G3 G4 G5 G6
6x Orange LD (µl) 3 3 3 3 3 3 3 3 3 3
Plasmid DNA (µl) 1 1 1 1 5 5 5 5 5 5
Nuclease-free H20 (µl) 16 16 16 16 12 12 12 12 12 12

Gel was loaded as follows:

Easyladder II A B C E G1 G2 G3 G4 G5 G6
10µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl 20µl

Transformation of TOP10 with 1)G1 and 2)j1

Followed protocol on p13+14, however, we transformed with 10µl Gibson reaction instead of 2µl. Plated 150µl on LB agar plates with Chl. Incubated at 30°C overnight.

Result: All 4 plates blank after overnight :( All 4 growth after 2 days, RFP present, no glow.


Results: No colonies observed from above transformation.

64. Expt: Transfer of promoter+rbs+P.P.Luc into pSB1C3 for submission to registry (Emily + Anja)

Followed protocol on p31 (nanodrop:[plasmid]=26.5ng/µl)

Restriction enzyme digest

Prepated at RT in the following order:

nuclease-free H20 1µl
10x Fast Digest Buffer 2µl
Plasmid DNA 15µl
FD Enzyme EcoRI 1µl
FD Enzyme PstI 1µl

The digest was prepared twice. It was checked that 15µl of plasmid DNA would not contain more than 1µg of DNA. The reaction was mixed gently, spun down and incubated at 37°C for 4h45min (in PCR machine).


Nanodrop measurements: Digest 1 -> 18.3ng/µl Digest 2 -> 22.8ng/µl

pSB1C3 supplied at 25ng/µl. 10-100ng of linearised vector DNA should be added to ligation mix. 3µl give 75ng. 3:1 molar excess of insert DNA should be added.

75ng/2035b x 1727b x 3 = 190ng => 9µl

To a PCR tube add:

promoter + rbs + luc digest 2 9µl
pSB1C3 3µl
5x rapid ligation buffer 4µl
T4 DNA ligase 1µl
nuclease-free H20 3µl

The ligation was prepared twice. Mix was vortexed, spun down and incubated at 22°C for 1h45min (in PCR machine).


Followed protocol on p13+14. Transformed 2x50µl TOP10cc with ligation 1 and ligation 2 (10µl of ligation rather than 2µl). Plated on LB agar plates with Chloramphenicol (plated 150µl).

Results: No colonies from TOP10 transformation with ligation. Plate 1 of TOP10 cells transformed with ligation 1: 2 colonies. Plate 2: 5 colonies.

65. Expt: Gibson assembly of pBAD, luxCDABEG (amplified in one fragment) and pSB1C3 (Will and Anja)

Template Forward Primer Reverse Primer Fragment Amplified
I0500 prefix.f.pBadstart luxCstart.r.pBadend pBAD
pJS555 pBADend.f.luxCstart suffix.rev.luxGend luxCDABEG
BBa_J04450 luxGend.for.suffix pBadstart.r.prefix pSB1C3

(BBa_J04450 had one TOP10 colony in DI H20)

PCR mix made up as on p38.

Program of PCR machine:

For pBAD and luxCDABEG:

98°C 30s
Start cycle (30x) 98°C 10s
55°C 15s
End cycle 72°C 3min
72°C 7.5min
10°C forever

For pSB1C3:

98°C 30s
Start cycle (30x) 98°C 10s
71°C 15s
End cycle 72°C 1.45min
72°C 7.5min
10°C forever

Gel Electrophoresis

1% (self-cast) Agarose gel loaded as follows:

Easyladder II pBAD luxCDABEG 1 luxCDABEG 2 pSB1C3
20µl 25µl 25µl 25µl 25µl

+ 5µl 6x orange LD (mixed before adding to gel) to everything except the ladder.

run at 120V

Results: Only for pBAD did we observe a band (this was of correct size).

=> PCR of luxCDABEG from pJS555 failed

=> PCR of pSB1C3 from BBa_J04450 transformed colony failed.

Following the 'MinElute Gel Extraction' protocol pBAD was isolated (using MinElute columns) and stored at 4°C.

66. Expt: PCR of pJS555 colony PCR of cells containing pSB1C3 (&RFP biobrick), PCR of pBAD (Will & Hannah)


1. pJS555 was diluted 10x in nuclease free water (taken from vial sent by James Slock), and PCRed in 3 fragments: CD, AB, EG using primers ordered on 17.08.10.

2. A colony grown up with a pSB1C3 plasmid (with RFP biobrick) was suspended in 20µl DI autoclaved water. 2µl of this was added to standard PCR mix as "template".

3. Purified I0500 (from Shuna)

Mixture was:

2x Phusion Master Mix 27.5µl
Forward Primer 0.25µl
Reverse Primer 0.25µl
Template DNA 2µl
DI (autoclaved) H20 25µl

Naming system is as on pp38-41.

A, C, b, d in machine (2)

e in machine (3)

In addition, another b was run in machine (3) in an attempt to get rid of the problematic secondary structure in the template DNA (hypothesised). This tube was labelled B72.

After PCR tubes were run on Agarose on a single gel

Gel Preparation

  • 150ml TAE + 1.5g Agarose + 10µl SYBERSAFE were prepared
  • 8 Tooth comb was used
  • each well could house 30µl liquid

Machine (2) did not have top screwed on properly so tube containing D was lost. For the purposes of this assembly a aprevious PCR product of D was used, though there was only 10µl of this product left, so a reduced amount was used.

  • To D: 10µl PCR product + 2µl gel loading buffer was put in a well.
  • To A,B,C,E,B27: 35µl PCR product + 7µl Gel loading buffer, 30µl of which was loaded into a well.
  • 10µl EZ ladder II was loaded.

The layour was: EZ ladder II, A, B, C, D, E, B72

After running for an hour, no banding was produced by E and B72.

But good bands of A, B, C, D were produced, including the CORRECT SIZED B BAND! :) :)

These 4 bands were extracted and purified according to Qiagen "Qiagen gel extraction kit", final ste 10µl of EB was added, although a normal column was used.

Tube Amount of band extracted (mg) Nanodrop after purification (ng/µl)
A 94 13.4
B 124 11.0
C 89 7.9
D 53 12.2

67. Expt: Gibson assembly of above fragments (Will)

A previously gel extracted E was used to replate the failed band (p41 original E).

2µl A, B, C, D, E

+30µl 1.33x Gibson master mix was added.

Incubated at 50°C for 60m.

68. Expt: Transformation of TOP10 with Gibson product above (Will)

Followed protocol on pp13-14.

  • 10µl mixture was added to 50µl cells
  • ice 30mins
  • heat shock 80s 42°C
  • rotating 37°C
  • plate 100µl onto 3 chloramphenicol plates, incubate 30°C overnight.