Team:UNIPV-Pavia/Calendar/July/settimana4

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UNIPV TEAM 2011

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June
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July
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JULY: WEEK 4

July, 18th

BBa_R0040 in BBa_J61002 plasmid purification and quantification was carried out:

Plasmid DNA (ng/μl)
BBa_R0040 in BBa_J61002 37.3

Digestions of previously purified plasmids were performed for ligations:

Plasmid Kind DNA (μl) H2O (μl) Enzyme 1 (μl) Enzyme 2 (μl) Buffer H (μl) Final Volume (μl)
E9-2 Insert 11.5 9 1 Xbal 1 Pstl 2.5 25
E10-1 Insert 10 10.5 1 Xbal 1 Pstl 2.5 25
E11-1 Insert 4 16.5 1 Xbal 1 Pstl 2.5 25
E12-1 Insert 10 10.5 1 Xbal 1 PstI 2.5 25
E13-1 Insert 6 14.5 1 EcoRl 1 Pstl 2.5 25
E16-1 Insert 4 16.5 1 EcoRl 1 Pstl 2.5 25
E21-1 Insert 7.5 13 1 EcoRl 1 Pstl 2.5 25
E22-2 Insert 10 10.5 1 EcoRl 1 Pstl 2.5 25
BBa_I13521 Insert 12.5 8 1 EcoRl 1 Pstl 2.5 25
BBa_R0040 in BBa_J61002 Vector 20.5 0 1 EcoRl 1 Pstl 2.5 25

Reactions were incubated at 37°C for three hours; meanwhile two medium-size agarose gels were prepared according to protocols.
According to protocols, 120 μl of 1kb Plus DNA ladder were prepared.

In the afternoon gel electrophoresis was performed.

Medium size gel
Medium size gel

As shown in figure, all clones were positive (apart from E13-1 run where it is possible to recognize only a band at approximately 2800 bp, corresponding to the linearized plasmid), so we cut and purified the bands of interest.

After gel extraction, digested DNA was quantified:

Part DNA (ng/μl)
E9-2 (X-P) 5.9
E10-1 (X-P) 4.2
E11-1 (X-P) 5.2
E12-1 (X-P) 5.2
E16-1 (E-P) 6.4
E21-1 (E-P) 5.8
E22-2 (E-P) 6.5
E23-1 (E-P) 4.6
BBa_I13521 6.1
BBa_R0040 in BBa_J61002 (E-P) 2.1

Then ligations were performed in a final volume of 10 μl:

Ligation Name Vector Vector volume (μl) Insert Insert volume (μl) Buffer (μl) T4 Ligase (μl)
E24 BBa_R0040 (S-P) 1.5 E9-2 (X-P) 6.5 1 1
E25 BBa_R0040 (S-P) 1.5 E10-1 (X-P) 6.5 1 1
E26 BBa_R0040 (S-P) 1.5 E11-1 (X-P) 6.5 1 1
E27 <partinfo>BBa_R0040</partinfo> (S-P) 1.5 E12-1 (X-P) 6.5 1 1
E31 BBa_R0040 (E-P) 2.5 E16-1 (E-P) 5.5 1 1
E32 pSB4C5 (E-P) 2 E21-1 (E-P) 6 1 1
E33 pSB4C5 (E-P) 2 E22-2 (E-P) 6 1 1
E34 pSB4C5 (E-P) 6.5 E23-1 (E-P) 1.5 1 1
E35 pSB4C5 (E-P) 2 BBa_I13521 (E-P) 6.5 1 1
E36 pSB4C5 (E-P) 1 BBa_R0040 in BBa_J61002 (E-P) 7 1 1

Ligations were incubated ON at 16°C.
Inoculum of E. coli MGZ1 in 10 ml of LB for competentization.

July, 19th

According to protocols 200 ml of Buffer 1 and 100 ml of Buffer 2 were prepared for MGZ1 strain competentization.
E13-1 was newly digested.

Plasmid Kind DNA (μl) H2O (μl) Enzyme 1 (μl) Enzyme 2 (μl) Buffer H (μl) Final Volume (μl)
E13 Insert 6 14.5 1 EcoRI 1 Pstl 2.5 25

After gel electrophoresis, E13-1 insert was succesfully identified.

Small size gel

E13-1 digested DNA was gel-extracted and quantified:

Part DNA (ng/μl)
E13-1 (E-P) 4.3

E28 ligation was performed in a final volume of 10 μl:

Ligation Name Vector Vector volume (μl) Insert Insert volume (μl) Buffer (μl) T4 Ligase (μl)
E28 pSB4C5 (E-P) 2 E13 (X-P) 6 1 1

Ligation was incubated ON at 16°C.

250 ml of M9 were prepared, according to protocols.

July, 20th

E24, E25, E26 and E27 were transformed in 100 μl of TOP10 competent cells according to protocols. Moreover E28, E31, E32, E33, E34, E35, E36 and BBa_B0032 (transformation efficiency positive control) were transformed in 100 μl of MGZ1 competent cells according to protocols. Plates were incubated ON at 37°C.

In the afternoon 500 ml of LB with chloramphenicol 12.5 were prepared.

July, 21th

All plates showed a lot of colonies, except for E28 and E31 (2 colonies).

A 26x mix was prepared in order to perform PCR on E24-1, E24-2, E25-1, E25-2, E26-1, E26-2, E27-1, E27-2, E28-1, E28-2, E31-1, E31-2, E32-1, E32-2, E33-1, E33-2, E34-1, E34-2, E35-1, E35-2, E36-1, E36-2:

H2O (μl) Buffer 10x (μl) MgCl2 (μl) VF2 (BBa_G00100) μl VR (BBa_G00101) μl dNTPs (μl) Taq polymerase (μl)
468 65 26 13 13 13 26

25 μl were aliquoted in each tube, together with 1 μl of each liquid culture. PCR cycles parameters were set as follows:

  • 94°C 30 seconds (denaturing)
  • 60°C 1 minute (annealing)
  • 72°C 2 minutes (elongation)
35 cycles were performed.

dubbio: diciamo dei sequenziamenti?!!

After the PCR, two medium size agarose gels were prepared in order to carry out DNA samples:


inserire immagini


All the band lengths were correct, except E31-1; 750 μl of E24-2, E25-1, E26-2, E27-2, E28-1, E31-1, E32-2, E33-2, E34-1 and E35-2 liquid cultures were used to prepare glycerol stocks.

July, 22th

E36 was transformed in 100 μl of TOP10 competent cells according to protocols. Plates were incubated ON at 37°C. E24-2, E25-1, E26-2, E27-2, E28-1, E31-1, E32-2, E33-2 and E34-1 plasmid purification was carried out, in order to prepare samples for sequencing.

Plasmid DNA (ng/μl)
E24-2 76.8
E25-1 75.1
E26-2 69.4
E27-2 81.4
E28-1 18.1
E31-1 19.4
E32-2 21.0
E33-2 23.4
E34-1 25.8

parte sequenziamenti