Friday, May 29, 2015

SOE PCR new prtocol 26_5_2015

5/26/2015
1-
1  μL      3` R primares
1  μL      3` F primares
2 μL        PCR(ClpB) from 4/10/2015
12.5 μL   supermix.
μL dd water.

Protocol:
 95 °C    3 minutes

95 °C   30 seconds
72 °C  2 minutes                    35 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.

2-
1  μL      5` R primares
1  μL      5` F primares
2 μL        PCR(ClpB) from 4/10/2015
12.5 μL   supermix.
μL dd water.

Protocol:
 95 °C    3 minutes

95 °C   30 seconds
72 °C  2 minutes                    35 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.




2-ClpB 5 prim(500bp)
empty
1-ClpB3 prim(500bp)

PCR for plasmidminipreb

5/20/2015
Plasmids from Plasmid minipreb for ClpX, ClpB and ChiT

Negative control: pJH1 with ClpB primares.
1% agrose run for 2 h.

ChiT4     (band)
ChiT3     (band)
ChiT2
ChiT1
ClpB4
B3
B2
ladder
empty
B1        (band)
pJH1
ClpX4
X3
X2
X1
ladder

Friday, May 22, 2015

Direct PCR for the insert clones

5/6/2015
Clones were grown on LB+ Hygromycin 250 mg/ml, direct sample was taken from the colony.

  • Clones: ClpX1, X2, X3, X4, X5, X6, X7,X8 ,X9 ,X10 and X11  
  • ClpX primar with pJH1 clone as a control.
  • ClpX PCR as a positive control.

  • ClpB1, B2,B3, B4, B5, B6, B7and B8 .
  • ClpB primar with pJH1 clone as a control.
  • ClpB PCR as a positive control.

  • ChiT1,T2,T3 and T4 
  •  ChiT primar with pJH1 clone as a control,ChiT primar with B/r E. coli clone as a control. 
  • ChiT PCR as a positive control.



1  μL      3` R primares
1  μL      5` F primares
12.5 μL   supermix.
10 μL dd water.

Protocol:
 95 °C    3 minutes

95 °C   30 seconds
55 °C  2 minutes                    30 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.




ChiT B/r
ChiT,pJH1
ChiT PCR 
ChiT3

ChiT2
ChiT1



ClpB,pJH1
ClpB,PCR
ClpB3
ClpB2
ClpB1
ClpX,pJH1
ClpX,PCR
ClpX3
ClpX2
ClpX1

ladder

Monday, April 20, 2015

SOE PCR for clpX, ClpB and ChiT

4/10/2015

1-
1.5  μL ClpX 3`           sample 1,     2/2/2015
1.5  μL ClpX 5`           sample 2,     2/11.2015  
1.5  μL ClpX 3` R primares
1.5  ClpX 5` F primares
20 micro supermix.
2-
1.5  μL ClpB 3`           sample 1,     2/8/2015
1.5  μL ClpB 5`           sample 3,     2/11.2015  
1.5  μL ClpB 3` R primares
1.5  ClpB 5` F primares
20 micro supermix.

3-
1.5  μL ChiT 3`           sample ,     3/3/2015
1.5  μL ChiT 5`           sample 4,     2/11.2015  
1.5  μL ChiT 3` R primares
1.5  ChiT 5` F primares
20 micro supermix.

Protocol:
 95 °C    3 minutes

95 °C   30 seconds
55 °C  2 minutes                    30 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.



Friday, April 17, 2015

Transformation using chemically competent cells for ClpX,ClpB and ChiT + pJH1

4/1/2015
ClpX,ClpB and ChiT + pJH1

One Shot® Mach1™-T1R Chemically Competent E. coli
Transforming Competent Cells Perform the following before starting the transformation procedure:
 • Equilibrate a water bath to 42°C. 
• Warm the vial of S.O.C. Medium (supplied with the kit) to room temperature. 
• Spread X-Gal onto LB agar plates containing antibiotic, if desired. 
• Warm the selective plates in a 37°C incubator for 30 minutes (use one plate for each transformation). 
If you are including the pUC19 control, make sure that you have one LB agar plate containing 100 µg/ml ampicillin.

 Note: For optimal growth of Mach1™-T1R E. coli cells, it is essential that selective plates are prewarmed to 37°C prior to spreading. Transformation Procedure We recommend including the pUC19 control plasmid DNA supplied with the kit in your transformation experiment to verify the efficiency of the competent cells.

1. Thaw, on ice, one vial of One Shot® Mach1™-T1R Chemically Competent E. coli for each transformation. 
2. Add 1 to 5 µl of the DNA (10 pg to 100 ng) into a vial of One Shot® cells and mix gently. Do not mix by pipetting up and down. If you are transforming the pUC19 control, add 1 µl (10 pg) into a separate vial of One Shot® cells and mix gently.
 3. Incubate the vial(s) on ice for 30 minutes.
 4. Heat-shock the cells for 30 seconds at 42°C without shaking. 
5. Remove the vial(s) from the 42°C bath and place them on ice for 2 minutes.
 6. Add 250 µl of room temperature S.O.C. Medium to each vial. 
7. Cap the vial(s) tightly and shake horizontally at 37°C for 1 hour at 225 rpm in a shaking incubator.
 8. Spread 25-100 µl of the transformation mix on a prewarmed selective plate. Store the remaining transformation mix at +4°C. Additional cells may be plated out the next day, if desired. 
9. Invert the plate(s) and incubate at 37°C. If you are using ampicillin selection, visible colonies should appear within 8 hours, and blue/white screening can be performed after 12 hours. If you are selecting transformants with an antibiotic other than ampicillin, incubate plates overnight.
 10. Select overnight-grown colonies and analyze by plasmid isolation, PCR, or sequencing.
 For plasmid isolation, inoculate a single, overnight-grown colony in 2 ml of prewarmed selective media .
 For optimal results, we recommend inoculating as much of the single colony as possible. Shake at 37°C for 4 hours before isolating the plasmid. 

Result
1-ClpX  + pJH1 ,on LB+ Hygromycine (+)
2-ClpB  + pJH1 , on LB+ Hygromycine(+)
3- ChiT + pJH1, on LB+ Hygromycine (+)
4- PUC 19 on LB+ Ampenicillin, (+)  positive control.
5- DH5 alfa on LB+ Ampenicillin (-) negative control.
6-PUC 19 and DH5 alfa on LB+ Hygromycine (-)





Ligation SOE PCR with pJH1

3/30/2015
ClpX, ClpB (insert)
pJH1 ,Δ dephosphatase and Δ SmaI (vector)
ClpX Insert 3 μL : pJH1 1 μL + 6 dH2O = total 10  μL 
ClpB Insert 3 μL : pJH1 1 μL+ 6 dH2O = total 10  μL  , brief centerfugation 

Ligation using .neb.com/protocols

Quick Ligation Protocol (M2200)

Buffers


Quick Ligation Reaction Buffer

Protocol

  1. Combine 50 ng of vector with a 3-fold molar excess of insert. Use NEBioCalculator to calculate molar ratios. Adjust volume to 10 μl with dH2O.
  2. Add 10 μl of 2X Quick Ligation Buffer and mix.
  3. Add 1μl of Quick T4 DNA Ligase and mix thoroughly.
  4. Centrifuge briefly and incubate at room temperature (25°C) for 5 minutes.
  5. Chill on ice, then transform or store at -20°C.
  6. Do not heat inactivate. Heat inactivation dramatically reduces transformation efficiency.

Wednesday, April 8, 2015

End repair for SOE (Clpx,ClpB and Chit) PCR.

3/6/2015
ClpX
  • DNA                        12 μL 
  • End repair enzyme (0.5μL  )  from life tech.
  • Buffer                      ( 2 μL )
  • dH2O                      ( 5 μL )

ClpB
  • DNA                        20 μL 
  • End repair enzyme (0.5μL  )
  • Buffer                      ( 2 μL )

Chit
  • DNA                        20 μL 
  • End repair enzyme (0.5μL  )
  • Buffer                      ( 2 μL)
Incubate 37 °C    for 15 minutes, inactivation 75  °C   for 10 minutes.

Enzyme digest and treatment pJH1 with SmaI, and Antarctic Phosphatase

3/13/2015

1-In a 1.5mL tube combine the following:

  • DNA     15 μL (1-5 mg) 
  • Restriction Enzyme(1μL SmaI )
  • Buffer_cutsmart_( 2 μL )
  • dH2O ( 2 μL )
              20 μL total.Incubate 25 °C    for 2 hours, inactivation 65  °C   for 20 minutes.
2-Antarctic Phosphatase catalyzes the removal of 5´ phosphate from DNA.
  • DNA     15 μL (from #1 above Δ SmaI
  • Antarctic Phosphatase(1μL SmaI )
  • Buffer ( 2 μL )
  • dH2O ( 2 μL )
              20 μL total.Incubate 37 °C    for 15 minutes, inactivation 70  °C   for 5 minutes.


Tuesday, April 7, 2015

Plasmid miniprep. pJH1

3/2/2015
E.coli with pJH1 grew on LB+ Hygromycine 250 mg/ml, after 24h incubation at 37 C a single colony was inculated into 150 ml LB broth + Hygromycine 250 mg/ml.

FosmidMAX™ DNA Purification Kit Cat. No. FMAX046 used Protocol






1% agarose







pJH1
                                                     

Friday, March 6, 2015

PCR for LVS chiT3 .

3/3/2015
Protocol 

95 c                    3 minutes

95 c                    30 second
41 c                     1.5 minutes                                35 cycle

68 c                    1.5 minute
Final elongation 5 minutes, total volume 25 microliter.
Samples:
1-chiT3

1.5 mico primares x 2
1.5
micro g DNA
20 micro supermix.
Run on 1% gel for 3 hours.



SOE PCR for clpB

clpB3 R primer 1.5 μL
clpB5 F primer 1.5 μL
supermix 21 μL


Protocol:
 95 °C    3 minutes

95 °C   30 seconds
55 °C  2 minutes                    30 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.

1% agarose run for 4 hours.

Wednesday, February 25, 2015

SOE PCR for clpX

2/23/2015

3 PCR 1.5 μL (PCR product from clpX 3)
5 PCR 1.5  μL (PCR product from clpX 5)
clpX3 R primer 1.5 μL
clpX5 F primer 1.5 μL
supermix 21 μL


Protocol:
 95 °C    3 minutes

95 °C   30 seconds
55 °C  2 minutes                    30 cycles
68 °C  1.5 minutes

Final elongation 68 °C  for 5 minutes.

1% agarose run for 4 hours.



Tuesday, February 24, 2015

PCR for LVS chiT3, clpX3,, clpB5 and chiT5

2/11/2015
Protocol 5

95 c                    3 minutes

95 c                    30 second
44 c                     1.5 minutes                                35 cycle

68 c                    1.5 minute
Final elongation 5 minutes, total volume 25 microliter.
Samples:
1-chiT3
2-clpX3
3- clpB5
4
- chiT5
1.5 mico primares x 2
2 micro g DNA
20 micro supermix.
Run on 1% gel for 3 hours.

PCR for LVS clpB3, chiT3, clpX5, clpB5 and chiT5

2/8/2015
Protocol 4

95 c                    3 minutes

95 c                    30 second
46 c                     30 seconds                                  35 cycle

68 c                    1 minute

Final elongation 5 minutes, total volume 25 microliter.
Samples:
1- clpB3
2-chiT3
3-clpX5
4- clpB5
5- chiT5
1.5 mico primares x 2
2 micro g DNA
20 micro supermix.
Run on 1% gel for 3 hours.

PCR for LVS clpX3, clpB5 and chiT5

2/2/2015
Protocol 3

95 c                    7 minutes

95 c                    30 second
49 c                     30 seconds                                  35 cycle
68 c                    1 minute
Final elongation 5 minutes, total volume 25 microliter.
Samples:1- clpX 3
1- clpX 3
2-clpB 5
3-chiT 5
Result:  clpX 3 showed band
Run on 1% gel for 3 hours. 

Thursday, January 8, 2015