User:DavidC/2 October 2009
From 2009.igem.org
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+ | |||
+ | === Friday the 2nd === | ||
+ | |||
+ | ==== Restriction digest ==== | ||
+ | |||
+ | ==== Ligation between BBa_B0030 and BBa_R0010 ==== | ||
+ | |||
+ | Restriction digest of R0010 by SpeI and PstI (2279bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer H (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br>F | ||
+ | Spe1 (TAKARA) = 1µL <br> | ||
+ | Pst1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | Restriction digest of BBa_B0030 by PstI and XbaI (15bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer M (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br> | ||
+ | Pst1 (TAKARA) = 1µL <br> | ||
+ | Xba1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br> | ||
+ | |||
+ | ==== Ligation between BBa_B0014 and BBa_P1003 + BBa_B0014 ==== | ||
+ | |||
+ | Restriction digest of BBa_B0014 by EcoRI and SpeI (95bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer M (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br> | ||
+ | EcoR1 (TAKARA) = 1µL <br> | ||
+ | Spe1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | Restriction digst of BBa_P1003 + BBa_B0014 by EcoRI and XbaI (3770bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer M (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br> | ||
+ | EcoR1 (TAKARA) = 1µL <br> | ||
+ | Xba1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | ==== Ligation between COS and pSB1A2 ==== | ||
+ | |||
+ | Restriction digest of COS by XbaI and SpeI (250bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer M (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br> | ||
+ | Xba1 (TAKARA) = 1µL <br> | ||
+ | Spe1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | Restriction digest of pSB1A2 by SpeI and XbaI (2079bp): <br> | ||
+ | |||
+ | DNA (miniprep) = 30µL <br> | ||
+ | Buffer M (TAKARA) =4µL <br> | ||
+ | H20 = 4µL <br> | ||
+ | Spe1 (TAKARA) = 1µL <br> | ||
+ | Xba1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | ==== Ligation of the D protein (PrtD) with the adenovirus 5 penton base (ADV5pb) ==== | ||
+ | |||
+ | Restriction digest of PrtD by SpeI (385bp): <br> | ||
+ | |||
+ | DNA (PCR) = 5µL <br> | ||
+ | Buffer M (TAKARA) =2µL <br> | ||
+ | H20 = 12µL <br> | ||
+ | Spe1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | Restriction digest of ADV5pb by XbaI (1715bp): <br> | ||
+ | |||
+ | DNA (PCR) = 5µL <br> | ||
+ | Buffer M (TAKARA) =2µL <br> | ||
+ | BSA (TAKARA) = 2µL <br> | ||
+ | H20 = 10µL <br> | ||
+ | Xba1 (TAKARA) = 1µL <br> | ||
+ | 1 hour of incubation at 37°C. <br><br> | ||
+ | |||
+ | ==== DNA electrophoresis ==== | ||
+ | |||
+ | 85 Volt, 15 minutes. <br> | ||
+ | 105 Volt, 40 minutes. <br> | ||
+ | Ladder fermentas 1 Kb. <br> | ||
+ | |||
+ | |||
+ | Samples: BBa_R0010, BBa_B0030, BBaB0014, BBa_P1003, adenovirus penton base with BioBrick prefix and suffix (ADV5pb BBa), D protein with BioBrick prefix and suffix (D prt BBa) | ||
+ | <br> | ||
+ | |||
+ | [[image:F0210.png|center]] | ||
+ | <br> | ||
+ | |||
+ | Interpretation: | ||
+ | |||
+ | We obtain all the fragments but we always have a problem of mistmacth for ADV5 pb primers, and the B0030 fragment is impossible to see into the photo, in fact there is a few DNA, and the fragment is short around 15bp. | ||
+ | |||
+ | ==== DNA purification ==== | ||
+ | |||
+ | Kit Qiagen “gel extraction kit”, final volume = 50µL. <br> | ||
+ | |||
+ | ==== Ligation ==== | ||
+ | |||
+ | Ligation between COS and pSB1A2 plasmid backbone (TAKARA, DNA ligation kit) : <br> | ||
+ | |||
+ | First report : <br> | ||
+ | COS = 3,5µL <br> | ||
+ | pSB1A2 = 0,5µL <br> | ||
+ | Solution A = 16µL <br> | ||
+ | Solution B = 4µL <br> | ||
+ | |||
+ | Second report: <br> | ||
+ | COS = 6µL <br> | ||
+ | pSB1A2 = 1µL <br> | ||
+ | Solution A = 28µL <br> | ||
+ | Solution B = 7µL <br> | ||
+ | |||
+ | 1 hours of incubation at room temperature <br><br> | ||
+ | |||
+ | Ligation between the D protein and ADV5pb (NEB enzyme): <br> | ||
+ | |||
+ | First report : <br> | ||
+ | PrtD = 2,5µL <br> | ||
+ | ADV5pb = 5,5µL <br> | ||
+ | NEB T4 ligase buffer= 1µL <br> | ||
+ | NEB T4 ligase = 1µL <br><br> | ||
+ | |||
+ | Second report: <br> | ||
+ | |||
+ | PrtD = 3µL <br>ADV5pb = 5µL <br> | ||
+ | NEB T4 ligase buffer= 1µL <br> | ||
+ | NEB T4 ligase = 1µL <br><br> | ||
+ | |||
+ | Third report: <br> | ||
+ | PrtD = 4µL <br> | ||
+ | ADV5pb = 4µL <br> | ||
+ | NEB T4 ligase buffer= 1µL <br> | ||
+ | NEB T4 ligase = 1µL <br><br> | ||
+ | |||
+ | Fourth report: <br> | ||
+ | PrtD = 2µL <br> | ||
+ | ADV5pb = 2µL <br> | ||
+ | NEB T4 ligase buffer= 1µL <br> | ||
+ | NEB T4 ligase = 1µL <br> | ||
+ | |||
+ | 1 hour at room temperature <br><br> | ||
+ | |||
+ | Ligation between BBa_B0030 and BBa_R0010 (TAKARA, DNA ligation kit) : <br> | ||
+ | |||
+ | First report : <br> | ||
+ | Plasmid (R0010) = 0,5µL <br> | ||
+ | Insert (B0030) = 5µL <br> | ||
+ | Solution A = 22µL <br> | ||
+ | Solution B = 5,5µL <br><br> | ||
+ | |||
+ | Second report: <br> | ||
+ | Plasmid (R0010) = 0,5µL <br> | ||
+ | Insert (B0030) = 6µL <br> | ||
+ | Solution A = 26µL <br> | ||
+ | Solution B = 6,5µL <br> | ||
+ | |||
+ | 1 hour of incubation at room temperature. <br><br> | ||
+ | |||
+ | Ligation between BBa_B0014 and BBa_P1003 + BBa_B0014 (TAKARA, DNA ligation kit) : <br> | ||
+ | |||
+ | First report : <br> | ||
+ | Plasmid (P1003 + B0014) = 0,5µL <br> | ||
+ | Insert (B0014) = 5µL <br> | ||
+ | Solution A = 22µL <br> | ||
+ | Solution B = 5,5µL <br> | ||
+ | |||
+ | Second report : <br> | ||
+ | Plasmid (P1003 + B0014) = 0,5µL <br> | ||
+ | Insert (B0014) = 6µL <br> | ||
+ | Solution A = 26µL <br> | ||
+ | Solution B = 6,5µL <br> | ||
+ | |||
+ | 1 hour of incubation at room temperature. <br><br> | ||
+ | |||
+ | ==== Electroporation ==== | ||
+ | |||
+ | Electroporation cuvettes = 2mm ; inoculums of electrocompetent <i>E.coli</i> DH5alpha= 40µL; pulse = 2,5KVolt ; 1h of incubation. <br> | ||
+ | |||
+ | Spread 1mL of inoculums into a petri dish with LB + ampicillin (50mg/mL) (20/0,02mL). <br> |
Latest revision as of 16:05, 21 October 2009
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Friday the 2nd
Restriction digest
Ligation between BBa_B0030 and BBa_R0010
Restriction digest of R0010 by SpeI and PstI (2279bp):
DNA (miniprep) = 30µL
Buffer H (TAKARA) =4µL
H20 = 4µL
F
Spe1 (TAKARA) = 1µL
Pst1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Restriction digest of BBa_B0030 by PstI and XbaI (15bp):
DNA (miniprep) = 30µL
Buffer M (TAKARA) =4µL
H20 = 4µL
Pst1 (TAKARA) = 1µL
Xba1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Ligation between BBa_B0014 and BBa_P1003 + BBa_B0014
Restriction digest of BBa_B0014 by EcoRI and SpeI (95bp):
DNA (miniprep) = 30µL
Buffer M (TAKARA) =4µL
H20 = 4µL
EcoR1 (TAKARA) = 1µL
Spe1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Restriction digst of BBa_P1003 + BBa_B0014 by EcoRI and XbaI (3770bp):
DNA (miniprep) = 30µL
Buffer M (TAKARA) =4µL
H20 = 4µL
EcoR1 (TAKARA) = 1µL
Xba1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Ligation between COS and pSB1A2
Restriction digest of COS by XbaI and SpeI (250bp):
DNA (miniprep) = 30µL
Buffer M (TAKARA) =4µL
H20 = 4µL
Xba1 (TAKARA) = 1µL
Spe1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Restriction digest of pSB1A2 by SpeI and XbaI (2079bp):
DNA (miniprep) = 30µL
Buffer M (TAKARA) =4µL
H20 = 4µL
Spe1 (TAKARA) = 1µL
Xba1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Ligation of the D protein (PrtD) with the adenovirus 5 penton base (ADV5pb)
Restriction digest of PrtD by SpeI (385bp):
DNA (PCR) = 5µL
Buffer M (TAKARA) =2µL
H20 = 12µL
Spe1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
Restriction digest of ADV5pb by XbaI (1715bp):
DNA (PCR) = 5µL
Buffer M (TAKARA) =2µL
BSA (TAKARA) = 2µL
H20 = 10µL
Xba1 (TAKARA) = 1µL
1 hour of incubation at 37°C.
DNA electrophoresis
85 Volt, 15 minutes.
105 Volt, 40 minutes.
Ladder fermentas 1 Kb.
Samples: BBa_R0010, BBa_B0030, BBaB0014, BBa_P1003, adenovirus penton base with BioBrick prefix and suffix (ADV5pb BBa), D protein with BioBrick prefix and suffix (D prt BBa)
Interpretation:
We obtain all the fragments but we always have a problem of mistmacth for ADV5 pb primers, and the B0030 fragment is impossible to see into the photo, in fact there is a few DNA, and the fragment is short around 15bp.
DNA purification
Kit Qiagen “gel extraction kit”, final volume = 50µL.
Ligation
Ligation between COS and pSB1A2 plasmid backbone (TAKARA, DNA ligation kit) :
First report :
COS = 3,5µL
pSB1A2 = 0,5µL
Solution A = 16µL
Solution B = 4µL
Second report:
COS = 6µL
pSB1A2 = 1µL
Solution A = 28µL
Solution B = 7µL
1 hours of incubation at room temperature
Ligation between the D protein and ADV5pb (NEB enzyme):
First report :
PrtD = 2,5µL
ADV5pb = 5,5µL
NEB T4 ligase buffer= 1µL
NEB T4 ligase = 1µL
Second report:
PrtD = 3µL
ADV5pb = 5µL
NEB T4 ligase buffer= 1µL
NEB T4 ligase = 1µL
Third report:
PrtD = 4µL
ADV5pb = 4µL
NEB T4 ligase buffer= 1µL
NEB T4 ligase = 1µL
Fourth report:
PrtD = 2µL
ADV5pb = 2µL
NEB T4 ligase buffer= 1µL
NEB T4 ligase = 1µL
1 hour at room temperature
Ligation between BBa_B0030 and BBa_R0010 (TAKARA, DNA ligation kit) :
First report :
Plasmid (R0010) = 0,5µL
Insert (B0030) = 5µL
Solution A = 22µL
Solution B = 5,5µL
Second report:
Plasmid (R0010) = 0,5µL
Insert (B0030) = 6µL
Solution A = 26µL
Solution B = 6,5µL
1 hour of incubation at room temperature.
Ligation between BBa_B0014 and BBa_P1003 + BBa_B0014 (TAKARA, DNA ligation kit) :
First report :
Plasmid (P1003 + B0014) = 0,5µL
Insert (B0014) = 5µL
Solution A = 22µL
Solution B = 5,5µL
Second report :
Plasmid (P1003 + B0014) = 0,5µL
Insert (B0014) = 6µL
Solution A = 26µL
Solution B = 6,5µL
1 hour of incubation at room temperature.
Electroporation
Electroporation cuvettes = 2mm ; inoculums of electrocompetent E.coli DH5alpha= 40µL; pulse = 2,5KVolt ; 1h of incubation.
Spread 1mL of inoculums into a petri dish with LB + ampicillin (50mg/mL) (20/0,02mL).