Team:Tokyo Metropolitan/Project/Pattern/Protocol
From 2010.igem.org
PCR with Pho DNA Polymerase (NIPPON GENE)
<Materials>
10x reaction buffer</br> Forward primer (starting with 20µM)</br> Reverse primer (starting with 20µM)</br> Pho DNA Polymerase (starting with 2.5U/µl)</br> dNTP (starting with 2.5mM)</br> DW</br> DNA samples</br> ・Pellet of E-coli having BBa_I723901</br>
・Pellet of E-coli having BBa_K208017</br>
・Plasmid of BBa_I13521(starting with 20nM)</br> ・Pellet of JM109</br>
<Protocol></br>
1 Make the pellet with pre-colony.</br> 2 Thaw all required reagents completely and put them on ice. Mix all reagents well by inversion and spin them down prior to pipeting.</br> 3 Prepare the reaction mix to correct for dispensing losses prepare an excess of reaction mix (for example, a 100 reactions mix for 96 reactions)</br> 10x reaction buffer 12.5μl</br> Forward primer 2.5μl (starting with 20µM)</br> Reverse primer 2.5μl (starting with 20µM)</br> Pho DNA Polymerase 2.5µl (starting with 2.5U/µl)</br> dNTP 20μl (starting with 2.5mM)</br> DW 85µl</br> Total reaction Mix 125μl </br> 4 Add all components together, except for the template. Mix thoroughly by inversion. Spin down.</br> 5 Add the template DNA(pellet or Plasmid) for your samples in to PCR tubes</br> 6 Add 50μl of the reaction mix per tube and mix gently on a stirrer or spin down. Ensure that no bubbles are present in the reaction tube. Reaction set up can be done at room temperature.</br> 7 Program your Real-Time Thermocycler w/ “fast block” using the following recommended FAST parameters:</br> 95°C 5min. 95°C 30sec. 30cycle 55°C 30sec. 30cycle 76.5~68.0°C 3min and 45sec. 30cycle 72°C 5min. 4°C
Ligation with Ligation-convenience kit (NIPPN GENE)
<Materials>
DNA solution
2 × Ligation Mix (Ligation-convenience kit NIPPN GENE)
<Protocol>
1 Prepare 10 μl of DNA solution to contain DNA fragment with appropriate mole ratio against vector DNA.
2 Add 10μl of 2 × Ligation Mix to the DNA solution and mix well.
3 Ligation reaction. Incubate 5-30min at 16°C.
4 Apply DNA reaction mixture directly to transformation or in vitro packaging as it is.
DNA extraction with ISOPLANT(NIPPON GENE)
<Materials>
Extraction Buffer 0.3ml Lysis Buffer 0.15ml Sodium Acetate(pH5.2) 0.15ml 10mM Tris-HCl(pH8.0), 1mM EDTA 0.1ml 1mg/ml RNaseA 1µl E-coli culture H20 TE Buffer
<Protocol> 1 Centrifuge 1.5ml of E-coli culture at 4οC for 5min, and then aspirate the supernatant. 2 Add 0.3ml of Extraction Buffer to sample, and then vortex 1~2sec. 3 Add 0.15mlof Lysis Buffer to solution, and then vortex 5~6sec. 4 Incubate 15min at 50°C. 5 Add 0.15ml of Sodium Acetate(pH5.2) to solution, and then vortex 1~2sec. 6 Leave on ice for 15min 7 Centrifuge solution at 4οC for 15min, and then aspirate the supernatant. 8 Add 0.3ml of H2O to the tube having the pellets, and then vortex thoroughly. 9 Add 0.6ml of EtOH to solution, and then vortex thoroughly. 10 Centrifuge solution for 10min, and then aspirate the supernatant. 11 Add 70%EtOH to the tube having the pellets. 12 Dry the pellets in the speed-vac for 5min, or air dry. 13 Add TE Buffer to the dried pellets