Melbourne/Lab BL Notebook/20070916PCR1
From 2007.igem.org
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=Digestion of Second Round PCR product= | =Digestion of Second Round PCR product= | ||
Per PCR reaction: | Per PCR reaction: | ||
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| - | 6ul purified DNA | + | |- |
| + | ! Per 2° PCR | ||
| + | |- | ||
| + | |6ul purified DNA | ||
2ul 10x NEB Buffer 2 | 2ul 10x NEB Buffer 2 | ||
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8ul H<sub>2</sub>O | 8ul H<sub>2</sub>O | ||
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| + | |- | ||
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| + | | 20ul Total | ||
| + | |} | ||
Revision as of 15:46, 10 October 2007
Contents |
Protocol for PCR reactions A~G
For amplifying the photoreceptor and transmembrane domains of NpSopII-NpHtrII. All -ve controls were clean.
| PCR mix | PCR program | PrimerII |
|---|---|---|
| 5ul 10x buffer\\
5ul 10x Enhancer 0.6ul dNTPs (25mM stock) 2.5ul MgSO4 (Supplied in PCR kit) 1.5ul Primer BL_FP1_s (10uM stock) 1.5ul Primer II (10uM stock) 1ul Template (pJS010) 0.4ul Pfx Platinum (Invitrogen) 32.5ul ddH2O | 94°C - 5'
94°C - 30" 59°C - 35" 68°C - 1.5' (goto step 2 x30) 68°C -10' 4°C forever | Reaction A => Primer BL_Con1_as (Some non-specific bands)
Reaction B => Primer BL_Con2_as Reaction C => Primer BL_Con3_as (Some non-specific bands) Reaction D => Primer BL_Con4_as Reaction E => Primer BL_Con5_as Reaction F => Primer BL_Con6_as Reaction G => Primer BL_Con7_as |
| 50ul Total |
Protocol for PCR reactions 1-7
For amplification of the kinase domain of ComP
| PCR mix | PCR program | PrimerI |
|---|---|---|
| 5ul 10x buffer\\
2.5ul MgSO4 (Supplied in PCR kit) 1.5ul Primer I (10uM stock) 1.5ul Primer VR (10uM stock) 1ul Template (pJS010) 0.4ul Pfx 32.5ul ddH2O | 94°C - 5'
94°C - 30" 59°C - 35" 68°C - 1.5' (goto step 2 x30) 68°C - 10' 4°C forever | Reaction 1 => Primer BL_Con1_s
Reaction 2 => Primer BL_Con2_s Reaction 3 => Primer BL_Con3_s Reaction 4 => Primer BL_Con4_s Reaction 5 => Primer BL_Con5_s Reaction 6 => Primer BL_Con6_s Reaction 7 => Primer BL_Con7_s |
| 50ul Total |
Gel Purification of PCR products A~G and 1~7
PCR product of the expected size was excised from .8% agarose gel and gel purified using the Invitrogen gel purification kit. Protocol as detailed in the kit.
Second Round PCR
For stitching products A~G to 1~7. Gel purified PCR products from the above reaction were used.
| PCR mix | PCR program | <Reaction, TemplateI, TemplateII> |
|---|---|---|
| 5ul 10x buffer\\
2.5ul 10x Enhancer 0.6ul dNTPs (25mM stock) 2.5ul MgSO4 (Supplied in PCR kit) 1.5ul Primer BL_FP1_s (10uM stock) 1.5ul Primer VR (10uM stock) 5ul Template I {A~G} 5ul Template II {1-7} 0.4ul Pfx 27ul ddH2O | 94°C - 5'
94°C - 1' 50°C - 1' 68°C - 3' (goto step 2 x30) 68°C - 10' 4°C forever |
|
| 50ul Total |
Gel purification of second round PCR product
All the reactions had large smears, but we cut out a band around 2.3kb (expected size) and gel purified as above.
Digestion of Second Round PCR product
Per PCR reaction:
| Per 2° PCR |
|---|
| 6ul purified DNA
2ul 10x NEB Buffer 2 2ul 10x BSA 1ul XbaI 1ul PstI 8ul H2O |
| 20ul Total |
