# IGEM:Paris Bettencourt 2012/Notebooks/Semantic group/day by day//2012/07/27

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 Revision as of 12:32, 27 July 2012 (view source) (→Designing oligo for PCR Quick Change mutagenesis)← Previous diff Current revision (08:24, 13 August 2012) (view source) (→Designing oligo for PCR Quick Change mutagenesis (QCM)) (4 intermediate revisions not shown.) Line 11: Line 11: -> #29 (from #3) & #30 (from #5) -> #29 (from #3) & #30 (from #5) - ==Designing oligo for PCR Quick Change mutagenesis== + ==Designing oligo for PCR Quick Change mutagenesis (QCM)== + + The following oligos anneal with the BB P1003, carried by plasmid pSB1A2. Oligo 1 Fw PCR QCM : Oligo 1 Fw PCR QCM : Line 22: Line 24: To calculate other Tm, you can change/copy/paste in Python the following code : To calculate other Tm, you can change/copy/paste in Python the following code : - + + N = 36 gc = 44.4 gc = 44.4 mut = 1 mut = 1 Line 29: Line 32: which give : which give : - In [23]: Tm + In [23]: Tm - Out[23]: 78.92622222222222 + Out[23]: 78.92622222222222 - Which is good, since Tm has to be ≥78°C and %GC = 40% + Which is good, since Tm has to be ≥78°C and %GC > 40%

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## pSC008

-80°C and -20°C stocks are made !

-> #29 (from #3) & #30 (from #5)

## Designing oligo for PCR Quick Change mutagenesis (QCM)

The following oligos anneal with the BB P1003, carried by plasmid pSB1A2.

Oligo 1 Fw PCR QCM :

```GCGCCGGTTACATTAGATTCCTGTTTGTAATTGTCC
```

Tm = 78.9°C

Calculate thanks to the formula given in the kit documentation :

To calculate other Tm, you can change/copy/paste in Python the following code :

```N = 36
gc = 44.4
mut = 1
Tm = 81.5 + 0.41*gc-675/N-((mut*100.0)/N)
```

which give :

```In [23]: Tm
Out[23]: 78.92622222222222
```

Which is good, since Tm has to be ≥78°C and %GC > 40%