User:Howard Boland/Notebook/Art from Synthetic Biology/2010/10/18

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pfu Taq Polymerase arrives
My long-range pfu Taq polymerase arrived from stratagen! Finally we can setup the PCRs. Interestingly it arrived in a massive box of dry ice and was then placed directly in -80ºC. I wish Halloween was a bit closer so the dry ice could come to some use...

I set up to PCR reactions with the new primer set and using my plasmids as templates.

pMAK512, pBR322 extract
To check conditions I prepared two tubes (not master mix)

PCR mix
 * 1) 40.1µl H20
 * 2) 4µl 10xpfu Polymerase Buffer
 * 3) 0.4 10mM dNTP (not supplied with kit)
 * 4) 1µl pMAK512 plasmid template (100ng/µl)
 * 5) 1.25µl Primer forward
 * 6) 1.25µl Primer reverse
 * 7) 1µl pfu Polymerase

PCR conditions Cycles: 32x Lid: 100ºC Volume: 50µl (each)


 * 1) Initial: 94ºC, 10 min
 * 2) Denature: 94ºC, 1 min
 * 3) Annealing: 63ºC, 50sec
 * 4) Extension: 70ºC, 1min 12sec
 * 5) Goto 2, 32 times
 * 6) Final: 70ºC, 10 min
 * 7) Rest: 8ºC, forever

Expected product size: 790b

Calculation of Extension time: 0.79kb*1.5min/kb = 1min 12 sec

Calculation of Annealing temperature:

CTGCGGCGAGCGGTATCAGC => G/C = 14, A/T = 6 => 14*4ºC + 6*2ºC = 68ºC => Lower by 5ºC => 63ºC TCCCTTAACGTGAGTTTTCGTTCCAC => G/C = 12, A/T = 14 => 12*4ºC + 14*2ºC = 72ºC => Lower by 5ºC => 67ºC

Select minimum of the two gives us the annealing temerature of 63ºC

pUA66katE, sensor part extract
To check conditions I prepared two tubes (not master mix)

PCR mix
 * 1) 40.1µl H20
 * 2) 4µl 10xpfu Polymerase Buffer
 * 3) 0.4 10mM dNTP (not supplied with kit)
 * 4) 1µl pUA66katE plasmid template (20ng/µl)
 * 5) 1.25µl Primer forward
 * 6) 1.25µl Primer reverse
 * 7) 1µl pfu Polymerase

PCR conditions Cycles: 32x Lid: 100ºC Volume: 50µl (each)


 * 1) Initial: 94ºC, 10 min
 * 2) Denature: 94ºC, 1 min
 * 3) Annealing: 61ºC, 50sec
 * 4) Extension: 70ºC, 2min 7sec
 * 5) Goto 2, 32 times
 * 6) Final: 70ºC, 10 min
 * 7) Rest: 8ºC, forever

Expected product size: 2359b

Calculation of Extension time: 02.359kb*1.5min/kb = 2min 7sec

Calculation of Annealing temperature:

GCGGCAACCGAGCGTTCTGA => G/C = 13, A/T = 7 => 13*4ºC + 7*2ºC = 66ºC => Lower by 5ºC => 61ºC GCCCAGTCTTTCGACTGAGCCT => G/C = 13, A/T = 9 => 13*4ºC + 9*2ºC = 70ºC => Lower by 5ºC => 65ºC

Select minimum of the two gives us the annealing temerature of 58ºC


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