Editing Overlap extension PCR

== Primer Design<br>  ==

15 to 21 bp overlap 

no self-pairing and low G/C content.<br>The length of the overlapping primers: 27 bp to 40 bp, with a minimal overlapping region of 15 bases.<br>The outer primers for the full-length ORF amplification do not contain any overlapping sequence 

== Asymmetric&nbsp; Overlap extension PCR<br>  ==
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1. PCR 

PCR reaction 1 &amp; 2 

1 ng plasmid DNA<br>0.5 ÎŒL 10 mM dNTP<br>200 nM Outer primer<br>20 nM mutant primer (20% or 10% of outer primer)<br>1 U Phusion<br>5 ÎŒL 5X Phusion buffer<br>water to 25 ÎŒL. 

2. Mix two PCR reactions, 94 <sup>o</sup>C 1 min, incubate at 60°C for 1 min and 72°C for 5 to 15 min. 

3. Gel purify, digestion then transformation. 
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== Fusion of 3 PCR fragments<br>  ==

1. PCR three fragments using Phusion or Deep Vent. Primers should have overlap regions. 

2. Fusion 

10 ÎŒl ThermoPol reaction buffer<br>5 ÎŒl 10 mM dNTP mix<br>20 ÎŒl (100 ng) fragment 1<br>20 ÎŒl (100 ng) fragment 3<br><span style="color:#ff0000">4 ÎŒl (20 ng) fragment 2 (middle one)</span><br>2 ÎŒl 100 mM MgSO4<br>0.8 ÎŒl Deep Vent DNA Polymerase<br>38.2 ÎŒl H2O 

94°C 2 min<br>94°C 15 s<br>56°C 20 s<br>72°C 1 min<br>10 cycles 

3. Amplification 

72 ÎŒl H2O,<br>10 ÎŒl ThermoPol reaction buffer<br>5 ÎŒl 10 mM dNTP mix<br>3 ÎŒl of unpurified PCR product from fusion step<br>2 ÎŒl 100 mM MgSO4 solution<br>2 ÎŒl F primer<br>2 ÎŒl R primer (both 2 ÎŒM)<br>0.8 ÎŒl Deep Vent DNA Polymerase. 

94°C 2 min<br>94°C 15 s<br>62°C 20 s<br>72°C 2 min 30 s<br>35 cycles<br>72°C 3 min 

== Fusion of PCR product with Vector without restriction digestion<br>  ==

1. Amplify insert using chimeric primers. 
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initial denaturation at 100°C for 2 min<br>denaturation at 94°C for 30 s<br>annealing at 60°C for 30 s<br>extension at 68°C for 90 s/kb for 30â32 cycles, with a final extension of 68°C for 10 min.<br>Gel purify PCR-amplified insert<br>The final PCR product has overlapping regions with the vector. 

2.&nbsp; Megaprime PCR<br>Mix acceptor plasmid vector (3â30 ng) with 250 Ã molar excess of insert DNA, in&nbsp; 10-ÎŒL total volume containing Phusion DNA polymerase, dNTP and buffer. 

PCR<br>Denature: 98°C for 30 s<br>annealing: 60°C for 30 s<br>extension: 98°C for 1.5 min per kb<br>15 cycles<br>one extra 10-min extension. 

Efficiency: Phusion &gt; KOD&nbsp; &gt; Pfu 

3. Add 10 units Dpn1 directly to PCR reaction, digest at 37 oC for 1 hr. 

4. Transform E. coli 

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== Original Overlap Extension PCR<br>  ==

== Ist round PCR<br>  ==

Run 25 to 35 cycles to check if PCR is going to work 

Run 10 cycles, use this reaction as 2nd PCR template 

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== 2nd Round PCR  ==

Mix 10 ul first round PCR reaction, add 1 ul two outer PCR primers, add 10XPCR buffer, dNTP, water (to 25 or 50 ul), Pfu or Phusion 

Run 20 to 25 cycles 

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Take 5 ul for gel electrophesis 

See if the size is good 

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Gel purify (if parent vector has the same antibiotics), or purify directly with spin column, elute with 20 ul H2O 

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== Digestion  ==

Digest with restriction enzymes, heat inactivate at 75 oC for 10 min, or purify by spin column 

Optionally, the PCR products can be digested with restriction enzymes without purification (using FastDigest buffer) if: 

*parent vector has different antibiotics 
*a single PCR band

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Add gel purified (digested) vector, DNA ratio (1:3 to 1:1, vector:insert, no need to use spectrophotometer for quantitation). 

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== Ligation  ==

Add 2.5 ul ligation buffer and 0.5 ul ligase, ligate 2 hours at RT. 

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Transformation 

Transform 10 ul ligation mix with 50 or 100 ul Top10 or STBL3. 

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== Grow cells O/N at 37 oC  ==

Spin down cells, plate on LB/Amp or LB/Kan 

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[[Category:Protocols]]