Has worked for Mike for various gene synthesis targets lengths ~300bp - 1500bp. More difficult for >1500bp. Use Josh's gene synthesis method or gBlocks and Gibson assembly for longer sequence genes.
Identify your target amino acid sequence. Plug it into DNAworks online software with your preferred excluded sequences (restriction sites, barcodes, screening primer sequences, etc.) and rough parameters - a rule of thumb that has worked in the past is 70 nt oligo length and ~63C annealing temp. You will get a set of primers out of the software.
PAN oligo synthesis works for ordering all of these primers with enough fidelity to get a working full synthesis. This set will be an even number of oligos 1 - n, oligo number #1 and #n are the full length amplification oligos.
The synthesis works by a two-step PCR process:
First run an assembly PCR with all the oligos excluding the full length amplification oligos #1 and #n. A quick recipe for this PCR is to mix 1ul from each of the assembly oligo stocks (diluted to 100mM) and use 5 ul of this mix as the input for the assembly PCR. Roche Expand polymerase has been the typical polymerase used in lab for the DNAworks PCR assembly. Run a small assembly reaction (25-50ul)
An example assembly PCR thermal cycle:
Use 1-3 ul of the product from this reaction as the template DNA for the second PCR reaction, which is basically a normal (30 cycle) PCR amplification reaction where you use the full length amplification oligos (#1 and #n from the DNAworks output).
Run 1ul of each of these reactions out onto a gel to assess the success of the assembly. You should see a smear of DNA from ~100bp up to full length as the product of the first reaction and a tight single band at the expected length as the product of the second reaction.
Isis will fill this out soon...
Save yourself the trouble and get it synthesized.