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I am trying to multi-fragment Gibson Assemblies and my PCR product concentrations are not high enough to yield plasmids every time. I am using a very low amount of elution buffer to maximise concentration, but in some cases I am getting ~10-20 ng/ul which is not conducive to a good assembly.

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Have you the other route: Eluting twice and do a simple ethanol precipitation (with glycogen when the concentration is low)? –  Chris May 16 at 13:58
why not run your pcr for more cycles and increase the amount of pcr product? –  shigeta May 16 at 14:29
I'm no expert but assuming you are using a kit to elite your plasmid from some sort of a column/filter, it always helps if you heat your elution buffer (e.g. 70 oC) but consult your protocol. For procedures similar to this (e.g. miniprep) I also wait for 60 sec before proceeding with elution using centrifugation, which helps the yield. Also are your enzymes (DNA polymerase etc) in good condition? Are your buffers or kit solutions in a good condition? –  Bez May 16 at 18:53
You have left out critical information: Exactly what is your Gibson assembly scheme? Where are you getting the template fragments? What protocol are you using to purify? Also the title is overly general. Your question is about Gibson assembly, not "PCR". –  Superbest May 17 at 7:32

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