Should I amplify my gBlocks Gene Fragments when I receive them?
We do not recommend amplifying gBlocks Gene Fragments >1 kb in length.
gBlocks fragments are synthesized from several smaller overlapping fragments. Even after purification the final prep will contain some of these smaller byproducts. During PCR, smaller products are more efficiently amplified than longer ones, and at the exponential phase of PCR, smaller products in the reaction will overwhelm the generation of the full-length correct product. When run on the gel, these amplification products appear as a smear or smaller bands than expected.
Most applications such as restriction digest, blunt end, and Gibson cloning can be performed with the material provided by IDT, and PCR amplification should not be necessary. If the purpose of the amplification is to add flanking bases to complete a cloning reaction, we strongly recommend ordering the gBlocks fragment with the required bases rather than adding them afterwards using PCR.
If you must amplify your gBlocks fragment, use the minimum amount of starting template required by your PCR kit protocol, limit the cycle number to 10–12, and use a high-fidelity polymerase.