Use a high-fidelity DNA polymerase and avoid over-amplification. We recommend Q5^® High-Fidelity DNA Polymerase formulations for maximal fidelity (NEB #M0491, #M0493), which is also available in Master Mix format (NEB #M0492, #M0494). Also, use the minimum number of cycles required to generate the amount of DNA required for assembly; this is usually 20 cycles or less.