Besides the introduction of mutations, Overlap Extension PCR is widely used to assemble complex DNA sequences without the introduction of undesired nucleotides at any position. This is possible since OE-PCR relies on the utilization of complementary overhangs to guide the scarless splicing of custom DNA fragments in a desired order. This is the main advantage of OE-PCR and other long-homology based cloning methos such as Gibson assembly, which overcome the limitations of traditional restriction enzyme digestion and ligation cloning methods. 
Assembly of custom DNA sequences with OE-PCR consists on three main steps. First, individual DNA sequences are amplified by PCR from different templates and flanked with the required complementary overhangs. Second, the formerly obtained PCR products are combined together into the overlap extension PCR reaction, where the complementary overhangs bind pair-wise allowing the polymerase to extend the DNA strand. Eventually, outer primers targeting the external overhangs are used and the desired DNA product is amplified in the final PCR reaction.