USER friendly DNA recombination (USERec) is based on near homology-independent recombination of DNA fragments (~40-400 bp) that are efficiently reassembled into full-length genes, proven for up to ten fragments. USERec requires a minimal crossover sequence (a 5'-AN(4-8)T-3' motif) of the fragments that can be implemented wherever structural or functional comparisons suggest a fragment boundary. The greatly reduced sequence constraints of this method facilitate directional assembly of gene fragments for applications such as exon or domain shuffling, loop grafting, reassembly of natural modular biosynthetic assembly lines, and rearrangement of structurally (but not sequence) homologous proteins.