Abstract: The present invention provides recombination based methods for assembling nucleic acids. In certain aspects the present invention provides hierarchical assembly methods for producing genome sized polynucleotide constructs. The methods may be used for assembling large polynucleotide constructs, for synthesizing synthetic genomes, or for introducing a plurality of nucleotide changes throughout the genome of an organism. In another aspect, the invention provides cells having increased genomic stability. For example, cells comprising alterations in at least a substantial portion of the transposons in the genome are provided.

Abstract: Disclosed are methods of assembling nucleic acid constructs from component parts in a manner that is not dependent on the sequence of the component parts. The methods may be used to assemble large nucleic acid constructs from multiple component parts in one or more reactions. The methods may also be used to assemble two or more nucleic acid constructs in the same reaction mixture. In exemplary embodiments, the methods involve formation of a Holliday junction or bridge structure using a junction oligonucleotide.