PCR reactions generate DNA fragments of interest. However, the reaction product also consists of contaminants that include excess dNTPs, primers, salts and failure products. In a typical cleanup the target double stranded DNA may be 2kb in length. PCR reactants and byproducts of 100 bp and smaller are eliminated. Yield and functionality are maintained while benefiting from high throughput automation. The purified PCR products are suitable for generating RNA by reverse transcription, cloning, hybridization reacts, and a host of other applications.