Concentration and cleanup of nucleic acid samples

A channel device used to separate one or more polynucleotide analytes from one or more contaminants, the channel device comprising:

• an injection channel and a separation channel, each channel having a first end and a second end, with said separation channel intersecting the injection channel at a region between the ends of the injection channel;
• a first reservoir disposed for fluid communication with one of said ends of said injection channel;
• and
• a first separation medium including a first polymer component held within said injection channel and a second separation medium including a second polymer component held within said separation channel said first polymer component in said injection channel being present at a higher concentration than the second polymer component in said separation channel;
• wherein said first polymer component concentration is sufficient to separate said one or more polynucleotide analytes from said one or more contaminants on the basis of differential eletrophoretic mobilities within the injection channel such that said one or more polynucleotide analytes are purified of the one more contaminants at the intersection of the injection channel and the separation channel, and the second polymer component concentration is sufficient to separate the purified polynucleotide analytes on the basis of differential eletrophoretic mobilities within the separation channel with reduced interference from the one or more contaminants.