Integrated systems for DNA sample preparation and detection in environmental samples

Field-portable sensor systems are currently needed for the detection and characterization of biological pathogens in the environment. Nucleic acid analysis is frequently the method of choice for discriminating between pathogenic and nonpathogenic bacteria in environmental samples, however standard protocols are difficult to automate and current microfluidic devices are not configured to analyze environmental samples. In this paper, we describe an automated DNA sample processing system and demonstrate its use for the extraction of bacterial DNA from water and sediment samples. Two challenges in environmental sample analysis are the need to process relatively large sample volumes (microliters to many milliliters) in order to obtain detectable quantities of DNA present at low concentrations, and the need to purify DNA from a complex sample matrix for downstream detection. These problems are addressed by using sequential injection fluid handling techniques for precise manipulation of the required volumes, and renewable separation columns for automatically trapping and releasing microparticles that are used for sample purification. The renewable microcolumns are used for both bacterial cell concentration and DNA purification. The purified bacterial DNA is then amplified using an on-line PCR module in order to produce detectable quantities of the target DNA.