An investigation into utilizing DNA hybridization kinetics and affinity chromatography to produce a DNA biosensor

A conceptual design has been developed for a biosensor, based on nucleic acid hybridization kinetics and affinity chromatography, for measurement of critical subpopulations within mixed culture bioreactors. The presence of small subpopulations in soil systems contaminated with polyaromatic hydrocarbons can have significent effects on the overall performance of the biodegradation kinetics. Nucleic acid hybridizations are discussed along with DMA probes and the problems presented by colony hybridization methods. The physical design of the affinity chromatography column is evaluated from a mass transfer, reaction kinetic, and detection sensitivity standpoint. The importance of hybridization reaction kinetics in sample preparation and between the sample and probe DMA in the column is discussed. Kinetic hybridization data for the NAH7 probe in solution are presented. The problems associated with securely immobolizing NAH7 onto a suitable solid support are discussed. Literature data is presented which shows that the reaction rate between free solution and immobolized DNA to be several orders of magnitude slower than solution hybridization, indicating that an unacceptable mass transfer situtation may exist within the conceived biosensor.