Modeling the kinetics of hybridization in microarrays

Abstract

Conventional fluorescent-based microarrays acquire data after the hybridization phase. In this phase the targets analytes (i.e., DNA fragments) bind to the capturing probes on the array and supposedly reach a steady state. Accordingly, microarray experiments essentially provide only a single, steady-state data point of the hybridization process. On the other hand, a novel technique (i.e., realtime microarrays) capable of recording the kinetics of hybridization in fluorescent-based microarrays has recently been proposed in [5]. The richness of the information obtained therein promises higher signal-to-noise ratio, smaller estimation error, and broader assay detection dynamic range compared to the conventional microarrays. In the current paper, we develop a probabilistic model of the kinetics of hybridization and describe a procedure for the estimation of its parameters which include the binding rate and target concentration. This probabilistic model is an important step towards developing optimal detection algorithms for the microarrays which measure the kinetics of hybridization, and to understanding their fundamental limitations.