Both the gel-based and surface microchips provide their own advantages but also show their own relative drawbacks. In particular, the hybridization kinetics on the surface microchips appears to be faster than that on the gel microchips. However, the immobilization of probes on a surface introduces the significant inhomogeneity into molecular interactions and leads to "smearing" association constants corresponding to the formation of complexes between probe and target molecules.

To avoid the surface effects, commonly one-stranded probe DNA is either the continuation of duplex linker of 15-30 base pairs in length or is the continuation of one-stranded linker like poly-T. Unlike surface microchips the molecular interactions on gel-based microchips remain approximately the same as that in solution and the linkers are not needed.

Moreover, despite the slower hybridization kinetics in gel pads both fluorescent signals and discrimination between perfect and mismatch complexes turn out higher for gel-based microchips still at the early stages of hybridization.

The binding kinetics may be accelerated about five times by mixing buffer solution with peristaltic pump, acoustic surface waves etc.