Lambda exonuclease pre-treatment for improved DNA-chip performance depends on the relative probe-target position

The hybridisation characteristics of DNA targets to solid phase bound probes, e.g. in DNA microarrays, depend on the probe-target position and on target renaturation if a dsDNA target is used. We investigated a lambda exonuclease treatment of a PCR amplified dsDNA target to produce ssDNA with regard to probe target position, treatment duration and inactivation time towards its impact on fluorescence or electrical signals on two DNA-chip formats. Surprisingly, the achieved amplification factors varied by three orders of magnitude, i.e. 2–1074 fold signal enhancement, depending on the relative probe-target position and readout scheme. The presented results can be used to design future studies involving lambda exonuclease preanalytic treatments.