Multiplex Color Coded Probe Pairs to Replace Microarrays

Source: Geiss et al. (2008). Direct multiplexed measurement of gene expression with color-coded probe pairs. Nat biotech 26(3):317-325.

This is a very cool paper with an exciting approach... The authors claim that their method is more sensitive compared to chip-based microarrays. Their method involves synthesizing two probes (a capture probe and a reporter probe). The capture probe is simply a biotinylated oligo with a 35-50 complementary region to the target mRNA; whereas, the reporter probe, in addition to a complementary region contains a series of sequences that can be targeted by colored probes. The sequence of these colors along the reporter oligo is unique for each mRNA (Figure a).

The pair of probes for each target is added to the mRNA solution along with the colored probes. Upon the formation of the complex, the oligos are bound to a surface from the biotin group on the capture probe and subjected to a electric field to extend all the molecules to alinear format. The resulting image is then analysed and the number of transcripts for each type is counted (see Figures b-c).


This method (as cool as it seems) is quite expensive and the fact that it is more sensitive does not make it a viable protocol. Specially, with the current emergence of RNA-seq it seems difficult to establish a competitive method.