Subtractive hybridization is a powerful technique to study gene expression in specific tissues or cell types or at a specific stage. Traditional procedures often are technically demanding and labor-intensive methods that require large amounts of mRNA and might give rise to falsely positive and unreproducible results.
Dynabeads Oligo(dT)25 can be used to produce subtracted cDNA probes for screening and isolation of rare, differentially expressed mRNAs. Instead of eluting the captured mRNA off the beads, the bead-bound oligo-dT sequence is used to prime cDNA synthesis to produce a solid-phase cDNA libraries specific for a particular cell type or tissue (1-11).
mRNA from the target material is hybridized with first-strand cDNA from the subtractor material immobilised on Dynabeads. The subtracted mRNA is left in the supernatant after magnetic separation of bead-bound subtractor cDNA with captured common mRNA, and the subtractor beads can be reused. After the final hybridisation step, the subtracted specific mRNA is reverse transcribed to radio-labelled cDNA and used to screen cDNA libraries (5, 10) or for cDNA cloning (9). When the difference between the subtractor and the target mRNA population is small, large amounts of target-specific mRNA may be difficult to obtain and the PCR-based method of Lambert (11) would be more appropriate. See this figure for how it works.
An alternative approach is to create immobilised cDNA libraries from both target and subtractor mRNA (2, 4). Second-strand cDNA is synthesised by random priming of target cDNA and the fragments eluted and mixed with excess immobilised subtractor cDNA. Common fragments are annealed and removed, while the unique fragments left in the supernatant are used as a probe to screen cDNA libraries (2, 8).If the amount of mRNA is limited or the two mRNA sources are very similar, the material might be insufficient for several rounds of subtraction to be performed, or the material remaining for screening purposes might be insufficient. This can be solved by allowing the subtracted cDNA fragments to reanneal back onto the immobilised subtractor cDNA. The double-stranded cDNA produced is then cut, linkers ligated and the fragments amplified by PCR (3). See this figure for how it works.