Will the 5 poly-A tracts in the aRNA interfere with downstream applications?
The 5′ poly-A tracts do not appear to interfere, at least as it applies to the ChIP-chip method. As far as microarray hybridization is concerned, as long as the microarray probes (i.e. the DNA probe adhered to the microarray surface) do not contain significantly large poly-A tracts, these poly-A tracts should not cause any problems. Furthermore, one can optionally follow the lead of gene expression profiling hybridization protocols by adding in poly(A) or poly(dA), which is used to block the poly-T tracts in the cDNA probe. Both poly(A) and poly(dA) are available from Sigma.
