In principle, the homopurine and homopyrimidine tracts uncovered have the capacity to form higher order structures, such as triple helices (35) . These tracts are known to alter the conformation and stabilities of RNA-DNA heteroduplexes (36, 37) , such as those formed between RNA targets and DNA probes in our system. Finally, we expect the ATM target to be especially rich in such sequence tracts given that both strands of the 3 0 -splice acceptor sequences, typically containing homopyrimidine tracts, for all 62 coding exons are included in the ATM target. This increases the likelihood that highly related sequence tracts in the ATM target can cross-hybridize to probes interrogating a particular homopurine or homopyrimidine sequence tract and reduce the overall hybridization specificity in this region.