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Could the differential effects of DAP versus MeC or MeU or the differential effects of DAP on different probe sequences also be related to structural consequences?
Finally, earlier studies have noted that methylation of cytosines (generating MeC) in ribopolynucleotides stabilizes duplexes to the same extent as substitution of thymine (MeU) for uracil [ 28 ] . Thus, although it is still surprising that MeC and MeU decrease hybridization intensities, it is not surprising that the magnitude of the effects generated by MeC and MeU residues are similar.
Those probes whose signal intensities were increased at least two-fold are summarized in Table 1. As Table 1shows, for a number of transcripts substitution with MeC or MeU may potentially augment hybridization signals more so than even DAP.
Why do we see differential effects of DAP, MeC, and MeU on hybridization intensities?
In contrast, both of the modified pyrimidine triphosphates (MeC and MeU) tested resulted in a decrease in overall signal intensities for nearly all of the probes tested when compared against unmodified control samples (Figures 2D& 2E).