I am currently trying to design a probe which should specifically bind to methylated CpGs in a certain gene promoter. The probe will probably cover 3-4 CpGs in its sequence, however, I do not know which CpGs are methylated. Is it possible for me to design a degenerate probe that binds to the first CpG if it's methylated and the rest(CpGs) will be designed as Y/5-nitroindole? How efficient will be the binding of the probe?

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