Figure 5.

A class of transcripts cleaved by RNase H can extend beyond the GAA·TTC repeat. (A) Primer extension provides high resolution mapping of the 3′ limit of the RNA·DNA hybrid within the transcript. The supercoiled (GAA·TTC)₈₈ template used in Figure 4 was transcribed in the presence or absence of RNase H to provide RNA for reverse transcriptase primer extension of an end-labeled 30 base oligonucleotide that annealed from 72 to 42 bases beyond the 3′ end of the repeat in the transcript. Full-length extension to the 5′ end of the transcript yields a 390 base product in both samples. The major RNase H cleavage endpoints are clustered within a couple of triplets from the promoter distal end of the repeat sequence (arrow). (B) Experimental design and interpretation.