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. 1998 Dec 8;95(25):14614–14621. doi: 10.1073/pnas.95.25.14614

Figure 5.

Figure 5

DMS modification data with synthetic and intracellular MFA2 mRNA. (A–D) DMS-treated intracellular mRNA and synthetic SP6A0 RNA were analyzed by primer extension as described in Materials and Methods. Synthetic SP6A0 RNA was modified with DMS as described in Fig. 2 (20-min reaction). Oligonucleotide primers used were complementary to the following RNA sequences: nucleotides 61–80 (A), nucleotides 132–151 (B), nucleotides 215–234 (C), and nucleotides 285–304 (D). Lanes 1 and 2 show the synthetic RNA with no and DMS modifications, and lanes 3 and 4 show the same with the in vivo RNA. Overall band labeling (S is a reverse transcriptase stall) is shown on the left and special modification sites referred to in the text on the right. Lanes 5 and 6 in each case show the DMS control and modification data with the SP6A0 synthetic RNA and lanes 7 and 8 show the results when ddATP and ddCTP, respectively, were added to the reverse transcriptase reaction mixtures of control RNA (as described in ref. 18). The U and G bands are labeled (right) and verify the DMS band labeling results (left). The analyses were run on 8% sequencing gels.