Biochemistry. In the article “A novel 3′-end repair mechanism in an RNA virus,” by Peter D. Nagy, Clifford D. Carpenter, and Anne E. Simon, which appeared in number 4, February 18, 1997, of Proc. Natl. Acad. Sci. USA (94, 1113–1118), Figs. 1, 2, 3, 4 were inadequately reproduced on press. The figures and their legends are reprinted below with greater contrast.

Figure 1.

Sequences and secondary structures of TCV and TCV-associated subviral RNAs. (A) Schematic representations of TCV, satellite RNA (sat-RNA) C, defective interfering (DI) RNA G, and sat-RNA D. Similar sequences are shaded alike. Positions of TCV-related sequence in the subviral RNAs are indicated. (B) Secondary structures of the 3′-terminal sequences of TCV, DI RNA G, sat-RNA D, sat-RNA C (16), and mutants derived from sat-RNA C. Plasmid-derived nucleotides present in the transcripts of sat-RNA C mutants containing 3′-terminal deletions are in lowercase letters. Point mutations that were generated in wild-type TCV and sat-RNA C are indicated, with names of mutants in parentheses.

Figure 2.

Model for the repair of deletions at the 3′ end of sat-RNA C. (A) Synthesis of abortive products by the RdRp at the 3′ end of (+)-strand TCV. (B) RNase-mediated damage at the single-stranded 3′ end of sat-RNA C (a deletion of six bases is shown). (C) Use of the “abortive” oligoribonucleotides by the RdRp to prime (−)-strand sat-RNA C synthesis, thereby repairing the damaged 3′ end.

Figure 3.

Analysis of aborted synthesis products generated in TCV RdRp reactions in vitro. Plus-strand RNA templates indicated above each lane (3 μg per lane) were added to partially purified TCV RdRp using reaction conditions as described, and using [α-³²P]ATP as the radioactive nucleotide. Products were separated through 20% polyacrylamide/8 M urea gels and analyzed by autoradiography. Lanes: TCV, wild-type TCV; TCVΔ5 and TCVΔ6, mutants of TCV with the 3′ terminal 5 (UGCCC-3′) and 6 (CUGCCC-3′) nucleotides, respectively, replaced with the sequence GGGGAUCCUCUAG-3′; G, DI RNA G; C, sat-RNA C; C/3′TCV, sat-RNA C with the 3′ 100 bases replaced with the corresponding region from TCV; D, sat-RNA D. (Left) Low and high molecular weight products. (Right) Overexposure of the lower portion of the gel shown at left to visualize low abundant oligoribonucleotide products. The migration positions of full-length subviral RNAs and oligoribonucleotides of 4–8 bases are shown. The sizes of the oligoribonucleotides products were determined by the use of labeled 5-, 6-, and 7-mer ribonucleotide size-markers. TCV migrates only slightly into these gels.

Figure 4.

Analysis of primer-extension products synthesized in TCV RdRp reactions in vitro. The (+)- or (−)-strand RNA templates indicated above each lane (3 μg per lane) were added to partially purified TCV RdRp reactions with or without the primers indicated, and the products were separated on 5% polyacrylamide/8 M urea gels and analyzed using a PhosphorImager. Lanes: C, sat-RNA C; CΔ5, CΔ6, and CΔ100, sat-RNA C with deletions of the 3′ terminal 5, 6, or 100 nt, respectively; CM4, sat-RNA C with four mismatch mutations that destabilize the base of the 3′ terminal hairpin (Fig. 1B); “+” or “−” indicate (+)-strand or (−)-strand template, respectively. (A–C) The mononucleotide label was omitted and replaced with the following oligoribonucleotide primers produced by T7 RNA polymerase transcription and labeled with [α-³²P]ATP: 6a, GACGGG-5′; 5, AAGGG-5′; 6b, CCCAGG-5′. One microgram of primer was used per reaction in A and B, and 10 μg of primer was used in C. Lanes 1 in A–C contain 356- and 256-nt markers. (D) The mononucleotide label was [α-³²P]ATP.