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. 1999 Aug;73(8):6307–6318. doi: 10.1128/jvi.73.8.6307-6318.1999

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Copyright © 1999, American Society for Microbiology

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FIG. 3 — Summary of nuclease digestion data for WT RSV RNA fragments. Lowest-free-energy secondary-structure diagrams for WT sequences are depicted (see Materials and Methods for a description of structure prediction). G residues (target of T₁ nuclease) in the viral RNA are underlined. Nucleotide sequences are numbered every 10 bases from the 5′ end of the RSV RNA genome. Brackets are used to designate several RNA-RNA duplexes. (A) Digestion of uncomplexed WT RNA fragments. A bold lowercase t indicates T₁ cleavages, where t t t t was the strongest cleavage site seen with 0.0009 U of T₁ per μl and t t t designates additional cleavage sites seen with 0.0009 U of T₁ per μl; t t describes moderate-cleavage sites seen with 0.003 U of T₁ per μl, and t describes slight cleavages with 0.003 U of T₁ per μl. A bold lowercase v indicates V₁ cleavages, where v v v was the strongest cleavage seen with 0.0001 U of V₁ per μl, v v was a strong cleavage seen with 0.0001 U of V₁ per μl, and v was a weak cleavage seen with 0.0001 U of V₁ per μl. A bold lowercase a indicates RNase A cleavages, where a a a a was the strongest cleavage seen with 0.3 pg of A per μl, a a a describes additional cleavages seen with 0.3 pg of A per μl, a a described additional cleavages seen with 1 pg of A per μl, and a designates cleavages seen only with 3 pg of A per μl. (B) Digestion of WT RNA fragments complexed with tRNA^Trp, where the tRNA^Trp sequences are shown in bold capital letters. Description of cleavages is as for panel A. (C) Changes in the digestion pattern when WT RNA fragments were complexed with tRNA^Trp. Arrows indicate how the nuclease digestion pattern changed as the WT fragments were complexed with the tRNA^Trp primer. Upward arrows indicate increased cleavage, while downward arrows indicate decreased cleavage. The number of arrows indicates the magnitude of the change. ↑ and ↓ indicate changes in the T₁ pattern, and indicate changes in the V₁ pattern, and and ↓ indicate changes in the A pattern. Absence of arrows means there was no change in the digestion pattern.

Inline graphic — Summary of nuclease digestion data for WT RSV RNA fragments. Lowest-free-energy secondary-structure diagrams for WT sequences are depicted (see Materials and Methods for a description of structure prediction). G residues (target of T₁ nuclease) in the viral RNA are underlined. Nucleotide sequences are numbered every 10 bases from the 5′ end of the RSV RNA genome. Brackets are used to designate several RNA-RNA duplexes. (A) Digestion of uncomplexed WT RNA fragments. A bold lowercase t indicates T₁ cleavages, where t t t t was the strongest cleavage site seen with 0.0009 U of T₁ per μl and t t t designates additional cleavage sites seen with 0.0009 U of T₁ per μl; t t describes moderate-cleavage sites seen with 0.003 U of T₁ per μl, and t describes slight cleavages with 0.003 U of T₁ per μl. A bold lowercase v indicates V₁ cleavages, where v v v was the strongest cleavage seen with 0.0001 U of V₁ per μl, v v was a strong cleavage seen with 0.0001 U of V₁ per μl, and v was a weak cleavage seen with 0.0001 U of V₁ per μl. A bold lowercase a indicates RNase A cleavages, where a a a a was the strongest cleavage seen with 0.3 pg of A per μl, a a a describes additional cleavages seen with 0.3 pg of A per μl, a a described additional cleavages seen with 1 pg of A per μl, and a designates cleavages seen only with 3 pg of A per μl. (B) Digestion of WT RNA fragments complexed with tRNA^Trp, where the tRNA^Trp sequences are shown in bold capital letters. Description of cleavages is as for panel A. (C) Changes in the digestion pattern when WT RNA fragments were complexed with tRNA^Trp. Arrows indicate how the nuclease digestion pattern changed as the WT fragments were complexed with the tRNA^Trp primer. Upward arrows indicate increased cleavage, while downward arrows indicate decreased cleavage. The number of arrows indicates the magnitude of the change. ↑ and ↓ indicate changes in the T₁ pattern, and indicate changes in the V₁ pattern, and and ↓ indicate changes in the A pattern. Absence of arrows means there was no change in the digestion pattern.