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. 2006 Sep 27;80(24):11920–11934. doi: 10.1128/JVI.01483-06

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FIG.4. — Ty1 LTR junction formation. (A) The structure of a Ty1 two-LTR junction molecule containing a circle junction (CJ). The LTR domains unique 3′ (U3), repeated (R), and unique 5′ (U5) are shown (6, 75). The positions of the PCR primers CJ5784w and CJ125c used to amplify LTR junction molecules and the positions of PPT (polypurine tract) (used to initiate plus-strand DNA synthesis) and the primer binding site (PBS) (tRNA-Met anneals to initiate minus-strand reverse transcription) are shown. Below are PCR products, separated by agarose gel electrophoresis, in the size range expected for a canonical circle junction (CJ = 259 bp) amplified with primers CJ5784w and CJ125c and genomic DNA from cells expressing wild-type Ty1 (WT, galactose), an in-2600 mutant (in-2600, galactose), cells grown under repressing conditions (WT, glucose), or a reaction mixture lacking yeast DNA (− template). When the in-2600 mutant was analyzed, a minor, bottom band (labeled B) was present in addition to a major, top band (T) that was closer to the size expected for a canonical CJ. Primers specific to the LEU2 gene were used to show that genomic DNA was PCR competent. (B) LTR junction molecules obtained from wild-type Ty1. Unidirectional deletions into U5 or U3 are at the top and designated by the arrow. A canonical CJ is depicted by the striped bar, and a canonical CJ with intervening DNA inserted between the LTR ends is shown by the open bar and asterisk. LTR junction molecules with deletions into U5 (PPT-proximal LTR; also refer to panel A) are on the left (filled bars, minus numbering), while those with deletions into U3 (PBS-proximal LTR) are on the right (filled bars, plus numbering). LTR junction molecules with intervening DNA are designated by asterisks (see file S1 in the supplemental material). (C) LTR junction molecules obtained from an in-2600 mutant enriched for T-band sequences (Fig. 4A). The resolution of the figure is about 5 bp.

FIG.4. — Ty1 LTR junction formation. (A) The structure of a Ty1 two-LTR junction molecule containing a circle junction (CJ). The LTR domains unique 3′ (U3), repeated (R), and unique 5′ (U5) are shown (6, 75). The positions of the PCR primers CJ5784w and CJ125c used to amplify LTR junction molecules and the positions of PPT (polypurine tract) (used to initiate plus-strand DNA synthesis) and the primer binding site (PBS) (tRNA-Met anneals to initiate minus-strand reverse transcription) are shown. Below are PCR products, separated by agarose gel electrophoresis, in the size range expected for a canonical circle junction (CJ = 259 bp) amplified with primers CJ5784w and CJ125c and genomic DNA from cells expressing wild-type Ty1 (WT, galactose), an in-2600 mutant (in-2600, galactose), cells grown under repressing conditions (WT, glucose), or a reaction mixture lacking yeast DNA (− template). When the in-2600 mutant was analyzed, a minor, bottom band (labeled B) was present in addition to a major, top band (T) that was closer to the size expected for a canonical CJ. Primers specific to the LEU2 gene were used to show that genomic DNA was PCR competent. (B) LTR junction molecules obtained from wild-type Ty1. Unidirectional deletions into U5 or U3 are at the top and designated by the arrow. A canonical CJ is depicted by the striped bar, and a canonical CJ with intervening DNA inserted between the LTR ends is shown by the open bar and asterisk. LTR junction molecules with deletions into U5 (PPT-proximal LTR; also refer to panel A) are on the left (filled bars, minus numbering), while those with deletions into U3 (PBS-proximal LTR) are on the right (filled bars, plus numbering). LTR junction molecules with intervening DNA are designated by asterisks (see file S1 in the supplemental material). (C) LTR junction molecules obtained from an in-2600 mutant enriched for T-band sequences (Fig. 4A). The resolution of the figure is about 5 bp.