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. 2003 Jan;77(2):1469–1480. doi: 10.1128/JVI.77.2.1469-1480.2003

FIG. 2.

FIG. 2.

HIV-1 2-LTR circle junction fragment sequence, with PCR and cloning primers, and the probe. A portion of the full-length 2-LTR junction sequence is presented, along with the locations of various primers and the probe. Nucleotide positions in the pNL4-3 sequence are denoted at the top in italics. The position of the 2-LTR junction is also shown. This sequence region contained in the pJB1041 plasmid was used as a standard template for real-time PCR. The legend depicting the various regions (R, U5, and U3) is shown at the bottom of the figure. The primers and probe used to quantify full-junction 2-LTR circles are HIV-SS-F4, HIV-LTR-R5, and P-HUS, SS1, respectively. Total 2-LTR circles are detected using HIV-SS-F4, HIV-LTR-R3, and P-HUS-SS1. The CJ-F and CJ-R primers have been described as the upstream and downstream primers, respectively, by Julias et al. (37).