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. Author manuscript; available in PMC: 2008 Nov 1.
Published in final edited form as: Microbes Infect. 2007 Sep 14;9(14-15):1581–1589. doi: 10.1016/j.micinf.2007.09.008

Figure 2. Identification of HIV-1 integration site in the lymphoma cells with genome walking.

Figure 2

(A) Sequence of the HIV-1 5’-LTR (upper panel) and 3’-LTR (lower panel) insertion site in the lymphoma genome. Whole sequences of PCR products are registered as GenBank DQ355432 (5’-LTR, 190 bp) and DQ117603 (3’-LTR, 1.5 kbp), respectively. The sequence of the lymphoma genome is shown in the lower line in black letters. The upper colored line indicates the HIV-1 LTR sequence (blue, GenBank K03455 or AF538307) and STAT3 genomic sequence (violet, GenBank AY572796). HIV-1 intervening sequence between 5’LTR and gag is indicated by green. Duplication of the cellular 5 bp (GAATC) and additional dinucleotides (TG in 5’-LTR and CA in 3’-LTR) by HIV-1 integrase are underlined. DraI site is indicated by italics. (B) PCR for the junction region of 3’LTR and STAT3 gene using HIV3LTR-F and Stat3intron-R primers (see Fig. 3D). 1, PBMCs from a healthy donor; 2, HIV-1-positive Molt4 cell line; 3, lymphoma cells with HIV-1integration; 4, KS lesion from the patient; 5, AIDS-related lymphoma from an unrelated patient; 6, lymphoma from a non-HIV-1infected patient; 7, BCBL-1 (KSHV-positive B cell line); 8, No DNA. The lower panel shows the results of an internal control (β-globin gene). (C) PCR of genomic DNA with a STAT3-intron forward primer (F in this figure, Stat3-intronF2) in combination with 5’ LTR reverse primers (lanes 1–6, 55R, 78R, 348R, 495R, 563R and 612R), and a reverse primer positioning between 5’LTR and gag (lane 7, 676R). The upper panel shows the positions of these primers. A 188 bp product was identified when the 676R primer was used with the STAT3 intron primer (lane 7). If the 5’LTR was intact, the predicted size of this amplicon would have been 777 bp. (D) Map of the defective HIV-1 insertion site in the STAT3 gene. Violet numbers indicate the number in GenBank AY572796 (STAT3). Blue boxes are HIV-1 genomes.