Structure and activity of LTR sequences from strains B1, B2, and subtype AE. A. Partial LTR sequence of subtypes B1, B2_S, B2_L, AE and X. The LTR region, spanning position -147 to +67 of reference strain B (LAI) is shown at the top. Dashes indicate nucleotides that are identical in subtype B(LAI), gaps are represented by dots. Restriction sites used in cloning are italicised and underlined. Boxes indicate motifs possibly involved in promoter function . Subtype AE has three unique transcription factor binding sites: an AP1 motif, a GABP motif and a CACCC box-binding factor motif [46,47]. The TAR hairpin sequence (position 176–232) is underlined. B. Structure of the TAR RNA secondary structure in different HIV-1 subtypes, using the structure of subtypes B(LAI) and X  as references. Nucleotide differences between the strains are boxed and nucleotide deletions are indicated by (black triangle). A detailed phylogenetic analysis of HIV-1 subtype B TAR sequences has been described previously [48,49]. C. Transcriptional activity of the HIV-1 LTR promoter sequences from strains B(LAI), X, B1, B2_S, B2_L, and AE. Transcriptional activity was tested in the presence of increasing concentrations of Tat. The value is the average of four independent measurements; the standard deviation is indicated.