Putative HIV and SIV G-Quadruplex Sequences in Coding and Noncoding Regions Can Form G-Quadruplexes

Figure 2

Strategy and searching criteria of putative G-quadruplex sequences. Randomly selected genomic sequences of HIV-1, HIV-2, and SIV from NCBI Gene database were analyzed (panel (a)). The criteria used to determine putative G-quadruplex sequences are listed in panel (b). represents the total number of nucleotide residues between G-runs (G₃ and G₂), and this value is restricted at the interval . Specific criteria were applied in cases in which G-runs consisted of more than four Gs (c); for instance, G₇ is formed of either two G₃ islands interrupted with one G (yellow square) or one G3 and G2 connected with two “yellow” Gs. The occurrence of putative sequences was researched by BLAST in other viruses listed in the Gene database. Positive and negative examples of the search procedure are shown in panels (d) and (e).

(a)

(b)

(c)

(d)

(e)