1. A HIV-1 -AUG1 DMS CMCT Control V1 +Mg2+ +Mg2+ -Mg2+ -Mg2+ C T A G G640 G650 A660 A665 A670 A675 C T A G 1 2 3 4 5 6 7

2. B HIV-1 AUG1 DMS CMCT V1 Control +Mg2+ +Mg2+ -Mg2+ -Mg2+ G C T A A500 C510 G520 C525 A530 C535 C T A G 1 2 3 4 5 6 7

3. C HIV-1-AUG1 DMS CMCT V1 Control +Mg2+ +Mg2+ -Mg2+ -Mg2+ G C T A G400 A410 U420 A430 A440 A450 C T A G 1 2 3 4 5 6 7

4. D SIVMAC-AUG1 DMS CMCT CONTROL V1 +Mg2+ +Mg2+ -Mg2+ -Mg2+ C T A G C880 G890 A895 A900 C T A G 1 2 3 4 5 6 7

5. S3 : Examples of a typical probing experiments. Probing experiments were performed as described in material and methods. RNAs were reverse sequenced with reverse transcriptase (lanes CTAG), and a mock-treated RNA was transcribed in standard RT buffer to monitor RNA specific RT stops (lane 1 - control). RNAse V1 probing revealing paired positions was conducted in native conditions only because its activity requires Mg2+ ions (lane 2, 0.01u; lane 3, 0.1u). DMS and CMCT probing were performed both in absence (lanes 4 and 6 respectively) and presence of Mg2+ ions (lanes 5 and 7 respectively). Hallmarks are indicated on the left side of the gel. A - HIV-1 region from 630 to 680 B - HIV-1 region from 500 to 535 C – HIV-1 region from 400 to 460 D – SIVMAC region from 880 to 905