Fig. 2

Secondary structure of the HIV-1 5´-UTR in wild type and Pr- HIV-1. (a) Secondary structure model for HIV-1 wild type 5´-UTR. The secondary structure model was built using RNAstructure software based on the reactivities determined in this study. The low reactivities seen for nucleotides G79 to C85 (grey box) were proposed to result from an interaction with downstream sequences G443 to C449 [19]. Similarly, The low reactivities of the grey-boxed nucleotides in the DIS loop (nts 257–262) have been proposed to result from pairing with a homologous viral RNA molecule in the viral RNA dimer. The AUG start codon is boxed in black. (b) The difference in SHAPE reactivities of Pr- viral 5´-UTR relative to the reactivities of wild type 5´-UTR. The difference in SHAPE reactivities between Pr- and wild type 5´-UTRs were calculated by subtracting the sum of the standard deviations at each nt position from the absolute value of the difference of reactivities at every position for each data set (|(reactivity^Pr-)-(reactivity^wt)|-(Std^Pr- + Std^wt)). A zero value was assigned to positions where the result was negative, implying that the error is higher than the difference in reactivities. Positive values indicate that the reactivity toward NMIA at the specified nucleotides is higher in the Pr- virions. The calculations and the graph plot were drawn using Excel from the Microsoft Office Package