Figure 4.

Location of the 226/227 dinucleotide pair in the higher-order structure. (A) Secondary structure of Ψ^CES [12], a minimal element for dimerization, NC binding, and packaging of HIV-1 RNA, are shown. Nucleotide sequence of the NL4-3 Ψ^CES [10], which is identical to that reported for the solution NMR structure of HIV-1 Ψ^CES (PDB code: 2N1Q) [11], was used to construct the secondary structure. Arrows indicate the 226/227 dinucleotide analyzed in this study. Arrow heads indicate a dinucleotide at positions 291 and 292, which were placed near the 226/227 dinucleotides in the three-dimensional structure. (B) Three-dimensional structure of the HIV-1 NL4-3 Ψ^CES [11] used for molecular dynamics (MD) simulations. The 226/227 dinucleotide is marked by red. Structural elements of the Ψ^CES were highlighted by different colors: U5-AUG stem (purple: positions 106–115 and 334–343), SL1 (yellow: positions 243–254 and 264–277), SL2 (cyan: 282–300), SL3 (green: 312–325), and PBS stem-loop (skin: 125–131 and 217–223). (C) Enlarged view of the Ψ^CES region around the G226/A227 dinucleotide.