The dimerization initiation site (DIS) is an essential RNA element responsible for dimerization of HIV-1 genomic RNA through a kissing loop interaction. The DIS loop contains six auto-complementary nucleotides stabilized by 5'- and 3'-flanking purines. NCp7 chaperone protein catalyzes conversion of an intermediate DIS kissing dimer to a more thermodynamically stable extended duplex dimer in the presence of Mg2+. Sequence constructs intended to model the extended duplex, (DIS 21), and the kissing dimer, DIS23(GA)*DIS23(HxUC), were designed to examine the structural information and biochemical behaviors during maturation. We introduced the fluorescent labeling, 2-aminopurine (2-AP) into these RNA constructs, to finely probe structural transition and local dynamics accompanied by the formation of the DIS dimer. The 2-AP nucleotides were inserted either in the DIS loop or junction to study loop-loop interaction or purine base stacking conformation at the junction responding to the metal ion effect. High resolution NMR methods were then used to probe structural changes associated with mono versus divalent cation binding to the DIS dimers and also determine the Mg2+ binding sites. Significant chemical shift perturbations (CSP) were found upon Mg2+ binding and used to map structural changes. Further Mn2+ paramagnetic relaxation enhancement (PRE) experiments provided evidence for specific Mg2+ ion binding are localized around the 5' purine bases in both the extended duplex and kissing dimers with profound line broadening effects. Mapping the CSP and PRE data onto the available X-ray crystal and NMR solution structures allowed localization of specific Mg2+ ions at binding sites on the DIS dimers created by the unpaired flanking DIS loop purine nucleotides. Our data indicates that the conformations that are metal cation dependent. These findings are consistent with previous results that suggested a role for divalent metal cations in stabilizing the DIS kissing dimer structure and influencing its maturation to an extended duplex form through interactions with the DIS loop.