Mg2+-induced variations in the conformation and dynamics of HIV-1 TAR RNA probed using NMR residual dipolar couplings

The effects of divalent Mg2+ on the conformation and dynamics of the stem-loop transactivation response element (TAR) RNA from HIV-1 have been characterized using NMR residual dipolar couplings (RDCs). Order matrix analysis of one bond C-13-H-1 RDCs measured in TAR at [Mg2+]:[TAR] stoichiometric ratios of similar to3:1 (TAR(3.0 Mg)) and similar to4.5:1 (TAR(4.5 Mg)) revealed that Mg2+ reduces the average inter-helical angle from 47(+/-5)degrees in TAR(free) to 5(+/-7)degrees in TAR(4.5 Mg). In contrast to the TAR(free) state, the generalized degree of order for the two stems in TAR(4.5 Mg) is found to be identical within experimental uncertainty indicating that binding of Mg2+ leads to an arrest of inter-helical motions in TAR(free). Results demonstrate that RDC-NMR methodology can provide new insight into the effects of Mg2+ on both the conformation and dynamics of RNA. (C) 2003 Elsevier Science Ltd. All rights reserved.