AN NMR-STUDY OF THE HIV-1 TAR ELEMENT HAIRPIN

The TAR hairpin is an important part of the 5' long terminal repeat of HIV-1 and appears to be recognized by a cellular protein. A 14-base m odel of the native TAR hairpin 5'-GAGC[CUGGGA]-GCUC3' (loop bases in s quare brackets) has been studied by proton, phosphorus, and natural ab undance carbon NMR; these results are compared to other published NMR studies of the TAR hairpin. Assignments of all nonexchangeable protons and of all the stem-exchangeable protons have been made, as well as a ll phosphorus and many carbon resonances. Large J1'2' and J3'4' proton -proton coupling in the C5, G8, and G9 sugars indicate an equilibrium between C2'- and C3'-endo forms; these data show a dynamic loop struct ure. We see three broad imino resonances that have not been reported b efore; these resonances are in the right region for unbonded loop imin o protons. These peaks suggest the protons are protected from fast exc hange with the solvent by the structure of the hairpin loop. Simulated annealing and molecular dynamics with 148 distance constraints, 11 hy drogen bonds, and 84 torsion angle constraints showed a wide variety o f structures. Certain trends are evident, such as continuation of the A-form helix on the 3' side of the hairpin loop. The ensemble of calcu lated structures agree with most chemical modification data.