THE STRUCTURE OF AN RNA KISSING HAIRPIN COMPLEX OF THE HIV TAR HAIRPIN LOOP AND ITS COMPLEMENT

We have used nuclear magnetic resonance (NMR) to obtain the structure of an RNA ''kissing'' hairpin complex formed between the HIV-2 TAR hai rpin loop and a hairpin with a complementary loop sequence. Kissing ha irpins are important in natural antisense reactions; their complex is a specific target for protein binding. The complex has all six nucleot ides of each loop paired to form a bent quasicontinuous helix of three coaxially stacked helices: two stems plus a loop-loop interaction hel ix. Experimental constraints derived from heteronuclear and homonuclea r NMR data on C-13 and N-15-labeled RNA led to a structure for the loo p-loop helix with an average root-mean-square deviation of 0.83 (+/-0. 10) A for 33 converged structures relative to the average structure. T he loop-loop helix of the kissing complex is distorted compared to A-f orm RNA. Its major groove is blocked by the phosphodiester bonds that connect the first loop residue of each hairpin with its own stem, and it is flanked two negatively charged phosphate clusters. The loop-loop helix has alternating helical twists between adjacent base-pairs. The base-pairs at the helix junctions are overwound and three base-pairs near the helix junctions adopt high propeller twists. All these change s reduce the distance needed for the bridging phosphodiester bends con necting each stem and loop to cross the major groove of the loop-loop helix, and result in a deformed RNA helix with localized perturbations in the minor groove surface. The alternating helical tu ist pattern, plus other distortions in the loop-loop helix may be important for Rom protein recognition of the kissing hairpin complex. (C) Academic Pres s Limited.