Global structure and flexibility of hairpin ribozymes with extended terminal helices

Global structure and flexibility of three different hairpin ribozyme constr ucts have been analyzed by measuring their electric dichroism decay in vari ous buffers at temperatures between 2 and 30 degrees C. The hairpin ribozym e is characterized by two independently folding domains A and B that are co nnected through a hinge and have to interact to enable catalysis. The analy zed constructs feature extended terminal helices 1 and 4 with 27 and 25 bp, respectively, to increase the sensitivity of the molecular rotational diff usion time constants with respect to the interdomain bending angle. Constru cts HP1 and HP2 cannot cleave because of a G(+1)A change at the 3'-side of the cleavage site; in HP1 the helices 2 and 3 that flank the hinge form a c ontinuous double helical segment; in HP2 and HP3, a six nucleotide bulge co nfers flexibility to the expected bending site; HP3 is a cleavable form of HP2 with a G(+1)-base. For comparison, a standard RNA double helix with 72 bp was included in our analysis. The dichroism decay curves of the hairpin constructs after pulses of low electric field strengths can be fitted to si ngle exponentials tau(s), whereas the curves after pulses of high field str engths require two exponentials. In all cases, time constants increase with RNA concentration, indicating intermolecular interactions. Extrapolation o f the tau(s) values measured in standard buffer (50 mM Tris (pH 7.5) and 12 mM MgCl2) to zero RNA concentration provide values of 112, 93, and 73 ns f or HP1, HP2 and HP3, respectively, at 30 degrees C, indicating increasingly compact structures. The 72 bp RNA reference under corresponding conditions did not show a dependence of its decay time constant on the RNA concentrat ion nor on the field strength; its time constant is 175 ns (standard buffer , 30 degrees C). The observation of two relaxation processes for the hairpi n constructs at high field strengths indicates stretching to a more elongat ed state; the fast process with a time constant of the order of 50 ns is as signed to reversion of stretching, the slow process to overall rotation. Th e overall rotational time of the stretched state at 20 degrees C is close t o that for a completely stretched rigid state; at 30 degrees C the experime ntal values are around 70% of that expected for a completely stretched rigi d state, indicating flexibility and/or residual bending. Bead models were c onstructed to simulate dichroism decay curves. The time constants observed for the 72 bp RNA are as expected for a rigid rod with a rise of 2.8 Angstr om per base-pair. Based on this rise per base-pair for models of a V and a Y-shape, we estimate average bending angles of 80(+/-20)degrees and 105 (+/ -25)degrees, respectively, for the catalytically active hairpin ribozyme HP 3. The energy required for stretching is of the order of the thermal energy . (C) 1999 Academic Press.