Self-association of adenine-dependent hairpin ribozymes.
Hairpin ribozymes are flexible molecules that catalyse reversible self-cleavage after the docking of two independently folded internal loops, A and B. The activities, self-association and structures in solution of two 85 base adenine-dependent hairpin ribozymes (ADHR1 and ADHR2) were studied by native gel electrophoresis, analytical centrifugation, and small angle neutron scattering. Bi-molecular RNA interactions such as linear-linear, loop-loop, loop-linear or kissing interactions have been found to be important in the control of various biological functions, and hairpin loops present rich potential for establishing both intra- and intermolecular interactions through standard Watson-Crick base pairing or non-canonical interactions. Similar results were obtained for ADHR1 and ADHR2. At room temperature, they indicated end-to-end self-association of the ribozymes in rod-like structures with a cross-section corresponding to two double strands side-by-side. Dimers, which predominate at low concentration ( approximately 0.1 mg/ml), associate into longer rods, with increasing concentration ( approximately 1 mg/ml). Above 65 degrees C, the dimers and rods dissociated into compact monomers, with a radius of gyration similar to that of tRNA (about 70 bases). The dimers were non-active for catalysis, which suggests that dimer formation, probably by preventing the correct docking of loops A and B, could act as an inhibition mechanism for the regulation of hairpin ribozyme catalysis.
Li
Yan-Li
YL
Institut Jacques-Monod,Université Paris VI, Tour 43, 2 place Jussieu, 75251, Paris Cedex 05, France.
Maurel
Marie-Christine
MC
Ebel
Christine
C
Vergne
Jacques
J
Pipich
Vitaliy
V
Zaccai
Giuseppe
G
D000225:Adenine / Q000378:metabolism*; D019281:Dimerization; D007700:Kinetics; D008954:Models, Biological; D009154:Mutation; D033363:Neutron Diffraction; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D053838:Scattering, Small Angle; D013696:Temperature; D014461:Ultracentrifugation
D016337:RNA, Catalytic; C418481:hairpin ribozyme; D000225:Adenine