NMR study on the impact of metal ion binding and deoxynucleotide substitution upon local structure and stability of a small ribozyme.
We have studied a very small ribozyme described earlier which requires the presence of soft metal ions like manganese or cadmium. It consists of only three uridines as ribozyme, cleaving the sequence 5'-GAAA-3' after the guanosine. We have set out to characterize the metal ion binding in this system by NMR spectroscopy and the impact of the ribose 2'-OH group of the cleavable nucleotide upon local structure. NMR results indicate a high degree of regularity and order in the pyrimidine-rich ribozyme strand, and high flexibility within the purine-rich substrate. The guanosine 2'-hydroxy group adjacent to the cleavage site was found to have a profound effect upon the structure, apparently destabilizing a stacked arrangement. Metal ions were found to bind in a rather unspecific way, however, in the presence of higher amounts of divalent ions a preference in the vicinity of the cleavage site could be observed. 113Cd NMR spectra suggest a specific binding of Cd2+ ions to the RNA.
Vogtherr
M
M
Laboratorium für Biochemie der Universität Bayreuth, Germany.
Limmer
S
S
D000241:Adenosine; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D002104:Cadmium / Q000378:metabolism*; D002413:Cations, Divalent; D014644:Genetic Variation; D006151:Guanosine; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry; D017354:Point Mutation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D002413:Cations, Divalent; D009843:Oligoribonucleotides; D016337:RNA, Catalytic; D002104:Cadmium; D006151:Guanosine; D000241:Adenosine