Nucleobase catalysis in the hairpin ribozyme.
RNA catalysis is important in the processing and translation of RNA molecules, yet the mechanisms of catalysis are still unclear in most cases. We have studied the role of nucleobase catalysis in the hairpin ribozyme, where the scissile phosphate is juxtaposed between guanine and adenine bases. We show that a modified ribozyme in which guanine 8 has been substituted by an imidazole base is active in both cleavage and ligation, with ligation rates 10-fold faster than cleavage. The rates of both reactions exhibit bell-shaped dependence on pH, with pK(a) values of 5.7 +/- 0.1 and 7.7 +/- 0.1 for cleavage and 6.1 +/- 0.3 and 6.9 +/- 0.3 for ligation. The data provide good evidence for general acid-base catalysis by the nucleobases.
Wilson
Timothy J
TJ
Cancer Research UK Nucleic Acid Structure Research Group, The University of Dundee.
Ouellet
Jonathan
J
Zhao
Zheng-Yun
ZY
Harusawa
Shinya
S
Araki
Lisa
L
Kurihara
Takushi
T
Lilley
David M J
DM
D000241:Adenosine / Q000737:chemistry / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites; D002384:Catalysis; D006151:Guanosine / Q000737:chemistry / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007093:Imidazoles / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry* / Q000378:metabolism
D007093:Imidazoles; D016337:RNA, Catalytic; C418481:hairpin ribozyme; D006151:Guanosine; C029899:imidazole; D000241:Adenosine