The mechanism of the hammerhead ribozyme.
The rate of cleavage of a 13-mer substrate by an all-RNA ribozyme with 2 10-mer hybridising arms (TAT RA), appears to be limited by a conformational change involving the longer than necessary arms. The same limitation does not apply to a similar ribozyme with DNA arms (TAT RB) or to an all-RNA ribozyme with only 6 hybridising bases on each arm (TAT RA 6x2). The limitation does not arise in the hybridisation step nor in the dissociation of products. An extra step involving a conformational change of the pre-formed ribozyme-substrate prior to cleavage is introduced to explain the observed kinetics.
Hendry
P
P
CSIRO, Division of Biomolecular Engineering, North Ryde, NSW, Australia.
McCall
M J
MJ
Lockett
T J
TJ
D001483:Base Sequence; D004247:DNA / Q000378:metabolism; D006863:Hydrogen-Ion Concentration; D007700:Kinetics; D008954:Models, Biological; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D009843:Oligoribonucleotides / Q000737:chemistry; D012313:RNA / Q000378:metabolism; D016337:RNA, Catalytic / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D013379:Substrate Specificity
D009838:Oligodeoxyribonucleotides; D009843:Oligoribonucleotides; D016337:RNA, Catalytic; D012313:RNA; D004247:DNA