Evidence for the role of solvated metal hydroxide in the hammerhead cleavage mechanism.
The log of the rate of the chemical step of hammerhead cleavage in Mg2+ increases linearly with pH between pH 5.7 and 8.9. A slope of approximately 1 indicates that a single deprotonation is required for cleavage. Hammerhead pH-rate profiles with Ca2+, Mn2+, Co2+, and Cd2+ correlate well with the pKa's of these ions in water. This relationship between the pKa's and the pH-rate profile suggests that a metal hydroxide bound to the hammerhead RNA acts as the base in the cleavage mechanism.
Dahm
S C
SC
Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.
Derrick
W B
WB
Uhlenbeck
O C
OC
D001483:Base Sequence; D002413:Cations, Divalent / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D006868:Hydrolysis; D006878:Hydroxides / Q000737:chemistry; D008670:Metals / Q000737:chemistry*; D008969:Molecular Sequence Data; D016337:RNA, Catalytic / Q000737:chemistry*; D012367:RNA, Viral / Q000737:chemistry; D012997:Solvents / Q000737:chemistry
D002413:Cations, Divalent; D006878:Hydroxides; D008670:Metals; D016337:RNA, Catalytic; D012367:RNA, Viral; D012997:Solvents