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Nucleic Acids Research, 1991, Vol. 19, No. 10 2747-2753
© 1991

CHEMISTRY

Rate limiting P-O(5') bond cleavage of RNA fragment: ab initio molecular orbital calculations on the base-catalyzed hydrolysis of phosphate

Kazunari Taira, Tadafumi Uchimaru1, Kazutoshi Tanabe1, Masami Uebayasi and Satoshi Nishikawa

Fermentation Research Institute Tsukuba Science City 305, Japan 1National Chemical Laboratory for Industry, Agency of Industrial Science & Technology, MITI Tsukuba Science City 305, Japan

Received December 28, 1990. Revised March 26, 1991. Accepted March 26, 1991.

In order to examine the energetics In base-catalyzed hydrolysis of RNA, a tentative pentacoordinated intermediate (3) has been characterized by molecular orbital calculations. Ab initio studies at the level of3-21G* indicate that, under the Cs symmetry restricted conditions, the P-O(2) bond possessing antiperiplanar (app) lone pair electrons (Ip) on the equatorial oxygen (O(3)) can be cleaved with almost no barrier (TS1 transition state; 0.08 kcal mol–1), from the pentacoordinated Intermediate (3) of base-catalyzed hydrolysis of phosphate, compared to the P-O(5) bond (TS2 transition state; 28.9 kcal mol–1) which lacks app Ip assistance from O(3). The dianionic intermediate, however, loses the TS1 transition state thus its property as an intermediate when the Cs restriction Is removed. The analysis of the entire potential energy surface enables us to conclude that, in a related system examined by Lim and Karplus ((1990) J. Am. Chem. Soc., 112, 5872–5873) for attack by OH– on ethylene phosphate monoanion, the TS1 transition state had also been lost and thus no intermediate had been found. These results further support our earlier conclusions (Taira et al. (1990) Protein Engineering, 3, 691 – 701) of rate limiting transition state possessing extended P-O(5') bond breaking character (the TS2 transition state) In the base-catalyzed hydrolysis of RNA (see also references 6 and 7). Finally, although the lack of 2',3'-migratlon of phosphate moieties in basic condition appears to be in accord with the short-lived intermediate, it really does not prove the absence of the intermediate. The detail will be discussed in the text.


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 Proc. Natl. Acad. Sci. USAHome page
D.-M. Zhou, L.-H. Zhang, and K. Taira
Explanation by the double-metal-ion mechanism of catalysis for the differential metal ion effects on the cleavage rates of 5'-oxy and 5'-thio substrates by a hammerhead ribozyme
PNAS, December 23, 1997; 94(26): 14343 - 14348.
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