Issue 2, 2010

Phosphorane intermediate vs. leaving group stabilization by intramolecular hydrogen bonding in the cleavage of trinucleoside monophosphates: implications for understanding catalysis by the large ribozymes

Abstract

Hydrolysis of 2′,3′-O-methyleneadenosin-5′-yl 5′-O-methyluridin-2′-yl 5′-O-methyl-2′-trifluoroacetamido-2′-deoxyuridin-3′-yl phosphate (1b) has been followed by HPLC over a wide pH range to study the effects of potential hydrogen bonding interactions of the 2′-trifluoroacetamido function on the rate and product distribution of the reaction. At pH < 2, decomposition of 1b (and its 3′,3′,5′-isomer 1a) is first-order in hydronium-ion concentration and cleavage of the P–O3′ bond of the 2′-trifluoroacetamido-modified nucleoside is slightly favored over cleavage of the P–O5′ bond. Between pH 2 and 4, the overall hydrolysis is pH-independent and the P–O3′ and P–O5′ bonds are cleaved at comparable rates. At pH 5, the reaction becomes first-order in hydroxide-ion concentration, with P–O3′ bond cleavage predominating. At 10 mmol L−1 aqueous sodium hydroxide, no P–O5′ bond cleavage is observed. Compared to the 2′-OH counterpart 2, a modest rate enhancement is observed over the entire pH range studied. The absence of P–O5′ fission under alkaline conditions suggests hydrogen bond stabilization of the departing 3′-oxyanion by the neighboring 2′-trifluoroacetamido function.

Graphical abstract: Phosphorane intermediate vs. leaving group stabilization by intramolecular hydrogen bonding in the cleavage of trinucleoside monophosphates: implications for understanding catalysis by the large ribozymes

Supplementary files

Article information

Article type
Paper
Submitted
19 Jun 2009
Accepted
13 Oct 2009
First published
19 Nov 2009

Org. Biomol. Chem., 2010,8, 349-356

Phosphorane intermediate vs. leaving group stabilization by intramolecular hydrogen bonding in the cleavage of trinucleoside monophosphates: implications for understanding catalysis by the large ribozymes

T. Lönnberg and M. Laine, Org. Biomol. Chem., 2010, 8, 349 DOI: 10.1039/B912042D

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