The cleavage and isomerisation of uridine 3'-alkylphosphates was studied in the presence of a dinuclear Zn(2+) complex, 3. The rate acceleration of the cleavage by 1 mM 3 is approximately 10(6)-fold under neutral conditions. Most remarkably, the complex also promotes the isomerisation of phosphodiester bonds, although the rate-enhancement is more modest: under neutral conditions complex 3 (1 mM) catalyses isomerisation by about 500-fold. The observation of this reaction shows that the reactions of these substrates catalysed by 3 proceed through a stepwise mechanism involving an intermediate phosphorane. A β(lg) value of -0.92 was determined for the 3-promoted cleavage reaction, and modest kinetic solvent deuterium isotope effects ranging from 1.5 to 2.8 were observed. Isomerisation was less sensitive to the nature of the esterifying group, with a β value of -0.5, and the kinetic solvent deuterium isotope effects were less than 1.5. Most of these characteristics of the 3-promoted cleavage are very similar to those for the cleavage of nucleoside 3'-phosphotriesters. These data are explained by a mechanism in which the complex primarily acts as an electrophilic catalyst neutralising the charge on the phosphate and stabilising an intermediate phosphorane, with general acid catalysis promoting the cleavage reaction. In contrast to the behaviour of triesters, isomerisation is significantly slower than cleavage; this suggests that the changes in geometry that occur during isomerisation lead to a much less stable complex between 3 and the phosphorane intermediate.

Background: Protein allostery can be communicated purely through altered entropy.Results: Altered cAMP binding strength in CAP results in changes to entropy-driven allostery.Conclusion: The requirement to maintain allostery constrains evolution of the ligand-binding site in CAP.Significance: Entropy-driven processes can constrain amino acid covariation in evolution.

Phosphoryl group transfer is central to genetic replication, cellular signalling and many metabolic processes. Understanding the mechanisms of phosphorylation and phosphate ester and anhydride cleavage is key to efforts towards biotechnological and biomedical exploitation of phosphate-handling enzymes. Analogues of phosphate esters and anhydrides are indispensable tools, alongside protein mutagenesis and computational methods, for the dissection of phosphoryl transfer mechanisms. Hydrolysable and non-hydrolysable phosphate analogues have provided insight into the nature and sites of phosphoryl transfer processes. Kinetic isotope effects and crystallography using transition state analogues have painted more detailed pictures of transition states and how enzymes work to stabilise them.

An azide-functionalized 12-armed Buckminster fullerene has been monosubstituted in organic media with a substoichiometric amount of cyclooctyne-modified oligonucleotides. Exposing the intermediate products then to the same reaction (i.e., strain-promoted alkyne–azide cycloaddition, SPAAC) with an excess of slightly different oligonucleotide constituents in an aqueous medium yields molecularly defined monofunctionalized spherical nucleic acids (SNAs). This procedure offers a controlled synthesis scheme in which one oligonucleotide arm can be functionalized with labels or other conjugate groups (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid, DOTA, and Alexa-488 demonstrated), whereas the rest of the 11 arms can be left unmodified or modified by other conjugate groups in order to decorate the SNAs’ outer sphere. Extra attention has been paid to the homogeneity and authenticity of the C 60 -azide scaffold used for the assembly of full-armed SNAs.

The transesterification of uridine 3'-phosphodiesters with a wide range of leaving group alcohols has been studied in the presence of monometallic and bimetallic complexes. The catalysis of isomerization of the phosphodiester bond was studied with a nucleoside 3'-phosphonate as a substrate. The results obtained are consistent with a step-wise mechanism, where metal ions are able to enhance both the nucleophilic attack and the departure of the leaving group. The mechanism of the catalysis depends on the acidity of the catalyst and of the leaving group alcohol: a change from general base catalysis to general acid catalysis is proposed. Catalysis of the isomerization requires efficient stabilization of the phosphorane by strong interactions with the catalyst. Catalytic strategies utilised by bimetallic complexes are also briefly discussed.

Studies on the mechanism of transesterification reactions of nucleoside 3′-phosphoesters using b LG values as a mechanistic tool are discussed in this mini review. Our recent observation that a dinuclear metal ion complex enhances both the cleavage and isomerisation is discussed in the light of previous studies. /journal/poc a Calculated from second-order rate constants determined NaOH solutions. b From second-order rate constants obtained from a non-linear fit of log k vs [H + ]. c From second-order rate constants determined in bicarbonate buffers.

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Additional information:Use policyThe full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that:• a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders.Please consult the full DRO policy for further details.