Phosphodiester models and mimics have been used widely to selleck inhibitor understand the mechanisms

of phosphodiesterases such as nucleases and ribozymes. This section discusses examples where one or more of the bridging or non-bridging oxygen atoms associated with the phosphodiester group has been exchanged for either sulfur or fluorine. The resulting analogues are often reactive, where their altered reactivity profiles are used to probe the nature of catalysis in enzyme active sites and/or binding to metal ions therein. Some of the most poignant recent additions to the mechanistic toolbox are the phosphorothiolates (Table 2, entry 1), where a bridging oxygen atom has been replaced by sulfur. These systems have received significant attention because synthetic advances have permitted their use in oligonucleotides [14, 15 and 16]. Phosphorothiolates can also elucidate O-Mg2+ ion interactions through soft metal ion GSI-IX chemical structure rescue experiments. More significantly, where a leaving

group oxygen is replaced by sulfur, the enhanced leaving group properties of thiolate anions accelerate their departure, sometimes obviating the need for catalysis, and potentially making previously kinetically silent processes rate-determining. In this vein, phosphorothiolate studies have illuminated HDV [17•] and VS [18] ribozyme systems alongside nucleobase substitutions to provide unequivocal evidence in support of general acid/base catalysis. Recent work in this area, primarily from the Piccirilli laboratory, has been reviewed [19•• and 20]. More subtle substitution of phosphodiesters can be effected through the use of isotopomeric compounds, such as 18-O

labelled species (Table 2, entry 2). Heavy atom isotope effects are challenging to determine aminophylline on a practical level, however, isotopic substitutions represent the least perturbing of all possible analogues. 5′-18O and 2′-18O isotopomeric analogues of the dinucleotide 5′-UpG-3′ were synthesised and the base-promoted cleavage kinetics of these phosphodiester systems were explored [21••]. Through these studies, the transition state for the 2′-O-transphosphorylation process was suggested to be late in nature, and solvent deuterium isotope effect studies suggest the prior formation of the 2′-alkoxide nucleophile rather than rate-determining general base catalysis by hydroxide ion. An extension of this, supplemented with computational studies, has been used to revisit the mechanism of ribonuclease A [22]. Fluorophosphonates present the possibility of concerted, diester-like transition states while offering the size and hydrogen bonding characteristics of monoesters [23]. This mixed character was used to explore the promiscuous proficiencies of phosphoryl transfer by alkaline phosphatase.