Phosphorothioate ion

Akerfeldt2 reported that the hydrolysis of the phosphorothioate ion in alkaline medium is catalyzed by silicone grease. It is therefore recommended that the ground-glass joints of the apparatus not be treated with silicone grease. 

Phosphorothioate ions are also 0,S-ambident. Their reactions with alkyl halides and sulfenyl chlorides occur at the sulfur (25). 

As in the case of inorganic phosphorothioate ions and salts of the type (RO)2POS M+, there arise three possible formnlae for salts of phosphinothioic acid R2POS" M. It appears from spectroscopic evidence that thiono, thiolo or mesomeric structures may exist in different salts, as weU as arrangements in which the metal atom is covalently bound to either the O or the S atom. The electronegativity of the metal atom and steric effects from the group R are liable to influence this situation. 

Puma, P., Duffey, D., and Dawidczyk, P., U.S. Patent appl. 94,944, Purification of oligodeoxyribonucleotide phosphorothioates using DEAE-5PW anion ion-exchange chromatography and hydrophobic interaction chromatography, 1994. 

The methanolyses of a series of <9,0-diethyl 0-aryl phosphates (101 X = O) and 0,0-diethyl 5-aryl phosphorothioates (101 X = S) promoted by methoxide and two metal ion systems, (La3+)2(MeO )2 and a complex of Zn2+ (MeO-) with 1,5,9-triazacyclododecane (79 M = Zn), has been studied in methanol at 25 °C. The kinetic data for the metal-catalysed reactions were analysed in terms of a common mechanism where there is extensive cleavage of the P-XAr bond in the transition state. The relevance of these findings to the mechanism of action of a phosphotriesterase enzyme present in a soil bacterium that hydrolyses paraoxon was discussed.100... 

Murphy AT, Brown-Augsburger P, Yu RZ, Geary RS, Thibodeaux S, Ackermann BL. Development of an ion-pair reverse-phase liquid chromatographic/tandem mass spectrometry method for the determination of an 18-mer phosphorothioate oligonucleotide in mouse liver tissue. Eur J Mass Spec 2005 11(2) 209-15. 

Metelev, V., and Agrawal, S. (1992). Ion-exchange high-performance liquid chromatography analysis of oligodeoxyribonucleotide phosphorothioates. Anal. Biochem. 200, 342-346. 

Figure 4.5 Structures of malathion impurities compound A, 0,0,S-trimethyl phosphorodithioate compound B, 0,0,S-trimethyl phosphorothioate compound C, 0,S,S-trimethyi phosphorodithioate compound D, 0,S-dimethyl S-l,2-di (ethoxycarbonyl) ethyl phosphorodithioate (also known as isoma lath ion).

The Gl ribozyme reaction depends on the presence of divalent metal ions but as indicated above, the binding of these ions plays multiple roles that include folding and enhancing substrate binding affinities (59). The rate of the chemical step is Mg(2- -) dependent, but these data do not distinguish between direct or indirect roles, or a combination of both. As indicated above, distinguishing active site metal ions from what has been referred to as the sea of other functionally important metal ion interactions presents a considerable challenge. For the GI ribozyme and other catalytic RNAs, site-specific evidence for active site metal interactions comes primarily from analyses of thiophilic metal ion rescue of phosphorothioate and other substrate modifications (e.g.. References 60 and 61). These analyses rely on the fact that substitution of a substrate phosphate by a phosphorothioate weakens the affinity of coordinated Mg(2- -) ions... 

Many ribozymes and proteins that catalyze phosphoryl-transfer reactions use a mechanism employing two metal ions, and early on group II introns were hypothesized to use a similar mechanism (17). However, evidence for the existence of two metal ions in the catalytic core was only found very recently (12, 13, 18). A direct Mg + coordination of the pro-Sv oxygen of the first nucleotide of the catalytic triad is evident based on phosphorothioate substitution experiments (18). Recently, an intact group II was successfully crystallized for the first time (12). This structure confirms the metal contact from the first nucleotide of the catalytic triad and shows additional contacts to this metal ion from the second nucleotide of the catalytic triad and from the first nucleotide upstream of the bulge (Fig. 4a). This nucleotide is additionally coordinated to the second Mg + ion in the core. The distance between the two Mg + ions in the crystal stmcture is 3.9 A, which is in agreement with the proposed two-metal-ion mechanism (17). 

During splicing, the two metal ions form additional contacts to the substrate. Evident from phosphorothioate substitution experiments are coordinative bonds to the pro-Rp oxygens of the scissile phosphates at both splice sites and to the 3 -oxygens of the leaving groups in both steps of splicing (Fig. 4). 

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