5 -Phosphoryl oligonucleotides

Nuclease SI Hydrolyzes single-stranded nucleic acids to form nucleotide monophosphates or 5 -phosphoryl oligonucleotides... 

The purchase of expensive phosphorylated oligonucleotides is unnecessary as the vector ends remain phosphorylated after the following ligation reaction. 

The phosphorylated oligonucleotide should be used immediately in the subsequent steps. 

This amide, readily formed from an amine and the anhydride or enzymatically using penicillin amidase, is readily cleaved by penicillin acylase (pH 8.1, A -methylpyrrolidone, 65-95% yield). This deprotection procedure works on peptides, phosphorylated peptides, and oligonucleotides, as well as on nonpeptide substrates. The deprotection of racemic phenylacetamides with penicillin acylase can result in enantiomer enrichment of the cleaved amine and the remaining amide. An immobilized form of penicillin G acylase has been developed. ... 

As mentioned in last year s Report, aromatic phosphoramidates have been used to protect 5 -phosphoryl groups in the stepwise synthesis of oligodeoxyribonucleotides. The appropriate monomer units are coupled with DCC and the phosphoramidate protecting group is removed when required with isoamyl nitrite. A rapid and general preparative method for oligonucleotides has been developed based on phosphoramidates of the highly lipophilic 4-aminophenyltriphenylmethane (25). Purification of... 

The fact that the 3,P-NMR signal of 183a can only be observed in pyridine-containing solution provides food for thought124). Viewed in conjugation with the idea that alkyl metaphosphates could form adducts such as 173 and 174 U9,120) as discussed above, formulation as a zwitterionic pyridine/metaphosphate adduct (188) seems reasonable. Similar adducts have also been found in the reaction of TPS with dinucleotides and trinucleoside diphosphate 126). In any case, the reactions of 183 or 188 are in full accord with the expected properties of a monomeric metaphosphate and its reactivity towards alcohols is far greater than that of all other reactive phosphorylation intermediates which can arise on reaction of TPS with oligonucleotides 126). 

On use of N,N -dicyclohexylcarbodiimide instead of sulfonyl chlorides as condensation reagent in oligonucleotide synthesis, then the pyro-, tri- and tetraphosphate stages are again involved 124). The metaphosphate 183 a is found in small amounts by 3iP-NMR spectroscopy, but again no cyclic trimetaphosphate 184 can be detected, which would also be a possible phosphorylation reagent. 

In an earlier study from Ken Beattie s group (then at the Houston Advanced Research Center), a similar conclusion was reached using a 9-mer oligonucleotide and triethylene glycol phosphoryl repeat unit as the spacer (1995). An optimal probe density leading to the greatest hybridization... 

Another anti-herpes compound is the remarkably simple foscarnet (9.15, phospho-noformate). This is an inorganic pyrophosphate compound that inhibits viral DNA polymerase and RNA polymerase without requiring activation by phosphorylation. Fomivirsen is an oligonucleotide that inhibits human cytomegalovirus (CMV) via an... 

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