Diastereomeric dinucleoside-methylphosphonates: determination of configuration with the 2-D NMR ROESY technique

Abstract

The determination of configuration at phosphorus in diastereomeric dinucleoside-methylphosphonates having the -O-P(= O)(-CH3)-O- internucleotide linkage with the NOE derived ROESY NMR technique is described for ApT, TpT, ApA, TpA and CpG. For this purpose ROE's from the P-CH3 group to the protons in the nearest neighbourhood were measured. These ROE's are different within diastereomeric pairs of a dimer enabling us to deduce the individual configuration. The validity of the method is proven in comparison with dimers of known configuration (ApT, TpT). Together with a recently published diastereoselective synthesis method a more homogeneous picture between physical properties and the corresponding configuration is provided. There is an improvement in our knowledge about the stereochemistry of these substances which could not be deduced from the data known before.

Role of a ribosomal RNA phosphate oxygen during the EF-G–triggered GTP hydrolysis

“…The replacement of a nonbridging phosphate oxygen by a methyl group was selected, as the latter has no proton acceptor capability and has no lone pair of electrons, thus erasing any possibility for classical hydrogen bond formation (28)(29)(30)(31)(32)(33). In addition, by replacing the oxygen through a methyl group, the negative charge at the rRNA backbone at this position is eliminated, which allows investigating the putative role of this charge at A2662 in affecting the acid-base behavior of the conserved His87 and its consequences on GTP hydrolysis.…”

“…The methylphosphonate modification generates chirality at the phosphor atom and results in two possible diastereomeric RNAs (R P and S P ; Cahn-Ingold-Prelog nomenclature is used throughout the manuscript) (28). Importantly, our experimental design allowed individual access to either of the two diastereomers (Fig.…”

Oligonucleotides with novel, cationic backbone substituents: aminoethylphosphonates

“…Stereochemistry at phosphorus A preliminary determination of the stereochemistry at phosphorus was obtained by an adaptation of the 2D-NMR method of Loschner and Engels [22]. These authors determined the stereochemistry about phosphorus of dinucleoside methylphosphonates based upon the level of interactions between the methylphosphonate and the C3 and C4, sugar protons.…”

Interactions of oligonucleotide analogs containing methylphosphonate internucleotide linkages and 2′-O-methylribonucleosides

“…Based on the similarity to d-ApT and the observation by others that the Rp methylphosphonate diastereoisomers have shorter retention times than the Sp diastereoisomers (25 -33), we have tentatively assigned the configuration of isomer 1 of oligomers 4 and 5 as Rp and the configuration of isomer 2 of oligomers 4 and 5 as Sp. Confirmation of these assignments awaits further physical characterization of the dimers by NMR spectroscopy (27).…”

“…In addition to the expected nucleosides, a peak whose mobility corresponded to one of the diastereoisomers of the diimer, d-ApT, was also observed. The dimer obtained from the first peak corresponded to authentic Rp-d-ApT, whereas the dimer obtained from the second peak corresponded to authentic Sp-d-ApT (25)(26)(27). The retention times of these two diastereomers differed by 0.22 min on the C-18 column using a linear gradient of 2-3 % acetonitrile for the first 12 min of elution followed by a linear gradient of 3-30% acetonitrile for the next 8 min.…”