Significance of stereochemistry of 3'-terminal phosphorothioate-modified primer in DNA polymerase-mediated chain extension

Quantification of total phosphorothioate in bacterial DNA by a bromoimane-based fluorescent method

The discovery of phosphorothioate (PT) modifications in bacterial DNA has challenged our understanding of conserved phosphodiester backbone structure of cellular DNA. This exclusive DNA modification in bacteria is not found in animal cells yet, and its biological function in bacteria is still poorly understood. Quantitative information about the bacterial PT modifications is thus important for the investigation of their possible biological functions. In this study, we have developed a simple fluorescence method for selective quantification of total PTs in bacterial DNA, based on fluorescent labeling of PTs and subsequent release of the labeled fluorophores for absolute quantification. The method was highly selective to PTs and not interfered by the presence of reactive small molecules or proteins. The quantification of PTs in an E. coli DNA sample was successfully achieved using our method and gave a result of about 455 PTs per million DNA nucleotides, while almost no detectable PTs were found in a mammalian calf thymus DNA. With this new method, the content of phosphorothioate in bacterial DNA could be successfully quantified, serving as a simple method suitable for routine use in biological phosphorothioate related studies.

The effect of divalent cations on the catalytic activity of the human plasma 3'-exonuclease

The 3'-exonuclease from human plasma is a soluble form of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) (EC 3.1.4.1/EC 3.6.1.9). Here, the possibility of divalent cation influence for the 3'-exonuclease activity was investigated using the phosphorothioate congener of oligonucleotide containing all phosphorothioate internucleotide linkages of the [R(P)]-configuration ([R(P)-PS]-d[T(12)]) as the substrate for this enzyme. It was found that the 3'-exonuclease is a metalloenzyme, i.e. its phosphodiesterase activity was completely abolished at 0.8 mM concentration EDTA and, in turn, it was restored in the presence of Mg(2+) or Mn(2+) ions. In addition, Mg(2+) can be replaced effectively by Ca(2+), Mn(2+), or Co(2+), but not by Ni(2+) and Cd(2+) during the hydrolysis of the phosphorothioate substrate in human plasma. In addition, the mechanism is postulated, by which a single internucleotide phosphorothioate bond of the S(P)-configuration at the 3'-end of unmodified phosphodiesters (PO-oligos), or their phosporothioate analogs (PS-oligos) protects these compounds against degradation in blood.

DNA oligonucleotides containing stereodefined phosphorothioate linkages in selected positions

This unit describes a method for the synthesis of DNA chimeric PO/PS-oligonucleotides with a stereodefined phosphorothioate bond in the selected position. Diastereomerically pure 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s obtained according to the previously described protocol (UNIT 4.17) are transformed via a stereospecific 1,3,2-oxathiaphospholane-ring opening condensation into the corresponding dinucleoside phosphorothioates. Such dimers cannot be introduced into an oligonucleotide chain via the phosphoramidite approach since the unprotected P-S(-) bond is easily oxidized during routine I(2)/Py/water oxidation of the phosphite function. In the methodology described here, the reversible alkylation of the PS function is applied. Subsequently, the 3'-phosphoramidites of such PS-protected dimers prepared in situ are used for routine synthesis of chimeric PO/PS-oligonucleotides according to the phosphoramidite method. The presence of the alkylated PS-function requires modified conditions for oligonucleotide deprotection and cleavage from the solid support. Detailed procedures for the synthesis of PS-dimers and their incorporation into an oligonucleotide chain, as well as deprotection/purification steps are presented.