IP RP LC separation of PS ONs was investigated in temperature range 20 – 90 °C.

Separation of PS ONs diastereomers is suppressed at high temperature.

Suppression of isomeric separation leads to narrower peaks.

n/n-x resolution of PS ONs is enhanced at elevated temperature.

Higher temperature does not lead to ONs retention decrease for all IP systems.

Analysis of diastereomers of phosphorothioate oligonucleotides in ion-pairing reversed-phase liquid chromatography is affected not only by the character and concentration of ion-pairing system, but also by the separation temperature. In this work, eight ion-pairing systems at two concentrations buffered with acetic acid were used with octadecyl column to investigate the effects of temperature (in the range from 20 °C to 90 °C) on retention, diastereomeric separation, resolution of mers of different length and resolution of oligonucleotides with different number of phosphorothioate linkages. It was observed that elevated temperature suppresses the diastereomeric separation and oligonucleotide peaks become narrower. This improves the resolution of n and n-1 mers at elevated temperature. Plots of ln k (k = retention factor) versus reciprocal absolute temperature show that for 100 mM ion-pairing systems the increase in temperature does not lead to simple decrease in oligonucleotides retention as generally observed in reversed-phase liquid chromatography. The aim of this work is to improve chromatographic method for analysis of phosphorothioate oligonucleotides.

Phosphorothioate oligonucleotides

Ion-pairing reversed-phase chromatography

Diastereomeric separation

Temperature

Resolution

The data are available as on-line Supporting material to the article.

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