Partitioning of pyrimidine single stranded oligonucleotide using polyethylene glycol - sodium sulfate aqueous two-phase systems; experimental and modeling

In this work partitioning of TAMRA (Tetramethyl-6-Carboxyrhodamine) - oligonucleotide in systems containing 18% (w/w) polyethylene glycol (PEG 600, PEG 1000, PEG 1500 and PEG 4000) and 15% (w/w) sodium sulfate (designated as 18/15) was investigated. To find the optimum condition, effective parameters on biomolecule partitioning including polymer molecular weight, pH, temperature and addition of a second salt were studied. The results showed that as pH increases and molecular weight of polymer decreases, the affinity of TAMRA oligonucleotide to accumulate in the top PEG-rich phase increases. In order to find the temperature effects, partitioning of TAMRA oligonucleotide was studied at two different temperatures 20 and 30 °C). At this range, no significant change was observed. Meanwhile, it is found that addition of 0.5% (w/w) of KH2PO4 as the second salt reversed the partitioning behavior of the oligonucleotide. A similar trend with smaller gradients was observed when KH2PO4 was substituted by KCl; whereas, substitution by MgSO4 increased the affinity of the oligonucleotide to partition to top phase. The best results achieved using PEG 600 at pH = 6. In this case, almost 100% of TAMRA oligonucleotide was recovered in the upper phase. Finally, the partitioning of the biomolecule was correlated using a model based on UNIFAC-FV group contribution. The results showed that the model can correlate the partitioning of the oligonucleotide with an acceptable accuracy.