Tuning the Solubility\nof Soluble Support Constructs\nin Liquid Phase Oligonucleotide Synthesis

Solubility of the growing oligonucleotide-soluble support\nconstructs\nin the liquid phase oligonucleotide synthesis (LPOS) is a critical\nparameter, which affects coupling efficiency, purity, and recovery\nof the growing oligonucleotides during the chain elongation. In the\npresent study, oligonucleotides have been assembled on a 4-oxoheptanedioic\nacid (OHDA) linker-derived tetrapodal soluble support using 5′-<i>O</i>-(2-methoxyprop-2-yl)-protected 2′-deoxyribonucleotide\nphosphoroamidite building blocks with different nucleobase protecting\ngroups [isobutyryl (Gua), 1-butylpyrrolidin-2-ylidene (Gua, Cyt),\n2,4-dimethylbenzoyl (Ade, Cyt), and Bz (Thy)]. The solubility of the\noligonucleotide-soluble support constructs (molecular mass varying\nbetween 3 and 10 kDa) as models of protected tetra-, octa-, dodeca-,\nhexadeca-, and eicosa-nucleotides was measured in different solvent\nsystems and in potential antisolvents. By tuning the nucleobase protecting\ngroup scheme, the solubility can be improved in aprotic organic solvent\nsystems, while the recovery of the constructs in the precipitation,\nused for the isolation and purification of the growing oligonucleotide\nintermediates in a protic antisolvent (2-propanol), remained near\nquantitative. The precipitation-based yield of the protected tetrapodal\noligonucleotides varied from a quantitative to 90% yield. Overall\nyield (for di-: 95%, tri-: 79–96%, tetra-: 82–88%, and\npentanucleotides: 68–75%) and purity of the LPOS were evaluated\nby RP HPLC and MS-spectroscopy of the released oligonucleotide aliquots.\nIn addition, the orthogonality of the OHDA linker was applied to release\nauthentic protected nucleotides from the soluble supports.