Structure-activity relationships in cell culture

The use of antisense oligonucleotides in cell culture relies on the development of potent modifications and cell delivery techniques. C-5 propyne pyrimidine phosphorothioate oligonucleotides bind selectively and with high affinity to RNA within cells, leading to potent antisense inhibition. The effect that increasing steric bulk of C-5-substituted deoxyuridine analogues has on the affinity for RNA and the ability to inhibit gene expression is discussed. The GS 2888 cytofectin agent delivers oligonucleotides to cells at high efficiency in the presence of serum in cell media. Modifications leading to the discovery of GS 2888 centered on the aliphatic chain length of the molecule and the pKa of the polar head group. Together, the C-5 propyne modifications and the GS 2888 cytofectin agent have been shown to be effective inhibitors of gene expression in cell culture, particularly in the area of cell cycle proteins involved in cancer progression.