Influence of backbone chemistry on immune activation by synthetic oligonucleotides

Depending on base sequence, DNA displays immunological activities relevant to the design of novel therapeutic agents. To determine the influence of backbone structure on these activities, we tested a series of synthetic phosphodiester and phosphorothioate oligonucleotides in in vitro cultures of murine spleen cells. These compounds were 30 bases long and consisted of either a single base or an immunostimulatory sequence (AACGTT) flanked on 5' and 3' ends by 12 nucleotides of each base. Cell activation was assessed by both thymidine incorporation and expression of cell surface CD69; production of interleukin-6 and interleukin-12 was used as a measure of cytokine stimulation. In these assays, phosphorothioate oligonucleotides induced much higher levels of proliferation, CD69 expression, and cytokine production than the comparable phosphodiester compounds and had activity at lower concentrations. The sequence for optimal stimulation by phosphorothioates varied among responses, however. For example, whereas compounds containing an immunostimulatory sequence all induced similar levels of proliferation and CD69 expression, cytokine production was greatest with compounds with dA and dT flanks. Furthermore, while single base dG oligonucleotides stimulated proliferation as both phosphodiesters and phosphorothioates, they failed to stimulate cytokine production. Together, these findings indicate that base sequence as well as backbone chemistry influence immune activation by synthetic oligonucleotides, with the effects varying among responses. While suggesting differences in the structure-function relationships of nucleic acids in their immune activities, these findings also raise the possibility of the design of agents with specific patterns of immune modulation.