Toll-like receptor 9 (TLR9), a member of the interleukin-1 (IL-1) family of pathogen-associated molecular pattern receptors, is activated by unmethylated CpGcontaining sequences in bacterial DNA or synthetic oligonucleotides (ODNs) in the endosomal compartment. The stimulation of an IL-1 response is thought to require the aggregation of its receptor. By analogy, we postulated that the potency of a TLR9 ligand should depend first on its ability to enter cells and gain access to TLR9 and second on its capacity to form a multimeric complex capable of cross-linking these receptors. Previously, we selected from a random library a series of phosphodiester ODNs with enhanced ability to permeate cells. Here, we studied the structural requirements for these penetrating ODNs to elicit a functional TLR9 response, as assessed by cytokine production from bone marrowderived mouse mononuclear cells. The presence of a prototypic murine immunostimulatory DNA hexameric sequence (purine-purine-CG-pyrimidine-pyrimidine) in the ODNs was not sufficient for stimulation. In addition, the TLR9-activating ODNs had to have the ability to form aggregates and often to form secondary structures near the core CpG motifs. Multimerization was promoted by the presence of a guanine-rich 3-terminus. The phosphodiester ODNs with CpG motifs that did not aggregate antagonized the effects of the multimeric TLR9 activators. These findings suggest that an optimal TLR9 agonist needs to contain a spatially distinct multimerization domain and a receptor binding CpG domain. This concept may prove useful for the design of new TLR9-modulating agents.The 10 members of the Toll-like receptor (TLR) 1 family have attracted intense interest, because they play key roles in the initiation of innate and adaptive immune responses (1-6). Many of the TLRs share common signaling pathways, mediated by the adapter proteins myeloid differentiation marker 88 (MyD88), Toll-interleukin 1 receptor (TIR) domain-containing adapter protein/MyD88 adaptor-like (7, 8), or TIR domaincontaining adaptor-inducing interferon- (9 -11). However, their cellular patterns of expression and their subcellular localization characteristics differ substantially. Thus, whereas most TLRs are expressed predominantly on the external plasma membrane, TLR7 and TLR9 are found mainly on the inner surface of endosomes (12-15). Hence, effective ligation of TLR7 and TLR9 might be intracellular events.The natural activating ligand for TLR9 is bacterial DNA containing unmethylated CpG dinucleotides, commonly referred to as immunostimulatory DNA or sequence (ISS) (15)(16)(17). Comparative studies of CpG oligonucleotides (ODNs) with different sequences have shown that the neighboring residues of the core CpG dinucleotides strongly influence immunostimulatory potency (18 -21). However, there are some differences between the optimal murine and human ISS. The central murine ISS motif for TLR9 activation has been shown to consist of the hexameric sequence purinepurine-CG-pyrimidine-pyrimidine in phosphodiester or ph...