Cyclic GMP-AMP containing a unique combination of mixed phosphodiester linkages (2′3′-cGAMP) is an endogenous second messenger molecule that activates the type-I IFN pathway upon binding to the homodimer of the adaptor protein STING on the surface of endoplasmic reticulum membrane. However, the preferential binding of the asymmetric ligand 2′3′-cGAMP to the symmetric dimer of STING represents a physicochemical enigma. Here we show that 2′3′-cGAMP, but not its linkage isomers, adopts an organized free-ligand conformation that resembles the STING-bound conformation and pays low entropy and enthalpy costs in converting into the active conformation. Our results demonstrate that analyses of free-ligand conformations can be as important as analyses of protein conformations in understanding protein-ligand interactions.T he presence of cytosolic DNA in mammalian cells is a danger signal that triggers the production of second messenger cGAMP by the DNA sensor protein cyclic GMP-AMP synthase (cGAS) (1, 2). cGAMP then activates the adaptor protein stimulator of IFN genes (STING, also known as TMEM173, MITA, ERIS, or MPYS) and induces the translocation of STING from the endoplasmic reticulum membrane to the Golgi, where it then recruits IκB kinase and TANK-binding kinase 1 (3, 4). The transcription factors nuclear factor κB and IFN regulatory factor 3 are subsequently activated, leading to the production of antiviral and proinflammatory cytokines, including type I interferons (IFNs). This cGAMP-mediated immune response is a fundamental defense mechanism against viral infection (5-7), making cGAMP and its structural derivatives potential vaccine adjuvants and immunotherapeutic agents against cancer (6,8).cGAMP is a hybrid cyclic dinucleotide that contains a guanosine unit and an adenosine unit joined by two phosphates in a macrocycle (Fig. 1). In contrast with the well-known bacterial signaling molecules cyclic di-GMP (c-di-GMP) and cyclic di-AMP (c-di-AMP) that contain a pair of (3′→5′)-phosphodiester linkages, the endogenous cGAMP molecule in mammalian cells contains unprecedented mixed phosphodiester linkages (9-12). Its two phosphate groups connect the two nucleosides from the 2′-and 5′ positions of guanosine and the 3′-and 5′ positions of adenosine. Denoted as 2′3′-cGAMP, this asymmetric ligand binds to the symmetric dimer of STING with an affinity significantly higher than its linkage isomers 2′2′-cGAMP, 3′2′-cGAMP, and 3′3′-cGAMP (SI Appendix, Table S1) (9). Notably, 3′3′-cGAMP has been found to be produced by certain bacteria (13, 14), whereas 2′2′-cGAMP and 3′2′-cGAMP have yet to be found in nature. Recent studies have revealed the molecular basis for the selective formation of the mixed 2′3′-phosphodiester linkages by cGAS (10, 14-18). However, the function of this linkage isomerism remained unclear and crystallographic studies of the STING/cGAMP complexes provided no insight (9, 19). Here we show that the preferred binding of 2′3′-cGAMP originates from its favorable free-ligand instead of protein-bound conformatio...