Assembly of the SNARE complex is essential for neurotransmitter release at synapses. Target plasma membrane SNAREs (t-SNAREs) syntaxin 1A and SNAP-25 form the t-SNARE complex that serves as an intermediate toward final SNARE assembly with vesicle-associated SNARE (v-SNARE). Membrane topologies of syntaxin 1A and the t-SNARE complex were investigated using site-directed spin labeling EPR. EPR analysis revealed that the basic region at the membrane-water interface is unstructured but inserted into the membrane. Such membrane insertion leaves no gap between the t-SNARE core and the membrane. Yet the lack of structure could provide the flexibility necessary for the t-SNARE core. Further, the insertion of the basic interfacial region into the membrane may have profound implications for the mechanism of SNARE-induced membrane fusion.