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As one vital member of the biologically important nucleotides, guanosine-5′-triphosphate (GTP) monitoring in biological systems has become a key research field because its abnormal concentration promotes certain pathological states. Herein, we report two "cleft-form" amphiphilic pyridinium receptors based on isophthalamide (PyPh-C16) and 2,6-dicarboxamidopyridine (PyPy-C16) spacers for structure modulated sensitive and selective response to GTP via the indicator displacement assay (IDA) method. Both receptors bind with a fluorescent indicator uranine dye (UD) to form self-assembled non-fluorescent nano-aggregate ensembles, i.e., PyPh-C16/UD and PyPy-C16/UD , which can be used for the nM detection of GTP in aqueous solution and also imaging GTP in complicated living cells environment. The non-fluorescent UD becomes fluorescent with releasing from the nano-ensembles displaced by GTP. With the aid of this phenomenon, the nano-ensembles could successfully discriminate GTP from other structurally related anions, including ATP, PPi, and most nucleotide polyphosphates (NPPs). In addition, the structure-related sensing properties of receptors toward GTP were detailly discussed. Thus, we believe that the present work will allow for many important developments in the future based on IDAs with advanced nano-ensembles and different indicators to recognize various types of essential nucleoside polyphosphates. [Display omitted] • Two "cleft-form" nanostructured ensembles are reported. • They show fluorescence OFF-ON response to GTP via the IDA method. • They were able to detect GTP in aqueous solutions and living cells. • The spacer structure can modulate the sensitivity and selectivity of ensembles. [ABSTRACT FROM AUTHOR]