Various approaches have been used to modulate the fluorescence changes of sensors in the presence of target analytes, including intramolecular interaction between fluorophores or between fluorophore and other molecular species, like resonance energy transfer (RET). Here, we focus on fluorescence quenching by intramolecular heterodimer complex formation, which can be modulated over a shorter distance range than RET. We synthesized several conjugates of tricarbocyanine, which is a near-infrared fluorophore, with several quencher candidates via flexible short linker structure, and examined their fluorescence properties. Of our synthesized compounds, the dabcyl group proved to be the best quencher via heterodimer complex formation. The fluorescence of tricarbocyanine-dabcyl conjugates in aqueous media was almost completely quenched, and there was a dramatic fluorescence enhancement when heterodimer formation was blocked. These results suggested a design approach to develop fluorescence sensors for probing proximity relationships and structural transitions.