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Abstract Single wall carbon nanotubes (SWCNTs) functionalized with (bio-)polymers such as DNA are soluble in water and sense analytes by analyte-specific changes of their intrinsic fluorescence. Such SWCNT-based (bio-)sensors translate the binding of a molecule (molecular recognition) into a measurable optical signal. This signal transduction is crucial for all types of molecular sensors to achieve high sensitivities. Although there is an increasing number of SWCNT-based sensors, there is yet no molecular understanding of the observed changes in the SWCNT’s fluorescence. Here, we report THz experiments that map changes in the local hydration of the solvated SWCNT upon binding of analytes such as the neurotransmitter dopamine or the vitamin riboflavin. The THz amplitude signal serves as a measure of the coupling of charge fluctuations in the SWCNTs to the charge density fluctuations in the hydration layer. We find a linear (inverse) correlation between changes in THz amplitude and the intensity of the change in fluorescence induced by the analytes. Simulations show that the organic corona shapes the local water, which determines the exciton dynamics. Thus, THz signals are a quantitative predictor for signal transduction strength and can be used as a guiding chemical design principle for optimizing fluorescent biosensors. 

ABSTRACT Single‐walled carbon nanotubes (SWCNTs) are promising optical biosensing platforms due to their intrinsic near‐infrared fluorescence and environmental sensitivity. While DNA‐SWCNT hybrids have been widely studied, the structural arrangement of double‐stranded DNA (dsDNA) on SWCNTs and its impact on exciton–fluorophore interactions remain insufficiently characterized. Here, we introduce carbon nanotube energy transfer with vertical nucleic acids (CNETvNA), in which fluorophores are positioned at defined distances from SWCNTs using guanine‐defect anchored capture sequences hybridized with complementary oligonucleotides. By systematically varying the duplex length from 12 to 24 base pairs, we probe the distance dependence of dye–SWCNT interactions at the single‐molecule level. Fluorescence lifetime imaging microscopy reveals efficient quenching of ATTO542 and ATTO643 dyes, with lifetime distributions reflecting heterogeneous duplex conformations. Molecular dynamics simulations demonstrate that dsDNA duplexes adopt a predominantly perpendicular orientation relative to the SWCNT axis, with increasing tilt and conformational variability at longer lengths. Combining experimental and computational results, we establish a distance dependence of d⁻⁵with 7.4 ± 0.7 nm for 50% quenching efficiency, consistent with theoretical predictions for point dipole donors and 1D acceptors. These findings provide structural insights into DNA‐SWCNT conjugates and establish CNETvNA as a rational design principle for SWCNT‐based biosensors.