Distance-Dependent Energy Transfer Between Organic Fluorophores and Single-Walled Carbon Nanotubes

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−5 with 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.