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.