The interaction between single-molecule (SM) fluorescence and transparent conductive oxide interface presents unique opportunities for studying molecular motion dynamics and conformational changes. In this study, we investigate the quenching effect of indium-tin oxide (ITO) on SM fluorescence, focusing on the fluorescent dye Cy3 tethered to the 3′-end of single-stranded DNA (ssDNA). By examining the brightness variations of single Cy3 molecules, we are able to distinguish Cy3-ssDNA covalently attached onto the ITO surface from the case of adsorption. Additionally, we can evaluate the molecular motion dynamics of single ssDNA molecules of varying lengths and conformations on the ITO surface. We believe that our findings make significant contributions to the understanding of molecular interactions at ITO interfaces and offer valuable insights into the potential applications of novel fluorophore motion- and orientation-based biosensing strategies.
[1] Hosono H (2007) Recent progress in transparent oxide semiconductors: materials and device application. Thin Solid Films 515:6000-6014. https://doi.org/10.1016/j.tsf.2006.12.125
[2] Liu H, Avrutin V, Izyumskaya N, Özgür Ü, Morkoç H (2010) Transparent conducting oxides for electrode applications in light emitting and absorbing devices. Superlattices Microstruct 48:458-484. https://doi.org/10.1016/j.spmi.2010.08.011
[3] Minami T (2013) Transparent conductive oxides for transparent electrode applications. Semiconductors and Semimetals. Elsevier, USA, pp 159-200
[4] Afre RA, Sharma N, Sharon M, Sharon M (2018) Transparent conducting oxide films for various applications: a review. Rev Adv Mater Sci 53:79-89. https://doi.org/10.1515/rams-2018-0006
[5] Althumayri M, Das R, Banavath R, Beker L, Achim AM, Ceylan Koydemir H (2024) Recent advances in transparent electrodes and their multimodal sensing applications. Adv Sci 11:2405099. https://doi.org/10.1002/advs.202405099
[6] Moerland RJ, Hoogenboom JP (2016) Subnanometer-accuracy optical distance ruler based on fluorescence quenching by transparent conductors. Optica 3:112-117. https://doi.org/10.1364/OPTICA.3.000112
[7] Chance RR, Prock A, Silbey R (1978) Molecular fluorescence and energy transfer near interfaces. In: Prigogine I, Rice SA (eds) Advances in Chemical Physics, 1st edn. Wiley, New York, pp 1-65
[8] Dexter DL (1979) Two ideas on energy transfer phenomena: ion-pair effects involving the OH stretching mode, and sensitization of photovoltaic cells. J Lumin 18-19:779-784. https://doi.org/10.1016/0022-2313(79)90235-7
[9] Hayashi T, Castner TG, Boyd RW (1983) Quenching of molecular fluorescence near the surface of a semiconductor. Chem Phys Lett 94:461-466. https://doi.org/10.1016/0009-2614(83)85032-5
[10] Liang Y, Goncalves AMP (1985) Time-resolved measurements of the fluorescence of Rhodamine B on semiconductor and glass surfaces. J Phys Chem 89:3290-3294. https://doi.org/10.1021/j100261a025
[11] Hashimoto K, Hiramoto M, Sakata T (1988) Photo-induced electron transfer from adsorbed rhodamine B to oxide semiconductor substrates in vacuo: semiconductor dependence. Chem Phys Lett 148:215-220. https://doi.org/10.1016/0009-2614(88)80302-6
[12] Lu HP, Xie XS (1997) Single-molecule kinetics of interfacial electron transfer. J Phys Chem B 101:2753-2757. https://doi.org/10.1021/jp9634518
[13] Peterson EM, Harris JM (2013) Imaging fluorescent nanoparticles to probe photoinduced charging of a semiconductor-solution interface. Langmuir 29:11941-11949. https://doi.org/10.1021/la402468k
[14] Ma Y, Macmillan A, Yang Y, Gaus K (2022) Lifetime based axial contrast enable simple 3D-STED imaging. Methods Appl Fluoresc 10:035001. https://doi.org/10.1088/2050-6120/ac5e10
[15] Isbaner S, Karedla N, Kaminska I, Ruhlandt D, Raab M, Bohlen J et al (2018) Axial colocalization of single molecules with nanometer accuracy using metal-induced energy transfer. Nano Lett 18:2616-2622. https://doi.org/10.1021/acs.nanolett.8b00425
[16] Karedla N, Chizhik AI, Gregor I, Chizhik AM, Schulz O, Enderlein J (2014) Single-molecule metal-induced energy transfer (smMIET): resolving nanometer distances at the single-molecule level. ChemPhysChem 15:705-711. https://doi.org/10.1002/cphc.201300760
[17] Chizhik AI, Rother J, Gregor I, Janshoff A, Enderlein J (2014) Metal-induced energy transfer for live cell nanoscopy. Nat Photonics 8:124-127. https://doi.org/10.1038/nphoton.2013.345
[18] Szalai AM, Ferrari G, Richter L, Hartmann J, Kesici M-Z, Ji B et al (2024) Single-molecule dynamic structural biology with vertically arranged DNA on a fluorescence microscope. Nat Methods. https://doi.org/10.1038/s41592-024-02498-x
[19] Backlund MP, Lew MD, Backer AS, Sahl SJ, Moerner WE (2014) The role of molecular dipole orientation in single-molecule fluorescence microscopy and implications for super-resolution imaging. ChemPhysChem 15:587-599. https://doi.org/10.1002/cphc.201300880
[20] Lu J, Mazidi H, Ding T, Zhang O, Lew MD (2020) Single-molecule 3D orientation imaging reveals nanoscale compositional heterogeneity in lipid membranes. Angew Chem Int Ed 59:17572-17579. https://doi.org/10.1002/anie.202006207
[21] Nguyen TD, Chen YI, Chen LH, Yeh HC (2023) Recent advances in single-molecule tracking and imaging techniques. Annu Rev Anal Chem 16:253-284. https://doi.org/10.1146/annurev-anchem-091922-073057
[22] Moerner WE (2015) Single-molecule spectroscopy, imaging, and photocontrol: foundations for super-resolution microscopy (Nobel Lecture). Angew Chem Int Ed 54:8067-8093. https://doi.org/10.1002/anie.201501949
[23] Reinhardt SCM, Masullo LA, Baudrexel I, Steen PR, Kowalewski R, Eklund AS et al (2023) Ångström-resolution fluorescence microscopy. Nature 617:711-716. https://doi.org/10.1038/s41586-023-05925-9
[24] Weber M, Von Der Emde H, Leutenegger M, Gunkel P, Sambandan S, Khan TA et al (2023) MINSTED nanoscopy enters the Ångström localization range. Nat Biotechnol 41:569-576. https://doi.org/10.1038/s41587-022-01519-4
[25] Khanna K, Mandal S, Blanchard AT, Tewari M, Johnson-Buck A, Walter NG (2021) Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor. Biosens Bioelectron 190:113433. https://doi.org/10.1016/j.bios.2021.113433
[26] Shin S, Han S, Kim J, Shin Y, Song JJ, Hohng S (2023) Fast, sensitive, and specific multiplexed single-molecule detection of circulating tumor DNA. Biosens Bioelectron 242:115694. https://doi.org/10.1016/j.bios.2023.115694
[27] He H, Hao R (2024) Multiplexed fluoro-electrochemical single-molecule counting enabled by SiC semiconducting nanofilm. Nano Lett 24:11051-11058. https://doi.org/10.1021/acs.nanolett.4c03199
[28] Ovesný M, Křížek P, Borkovec J, Švindrych Z, Hagen GM (2014) ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging. Bioinformatics 30:2389-2390. https://doi.org/10.1093/bioinformatics/btu202
[29] Li H, Zhang J, Zhou X, Lu G, Yin Z, Li G et al (2010) Aminosilane micropatterns on hydroxyl-terminated substrates: fabrication and applications. Langmuir 26:5603-5609. https://doi.org/10.1021/la9039144
[30] Zandieh M, Patel K, Liu J (2022) Adsorption of linear and spherical DNA oligonucleotides onto microplastics. Langmuir 38:1915-1922. https://doi.org/10.1021/acs.langmuir.1c03190
[31] Jung GY, Li Z, Wu W, Chen Y, Olynick DL, Wang SY et al (2005) Vapor-phase self-assembled monolayer for improved mold release in nanoimprint lithography. Langmuir 21:1158-1161. https://doi.org/10.1021/la0476938
[32] Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR et al (2011) NUPACK: analysis and design of nucleic acid systems. J Comput Chem 32:170-173. https://doi.org/10.1002/jcc.21596
[33] Dekking FM, Kraaikamp C, Lopuhaä HP, Meester LE (2005) Exploratory data analysis: numerical summaries. In: Dekking FM, Kraaikamp C, Lopuhaä HP, Meester LE (eds) A Modern Introduction to Probability and Statistics: Understanding Why and How. Springer, London, pp 231-243. https://doi.org/10.1007/1-84628-168-7_16
