DNA-ORIGAMI APERTURED TILES SELF-ASSEMBLY AND SURFACE AFM-CHARACTERIZATION IN THE PRESENCE OF SPONTANEOUS ATTACHMENT OF SINGLE COLLOIDAL QUANTUM DOT

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Abstract

Modern photonics technologies are increasingly dealing with nanostructures of different chemical composition and morphology. DNA- origami is one of the most promising methods of colloidal synthesis since its self- assembling allows creating organic nanoparticles with controlled geometry. Yet the issue remains how to hybridize them with single emitters of light for photonics applications. In the paper we investigate an opportunity of spontaneous interaction of DNA- origami in the form of parallelepiped tiles (61 × 52 × 5.8 nm) containing rectangle apertures (15 × 9 nm) with colloidal core- shell quantum dots (CdSe/CdS/ZnS/oleic acid). We characterize the attachment probability (− 25%) as well as consider single DNA/QD hybrid geometry with atomic force microscopy using deep 2D deconvolution post- processing analysis for correction.

About the authors

A. I Arzhanov

Moscow Pedagogical State University; Lebedev Physical Institute, Troitsk Branch

Email: arzhanov.artyom@gmail.com
Moscow, Russia; Troitsk, Russia

M. E Stepanov

Moscow Pedagogical State University

Moscow, Russia

T. V Egorova

Moscow Pedagogical State University

Moscow, Russia

K. A Magaryan

Moscow Pedagogical State University

Moscow, Russia

R. A Akasov

Moscow Pedagogical State University

Moscow, Russia

E. V Khaydukov

Lebedev Physical Institute, Troitsk Branch

Troitsk, Russia

A. V Naumov

Moscow Pedagogical State University; Lebedev Physical Institute, Troitsk Branch

Moscow, Russia; Troitsk, Russia

References

  1. Porrati F., Barth S., Gazzadi G.C., Frabboni S., Volkov O.M., Makarov D., Huth M. Site-selective chemical vapor deposition on direct-write 3d nanoarchitectures // Acs Nano. 2023. V. 17. № 5. P. 4704−4715. https://doi.org/10.1021/acsnano.2c10968
  2. Tan C., Chen J., Wu X.-J., Zhang H. Epitaxial growth of hybrid nanostructures // Nature Reviews Materials. 2018. V. 3. № 2. P. 17089. https://doi.org/10.1038/natrevmats.2017.89
  3. Sorokin S.V., Klimko G.V., Sedova I.V., Galimov A.I., Serov Y.M., Kirilenko D.A., Prasolov N.D., Toropov A.A. Molecular-beam epitaxy of metamorphic inas/ingaas quantum-dot heterostructures emitting in the telecom wavelength range // JETP Letters. 2024. V. 120. № 9. P. 668−674. https://doi.org/10.1134/s0021364024603294
  4. Wang X., Dai X., Wang H., Wang J., Chen Q., Chen F., Yi Q., Tang R., Gao L., Ma L., Wang C., Wang X., He G., Fei Y., Guan Y., Zhang B., Dai Y., Tu X., Zhang L., Zhang L., Zou G. All-water etching-free electron beam lithography for on-chip nanomaterials // Acs Nano. 2023. V. 17. № 5. P. 4933−4941. https://doi.org/10.1021/acsnano.2c12387
  5. Gol’tsman G.N., Okunev O., Chulkova G., Lipatov A., Semenov A., Smirnov K., Voronov B., Dzardanov A., Williams C., Sobolewski R. Picosecond superconducting single-photon optical detector // Applied Physics Letters. 2001. V. 79. № 6. P. 705−707. https://doi.org/10.1063/1.1388868
  6. Shangina E.L., Smirnov K.V., Morozov D.V., Kovalyuk V.V., Gol’tsman G.N., Verevkin A.A., Toropov A.I. Concentration dependence of the intermediate frequency bandwidth of submillimeter heterodyne AlGaAs/GaAs nanostructures // Bulletin of the Russian Academy of Sciences: Physics. 2010. V. 74. № 1. P. 100−102. https://doi.org/10.3103/s1062873810010272
  7. Fan J., Qian L. Quantum dot patterning by direct photolithography // Nat Nanotechnol. 2022. V. 17. № 9. P. 906−907. https://doi.org/10.1038/s41565-022-01187-0
  8. Anscombe N. Direct laser writing // Nature Photonics. 2010. V. 4. № 1. P. 22−23. https://doi.org/10.1038/nphoton.2009.250
  9. Chichkov B.N., Momma C., Nolte S., Alvensleben F., Tünnermann A. Femtosecond, picosecond and nanosecond laser ablation of solids // Applied Physics A Materials Science & Processing. 1996. V. 63. № 2. P. 109−115. https://doi.org/10.1007/bf01567637
  10. Gurbatov S.O., Shevlyagin A.V., Zhizhchenko A.Y., Modin E.B., Kuchmizhak A.A., Kudryashov S.I. Photothermal conversion and laser-induced transformations in silicon–germanium alloy nanoparticles // JETP Letters. 2024. V. 119. № 12. P. 910−916. https://doi.org/10.1134/s0021364024601398
  11. Nastulyavichus A.A., Ulturgasheva E.V., Kudryashov S.I. Nanosecond fabrication of hyperdoped silicon // Bulletin of the Lebedev Physics Institute. 2025. V. 51. № 12. P. 583−588. https://doi.org/10.3103/s1068335624602036
  12. Chubich D.A., Kolymagin D.A., Kazakov I.A., Vitukhnovsky A.G. Morphology and structural parameters of three-dimensional structures created using STED nanolithography // Bulletin of the Russian Academy of Sciences: Physics. 2018. V. 82. № 8. P. 1012−1017. https://doi.org/10.3103/s1062873818080154
  13. Farsari M., Chichkov B.N. Two-photon fabrication // Nature Photonics. 2009. V. 3. № 8. P. 450−452. https://doi.org/10.1038/nphoton.2009.131
  14. Demina P.A., Khaydukov K.V., Rocheva V.V., Akasov R.A., Generalova A.N., Khaydukov E.V. Technology of infrared photopolymerization // PHOTONICS Russia. 2022. V. 16. № 8. P. 600−602. https://doi.org/10.22184/1993-7296.FRos.2022.16.8.600.602
  15. Balykin V.I., Borisov P.A., Letokhov V.S., Melentiev P.N., Rudnev S.N., Cherkun A.P., Akimenko A.P., Apel P.Y., Skuratov V.A. Atom “pinhole camera” with nanometer resolution // JETP Letters. 2006. V. 84. № 8. P. 466−469. https://doi.org/10.1134/s0021364006200124
  16. Marago O.M., Jones P.H., Gucciardi P.G., Volpe G., Ferrari A.C. Optical trapping and manipulation of nanostructures // Nat Nanotechnol. 2013. V. 8. № 11. P. 807−819. https://doi.org/10.1038/nnano.2013.208
  17. Shilkin D.A., Lyubin E.V., Soboleva I.V., Fedyanin A.A. Trap position control in the vicinity of reflecting surfaces in optical tweezers // JETP Letters. 2014. V. 98. № 10. P. 644−647. https://doi.org/10.1134/s0021364013230124
  18. Kaur A., Bajaj B., Kaushik A., Saini A., Sud D. A review on template assisted synthesis of multi-functional metal oxide nanostructures: Status and prospects // Materials Science and Engineering: B. 2022. V. 286. P. 116005. https://doi.org/10.1016/j.mseb.2022.116005
  19. Apel P. Track etching technique in membrane technology // Radiation Measurements. 2001. V. 34. № 1−6. P. 559−566. https://doi.org/10.1016/s1350-4487(01)00228-1
  20. Kozhina E.P., Bedin S.A., Nechaeva N.L., Podoynitsyn S.N., Tarakanov V.P., Andreev S.N., Grigoriev Y.V., Naumov A.V. Ag-nanowire bundles with gap hot spots synthesized in track-etched membranes as effective sers-substrates // Applied Sciences. 2021. V. 11. № 4. P. 1375. https://doi.org/10.3390/app11041375
  21. Kozhina E.P., Andreev S.N., Tarakanov V.P., Bedin S.A., Doludenko I.M., Naumov A.V. Study of local fields of dendrite nanostructures in hot spots formed on sers-active substrates produced via template-assisted synthesis // Bulletin of the Russian Academy of Sciences: Physics. 2021. V. 84. № 12. P. 1465−1468. https://doi.org/10.3103/s1062873820120205
  22. Stepanov M.E., Khorkina S.A., Arzhanov A.I., Karabulin A.V., Matyushenko V.I., Naumov A.V. Near-field effects at the nodes of a gold nanonetwork grown by laser ablation in superfluid helium: Crossover between “tip and gap hot spots” // JETP Letters. 2024. V. 120. № 4. P. 223−229. https://doi.org/10.1134/S0021364024602161
  23. Murray C.B., Kagan C.R., Bawendi M.G. Synthesis and characterization of monodisperse nanocrystals and close-packed nanocrystal assemblies // Annual Review of Materials Science. 2000. V. 30. № 1. P. 545−610. https://doi.org/10.1146/annurev.matsci.30.1.545
  24. Huo D., Kim M.J., Lyu Z., Shi Y., Wiley B.J., Xia Y. One-dimensional metal nanostructures: From colloidal syntheses to applications // Chem. Rev. 2019. V. 119. № 15. P. 8972−9073. https://doi.org/10.1021/acs.chemrev.8b00745
  25. Arzhanov A.I., Savostianov A.O., Magaryan K.A., Karimullin K.R., Naumov A.V. Photonics of semiconductor quantum dots: Basic aspects // PHOTONICS Russia. 2021. V. 15. № 9. P. 622−641. https://doi.org/10.22184/1993-7296.FRos.2021.15.8.622.641
  26. Arzhanov A.I., Savostianov A.O., Magaryan K.A., Karimullin K.R., Naumov A.V. Photonics of semiconductor quantum dots: Applied aspects // PHOTONICS Russia. 2022. V. 16. № 2. P. 96−112. https://doi.org/10.22184/1993-7296.FRos.2022.16.2.96.112
  27. Rogach A.L., Franzl T., Klar T.A., Feldmann J., Gaponik N., Lesnyak V., Shavel A., Eychmüller A., Rakovich Y.P., Donegan J.F. Aqueous synthesis of thiol-capped cdte nanocrystals: State-of-the-art // The Journal of Physical Chemistry C. 2007. V. 111. № 40. P. 14628−14637. https://doi.org/10.1021/jp072463y
  28. Magaryan K.A., Mikhailov M.A., Karimullin K.R., Vasilieva I.A., Klimusheva G.V. Temperature dependence of the luminescence spectra of liquid crystal composites with cdse quantum dots // Bulletin of the Russian Academy of Sciences: Physics. 2014. V. 78. № 12. P. 1336−1340. https://doi.org/10.3103/s1062873814120193
  29. Galisteo-Lopez J.F., Ibisate M., Sapienza R., Froufe-Perez L.S., Blanco A., Lopez C. Self-assembled photonic structures // Adv Mater. 2011 V. 23. № 1. P. 30−69. https://doi.org/10.1002/adma.201000356
  30. Grzelczak M., Vermant J., Furst E.M., Liz-Marzan L.M. Directed self-assembly of nanoparticles // Acs Nano. 2010. V. 4. № 7. P. 3591−3605. https://doi.org/10.1021/nn100869j
  31. Kovalets N.P., Kozhina E.P., Razumovskaya I.V., Arzhanov A.I., Naumov А.V. Scratching of metallized polymer films by vickers indenter as a method for controlled production of SERS-active metasurfaces // Journal of Luminescence. 2024. V. 275. P. 120803. https://doi.org/10.1016/j.jlumin.2024.120803
  32. Dahoumane S.A., Jeffryes C., Mechouet M., Agathos S.N. Biosynthesis of inorganic nanoparticles: A fresh look at the control of shape, size and composition // Bioengineering. 2017. V. 4. № 1. P. 14. https://doi.org/10.3390/bioengineering4010014
  33. Klaus T., Joerger R., Olsson E., Granqvist C.G. Silver-based crystalline nanoparticles, microbially fabricated // Proc. Natl. Acad. Sci. USA. 1999. V. 96. № 24. P. 13611−13614. https://doi.org/10.1073/pnas.96.24.13611
  34. Sachin K., Karn S.K. Microbial fabricated nanosystems: Applications in drug delivery and targeting // Frontiers in Chemistry. 2021. V. 9. P. 617353. https://doi.org/10.3389/fchem.2021.617353
  35. Mukherjee P., Ahmad A., Mandal D., Senapati S., Sainkar S.R., Khan M.I., Parishcha R., Ajaykumar P.V., Alam M., Kumar R., Sastry M. Fungus-mediated synthesis of silver nanoparticles and their immobilization in the mycelial matrix: A novel biological approach to nanoparticle synthesis // Nano Letters. 2001. V. 1. № 10. P. 515−519. https://doi.org/10.1021/nl0155274
  36. Kowshik M., Ashtaputre S., Kharrazi S., Vogel W., Urban J., Kulkarni S.K., Paknikar K.M. Extracellular synthesis of silver nanoparticles by a silver-tolerant yeast strain mky3 // Nanotechnology. 2003. V. 14. № 1. P. 95−100. https://doi.org/10.1088/0957-4484/14/1/321
  37. Iravani S. Green synthesis of metal nanoparticles using plants // Green Chemistry. 2011. V. 13. № 10. P. 2638−2650. https://doi.org/10.1039/c1gc15386b
  38. Willner I., Baron R., Willner B. Growing metal nanoparticles by enzymes // Advanced Materials. 2006. V. 18. № 9. P. 1109−1120. https://doi.org/10.1002/adma.200501865
  39. Gholami-Shabani M., Shams-Ghahfarokhi M., Gholami-Shabani Z., Akbarzadeh A., Riazi G., Ajdari S., Amani A., Razzaghi-Abyaneh M. Enzymatic synthesis of gold nanoparticles using sulfite reductase purified from escherichia coli: A green eco-friendly approach // Process Biochemistry. 2015. V. 50. № 7. P. 1076−1085. https://doi.org/10.1016/j.procbio.2015.04.004
  40. Mao C., Solis D.J., Reiss B.D., Kottmann S.T., Sweeney R.Y., Hayhurst A., Georgiou G., Iverson B., Belcher A.M. Virus-based toolkit for the directed synthesis of magnetic and semiconducting nanowires // Science. 2004. V. 303. № 5655. P. 213−217. https://doi.org/10.1126/science.1092740
  41. Nam K.T., Kim D.W., Yoo P.J., Chiang C.Y., Meethong N., Hammond P.T., Chiang Y.M., Belcher A.M. Virus-enabled synthesis and assembly of nanowires for lithium ion battery electrodes // Science. 2006. V. 312. № 5775. P. 885−888. https://doi.org/10.1126/science.1122716
  42. Sandhage K.H., Dickerson M.B., Huseman P.M., Caranna M.A., Clifton J.D., Bull T.A., Heibel T.J., Overton W.R., Schoenwaelder M.E.A. Novel, bioclastic route to self-assembled, 3d, chemically tailored meso/nanostructures: Shape-preserving reactive conversion of biosilica (diatom) microshells // Advanced Materials. 2002. V. 14. № 6. P. 429−433. https://doi.org/10.1002/1521-4095(20020318)14:6<429::Aid-adma429>3.0.Co;2-c
  43. Kang F., Alvarez P.J., Zhu D. Microbial extracellular polymeric substances reduce ag+ to silver nanoparticles and antagonize bactericidal activity // Environ. Sci. Technol. 2014. V. 48. № 1. P. 316−322. https://doi.org/10.1021/es403796x
  44. Senapati S., Syed A., Moee S., Kumar A., Ahmad A. Intracellular synthesis of gold nanoparticles using alga Tetraselmis kochinensis // Materials Letters. 2012. V. 79. P. 116–118. https://doi.org/10.1016/j.matlet.2012.04.009
  45. Seeman N.C. DNA in a material world // Nature. 2003. V. 421. P. 427–431. https://doi.org/10.1038/nature01406
  46. Rothemun, P.W. Folding DNA to create nanoscale shapes and patterns // Nature. 2006. V. 440. № 7082. P. 297–302. https://doi.org/10.1038/nature04586
  47. Nangreave J., Han D., Liu Y., Yan H. DNA origami: A history and current perspective // Current Opinion in Chemical Biology. 2010. V. 14. № 5. P. 608–615. https://doi.org/10.1016/j.cbpa.2010.06.182
  48. Kuzyk A., Jungmann R., Acuna G.P., Liu N. DNA origami route for nanophotonics // ACS Photonics. 2018. V. 5. № 4. P. 1151–1163. https://doi.org/10.1021/acsphotonics.7b01580
  49. Dey S., Fan C., Gothelf K.V., Li J., Lin C., Liu L., Liu N., Nijenhuis M.A.D., Saccà B., Simmel F.C., Yan H., Zhan P. DNA origami // Nature Reviews Methods Primers. 2021. V. 1. № 1. P. 13. https://doi.org/10.1038/s43586-020-00009-8
  50. Zhan P., Peil A., Jiang Q., Wang D., Mousavi S., Xiong Q., Shen Q., Shang Y., Ding B., Lin C., Ke Y., Liu N. Recent advances in DNA origami-engineered nanomaterials and applications // Chemical Reviews. 2023. V. 123. № 7. P. 3976–4050. https://doi.org/10.1021/acs.chemrev.3c00028
  51. Tian Y., Wang T., Liu W., et al. Prescribed nanoparticle cluster architectures and low-dimensional arrays built using octahedral DNA origami frames // Nature Nanotech 2015 V. 10. P. 637–644. https://doi.org/10.1038/nnano.2015.105
  52. Engelen W., Dietz H. Advancing biophysics using DNA origami // Annu Rev Biophys. 2021. V. 50. P. 469–492. https://doi.org/10.1146/annurev-biophys-110520-125739
  53. Zhang Z., Ahamed M.A., Yang D. Biological properties and DNA nanomaterial biosensors of exosomal miRNAs in disease diagnosis // Sensors Diagnostics. 2025. V. 4. № 4, P. 273–292. https://doi.org/10.1039/d4sd00373j
  54. Huang J., Jaekel A., Van Den Boom, J., Podlesainski D., Elnaggar M., Heuer-Jungemann A., Kaiser M., Meyer H., Saccà B. A modular DNA origami nanocompartment for engineering a cell-free, protein unfolding and degradation pathway // Nature nanotechnology. 2024. V. 19. № 10. P. 1521–1531. https://doi.org/10.1038/s41565-024-01738-7
  55. Schreiber R., Do J., Roller E.M., Zhang T., Schüller V.J., Nickels P.C., Feldmann J., Liedl T. Hierarchical assembly of metal nanoparticles, quantum dots and organic dyes using DNA origami scaffolds // Nat Nanotechnol. 2014. V. 9. № 1. P. 74–78. https://doi.org/10.1038/nnano.2013.253
  56. Chen C., Wei X., Parsons M.F., Guo J., Banal J.L., Zhao Y., Scott M.N., Schlau-Cohen G.S., Hernandez R., Bathe M. Nanoscale 3d spatial addressing and valence control of quantum dots using wireframe DNA origami // Nat Commun. 2022. V. 13. № 1. P. 4935. https://doi.org/10.1038/s41467-022-32662-w
  57. Wang Z., Yan T.D., Susha A.S., Chan M.S., Kershaw S.V., Lo P.K., Rogach A.L. Aggregation-free DNA nanocage/quantum dot complexes based on electrostatic adsorption // Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2016. V. 495. P. 62–67. https://doi.org/https://doi.org/10.1016/j.colsurfa.2016.02.002
  58. Stepanov M.E., Khokhryakova U.A., Egorova T.V., Magaryan K.A., Naumov A.V. Shedding light on DNA-origami // PHOTONICS Russia. 2024. V. 18. № 1. P. 72–80. https://doi.org/10.22184/1993-7296.FRos.2024.18.1.72.80
  59. Stepanov M.E., Khokhryakova U.A., Egorova T.V., Magaryan K.A., Naumov A.V. Shedding light on DNA-origami: Practice // PHOTONICS Russia. 2024. V. 18. № 2. P. 166–174. https://doi.org/10.22184/1993-7296.FRos.2024.18.2.166.174
  60. Stepanov M.E., Khokhryakova U.A., Egorova T.V., Magaryan K.A., Naumov A.V. Shedding light on DNA-origami: Applications in photonics // PHOTONICS Russia. 2024. V. 18. № 5. P. 398–405. https://doi.org/10.22184/1993-7296.FRos.2024.18.5.398.405
  61. Kuzyk A., Schreiber R., Fan Z., Pardatscher G., Roller E.M., Hogele A., Simmel F.C., Govorov A.O., Liedl T. DNA-based self-assembly of chiral plasmonic nanostructures with tailored optical response // Nature. 2012. V. 483. № 7389. P. 311–314. https://doi.org/10.1038/nature10889
  62. Liu N., Liedl T. DNA-assembled advanced plasmonic architectures // Chem. Rev. 2018. V. 118. № 6. P. 3032–3053. https://doi.org/10.1021/acs.chemrev.7b00225
  63. Huang Y., Nguyen M.K., Natarajan A.K., Nguyen V.H., Kuzyk A. A DNA origami-based chiral plasmonic sensing device // ACS Appl Mater Interfaces. 2018. V. 10. № 51. P. 44221–44225. https://doi.org/10.1021/acsami.8b19153
  64. Tikhomirov G., Petersen P., Qian L. Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns // Nature. 2017. V. 552. № 7683. P. 67–71. https://doi.org/10.1038/nature24655
  65. Acuna G.P., Moller F.M., Holzmeister P., Beater S., Lalkens B., Tinnefeld P. Fluorescence enhancement at docking sites of DNA-directed self-assembled nanoantennas // Science. 2012. V. 338. № 6106. P. 506–510. https://doi.org/10.1126/science.1228638
  66. Douglas S.M., Dietz H., Liedl T., Hogberg B., Graf F., Shih W.M. Self-assembly of DNA into nanoscale three-dimensional shapes // Nature. 2009. V. 459. № 7245. P. 414–418. https://doi.org/10.1038/nature08016
  67. Martynenko I.V., Erber E., Ruider V., Dass M., Posnjak G., Yin X., Altpeter P., Liedl T. Site-directed placement of three-dimensional DNA origami // Nat Nanotechnol. 2023. V. 18. № 12. P. 1456–1462. https://doi.org/10.1038/s41565-023-01487-z
  68. Filippova Y.A., Papugaeva A.V., Panov D.V., Kozhina E.P., Razumovskaya I.V., Bedin S.A. Studying the geometry and physical characteristics of feni nanowires in ferrofluids // Bulletin of the Russian Academy of Sciences: Physics. 2023. V. 87. № 12. P. 1885–1889. https://doi.org/10.1134/s1062873823704142
  69. Wang H., Jin G., Tan Q. Microstructural characterization of v-defects in InGaN/GaN multiquantum wells // JETP Letters. 2020. V. 111. № 5. P. 264–267. https://doi.org/10.1134/s0021364020050021
  70. Masyutin A.G., Tarasova E.K., Onishchenko G.E., Erokhina M.V. Identifying carbon nanoparticles in biological samples by means of transmission electron microscopy // Bulletin of the Russian Academy of Sciences: Physics. 2023. V. 87. № 10. P. 1443–1448. https://doi.org/10.3103/s106287382370346x
  71. Sollier J., Stork C.T., Garcia-Rubio M.L., Paulsen R.D., Aguilera A., Cimprich K.A. Transcription-coupled nucleotide excision repair factors promote r-loop-induced genome instability // Mol Cell. 2014. V. 56. № 6. P. 777–785. https://doi.org/10.1016/j.molcel.2014.10.020
  72. Shapiro D.A., Yu Y.-S., Tyliszczak T., Cabana J., Celestre R., Chao W., Kaznatcheev K., Kilcoyne A.L.D., Maia F., Marchesini S., Meng Y.S., Warwick T., Yang L.L., Padmore H.A. Chemical composition mapping with nanometre resolution by soft X-ray microscopy // Nature Photonics. 2014. V. 8. № 10. P. 765–769. https://doi.org/10.1038/nphoton.2014.207
  73. Peddie C.J., Genoud C., Kreshuk A., Meechan K., Micheva K.D., Narayan K., Pape C., Parton R.G., Schieber N.L., Schwab Y., Titze B., Verkade P., Aubrey A., Collinson L.M. Volume electron microscopy // Nat. Rev. Methods. Primers. 2022. V. 2. P. 51. https://doi.org/10.1038/s43586-022-00131-9
  74. Rust M.J., Bates M., Zhuang X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (storm) // Nat. Methods. 2006. V. 3. № 10. P. 793–796. https://doi.org/10.1038/nmeth929
  75. Genty G., Salmela L., Dudley J.M., Brunner D., Kokhanovskiy A., Kobtsev S., Turitsyn S.K. Machine learning and applications in ultrafast photonics // Nature Photonics. 2021. V. 15. № 2. P. 91–101. https://doi.org/10.1038/s41566-020-00716-4
  76. Lelek M., Gyparaki M.T., Beliu G., Schueder F., Griffie J., Manley S., Jungmann R., Sauer M., Lakadamyali M., Zimmer C. Single-molecule localization microscopy // Nat. Rev. Methods Primers. 2021. V. 1. P. 39. https://doi.org/10.1038/s43586-021-00038-x
  77. Eremchev I.Y., Prokopova D.V., Losevskii N.N., Mynzhasarov I.T., Kotova S.P., Naumov A.V. Three-dimensional fluorescence nanoscopy of single quantum emitters based on the optics of spiral light beams // Physics-Uspekhi. 2021. V. 65. № 6. P. 617–626. https://doi.org/10.3367/UFNe.2021.05.038982
  78. Dahlberg P.D., Moerner W.E. Cryogenic super-resolution fluorescence and electron microscopy correlated at the nanoscale // Annual Review of Physical Chemistry. 2021. V. 72. № 1. P. 253–278. https://doi.org/10.1146/annurev-physchem-090319-051546
  79. Eremchev M.Y., Naumov A.V. Determination of the character of the interaction of bioactive ions with phospholipid membranes using nonlinear microscopy methods // JETP Letters. 2025. V. 121. № 3. P. 225–230. https://doi.org/10.1134/s0021364024605098
  80. Giessibl F.J. Advances in atomic force microscopy // Reviews of Modern Physics. 2003. V. 75. № 3. P. 949–983. https://doi.org/10.1103/RevModPhys.75.949
  81. Golovanova A.V., Domnina M.A., Arzhanov A.I., Karimullin K.R., Eremchev I.Y., Naumov A.V. AFM characterization of track-etched membranes: Pores parameters distribution and disorder factor // Applied Sciences. 2022. V. 12. № 3. P. 1334. https://doi.org/10.3390/app12031334
  82. Verma P. Tip-enhanced Raman spectroscopy: Technique and recent advances // Chemical Reviews. 2017. V. 117. № 9. P. 6447−6466. https://doi.org/10.1021/acs.chemrev.6b00821
  83. Chernykh E.A., Kharintsev S.S. Sensing phase transitions in solids using thermoplasmonics // Bulletin of the Russian Academy of Sciences: Physics. 2023. V. 86. № S1. P. S37−S40. https://doi.org/10.3103/s1062873822700356
  84. Zhao X., Li M., Ma T., Yan J., Khalaf G.M.G., Chen C., Hsu H.Y., Song H., Tang J. Stable pbs colloidal quantum dot inks enable blade-coating infrared solar cells // Front Optoelectron. 2023. V. 16. № 1, P. 27. https://doi.org/10.1007/s12200-023-00085-0
  85. Lee J., Crampton K.T., Tallarida N., Apkarian V.A. Visualizing vibrational normal modes of a single molecule with atomically confined light // Nature. 2019. V. 568. № 7750. P. 78−82. https://doi.org/10.1038/s41586-019-1059-9
  86. Kasimov R.K., Arzhanov A.I., Sedykh K.O., Golikov A.D., Galanova V.S., Gladush Y.G., Kovalyuk V.V., Naumov A.V., Goltsman G.N. Single photon source based on CdSe/CdS/ZnS quantum dots on silicon nitride waveguides // Book Single photon source based on CdSe/CdS/ZnS quantum dots on silicon nitride waveguides. Editor. 2025.
  87. Rempel A.A., Ovchinnikov O.V., Weinstein I.A., Rempel S.V., Kuznetsova Y.V., Naumov A.V., Smirnov M.S., Eremchev I.Y., Vokhmintsev A.S., Savchenko S.S. Quantum dots: Modern methods of synthesis and optical properties //Russian Chemical Reviews. 2024. V. 93. № 4. P. RCR5114. https://doi.org/10.59761/rcr5114
  88. Castro C.E., Kilchherr F., Kim D.N., Shiao E.L., Wauer T., Wortmann P., Bathe M., Dietz H. A primer to scaffolded DNA origami // Nat. Methods // 2011. V. 8. № 3. P. 221−229. https://doi.org/10.1038/nmeth.1570
  89. Kolbeck P.J., Dass M., Martynenko I.V., van Dijk-Moes R.J.A., Brouwer K.J.H., van Blaaderen A., Vanderlinden W., Liedl T., Lipfert J. A DNA origami fiducial for accurate 3d afm imaging // bioRxiv. 2022. https://doi.org/10.1101/2022.11.11.516090
  90. Matsunaga Y., Fuchigami S., Ogane T., et al. End-to-end differentiable blind tip reconstruction for noisy atomic force microscopy images // Sci Rep. 2023. V. 13. P. 129. https://doi.org/10.1038/s41598-022-27057-2
  91. Villarrubia J.S. Algorithms for scanned probe microscope image simulation, surface reconstruction, and tip estimation // Journal of Research of the National Institute of Standards and Technology. 1997. V. 102. № 4. P. 425. https://doi.org/10.6028/jres.102.030
  92. Nečas D., Klapetek P. Gwyddion: An open-source software for spm data analysis // Open Physics. 2012. V. 10. № 1. P. 181−188. https://doi.org/10.2478/s11534-011-0096-2
  93. Weiden J., Basting M.M.C. DNA origami nanostructures for controlled therapeutic drug delivery // Current Opinion in Colloid & Interface Science. 2021. V. 52. P. 101411. https://doi.org/10.1016/j.cocis.2020.101411
  94. Wang W.X., Douglas T.R., Zhang H., Bhattacharya A., Rothenbroker M., Tang W., Sun Y., Jia Z., Muffat J., Li Y., Chou L.Y.T. Universal, label-free, single-molecule visualization of DNA origami nanodevices across biological samples using origamifish // Nat. Nanotechnol., 2024. V. 19. № 1. P. 58−69. https://doi.org/10.1038/s41565-023-01449-5
  95. Karimullin K.R., Arzhanov A.I., Eremchev I.Y., Kulnitskiy B.A., Surovtsev N.V., Naumov A.V. Combined photon-echo, luminescence and raman spectroscopies of layered ensembles of colloidal quantum dots // Laser Physics. 2019. V. 29. № 12. P. 124009. https://doi.org/10.1088/1555-6611/ab4bdb
  96. Karimullin K.R., Arzhanov A.I., Naumov A.V. Preparation and optical characterization of nanocomposites with semiconductor colloidal quantum dots // Bulletin of the Russian Academy of Sciences: Physics. 2017. V. 81. № 12. P. 1396−1400. https://doi.org/10.3103/S1062873817120164
  97. Kozhina E., Bedin S., Martynov A., Andreev S., Piryazev A., Grigoriev Y., Gorbunova Y., Naumov A. Ultrasensitive optical fingerprinting of biorelevant molecules by means of sers-mapping on nanostructured metasurfaces // Biosensors. 2023. V. 13. № 1. P. 46. https://doi.org/10.3390/bios13010046
  98. Li K., Qin W., Xu Y., Peng T., Li D. Optical approaches in study of nanocatalysis with single-molecule and single-particle resolution // Frontiers of Optoelectronics. 2015. V. 8. № 4. P. 379−393. https://doi.org/10.1007/s12200-014-0423-5
  99. Li S., Shi B., He D., Zhou H., Gao Z. DNA origami-mediated plasmonic dimer nanoantenna-based sers biosensor for ultrasensitive determination of trace diethylstilbestrol // Journal of Hazardous Materials. 2023. V. 458. P. 131874. https://doi.org/10.1016/j.jhazmat.2023.131874
  100. Prinz J., Heck C., Ellerik L., Merk V., Bald I. DNA origami based au–ag-core–shell nanoparticle dimers with single-molecule sers sensitivity // Nanoscale. 2016. V. 8. № 10. P. 5612−5620. https://doi.org/10.1039/c5nr08674d
  101. Rajendran A., Endo M., Sugiyama H. Single‐molecule analysis using DNA origami // Angewandte Chemie International Edition. 2011. V. 51. № 4. P. 874−890. https://doi.org/10.1002/anie.201102113
  102. Adhikari S., Smit R., Orrit M. Future paths in cryogenic single-molecule fluorescence spectroscopy // The Journal of Physical Chemistry C. 2023. V. 128. № 1. P. 3−18. https://doi.org/10.1021/acs.jpcc.3c06564
  103. Adhikari S., Orrit M. Progress and perspectives in single-molecule optical spectroscopy // The Journal of Chemical Physics. 2022. V. 156. № 16. P. 160903. https://doi.org/10.1063/5.0087003
  104. Naumov A.V., Gorshelev A.A., Gladush M.G., Anikushina T.A., Golovanova A.V., Köhler J., Kador L. Micro-refractometry and local-field mapping with single molecules // Nano Letters. 2018. V. 18. № 10. P. 6129−6134. https://doi.org/10.1021/acs.nanolett.8b01753
  105. Gladush M.G., Anikushina T.A., Gorshelev A.A., Plakhotnik T.V., Naumov A.V. Dispersion of lifetimes of excited states of single molecules in organic matrices at ultralow temperatures // Journal of Experimental and Theoretical Physics. 2019. V. 128. № 5. P. 655−663. https://doi.org/10.1134/s1063776119030038

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