One-step microchip for DNA fluorescent labeling

  • Yeongseok Jang
  • Hojun Shin
  • Jinmu JungEmail author
  • Jonghyun OhEmail author


In this study, we propose a microchip that is sequentially capable of fluorescently staining and washing DNAs. The main advantage of this microchip is that it allows for one-step preparation of small amounts of solution without degrading microscopic bio-objects such as the DNAs, cells, and biomolecules to be stained. The microchip consists of two inlets, the main channel, staining zone, washing zone, and one outlet, and was processed using a femtosecond laser system. High molecular transport of rhodamine B to deionized water was observed in the performance test of the microchip. Results revealed that the one-step procedure of on-chip DNA staining and washing was excellent compared to the conventional staining method. The one-step preparation of stained and washed DNAs through the microchip will be useful for preparing small volumes of experimental samples.


Staining DNA Microchip Femtosecond laser Diffusion 



This work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2017R1A4A1015681, NRF-2018R1D1A3B07047434, and 2019R1I1A3A01060695).

Author contributions

Conceptualization, Jinmu Jung and Jonghyun Oh; Data curation, Yeongseok Jang and Hojun Shin; Formal analysis, Yeongseok Jang and Hojun Shin; Investigation, Yeongseok Jang and Hojun Shin; Project administration, Jinmu Jung and Jonghyun Oh; Supervision, Jinmu Jung and Jonghyun Oh; Writing—original draft, Yeongseok Jang and Hojun Shin; Writing—review & editing, Jinmu Jung and Jonghyun Oh.

Compliance with ethical standards

Conflict of interest

The authors declare no conflict of interest.


  1. L. Schermelleh, R. Heintzmann, H. Leonhardt, A guide to super-resolution fluorescence microscopy. J. Cell Biol. 190, 165–175 (2010)CrossRefGoogle Scholar
  2. M. Gao, F. Yu, C. Lv, J. Choo, L. Chen, Fluorescent chemical probes for accurate tumor diagnosis and targeting therapy. Chem. Soc. Rev. 46, 2237–2271 (2017)CrossRefGoogle Scholar
  3. M. Ratz, I. Testa, S.W. Hell, S. Jakobs, Crispr/cas9-mediated endogenous protein tagging for resolft super-resolution microscopy of living human cells. Sci. Rep. 5, 9592 (2015)CrossRefGoogle Scholar
  4. F. Göttfert, T. Pleiner, J. Heine, V. Westphal, D. Görlich, S.J. Sahl, S.W. Hell, Strong signal increase in sted fluorescence microscopy by imaging regions of subdiffraction extent. Proc. Natl. Acad. Sci. U. S. A. 114, 2125–2130 (2017)CrossRefGoogle Scholar
  5. M. Pusey, J. Barcena, M. Morris, A. Singhal, Q. Yuan, J. Ng, Trace fluorescent labeling for protein crystallization. Acta Crystallogr. F Struct. Biol. Commun. 71, 806–814 (2015)CrossRefGoogle Scholar
  6. J.R. Simard, M. Getlik, C. Grütter, R. Schneider, S. Wulfert, D. Rauh, Fluorophore labeling of the glycine-rich loop as a method of identifying inhibitors that bind to active and inactive kinase conformations. J. Am. Chem. Soc. 132, 4152–4160 (2010)CrossRefGoogle Scholar
  7. T. Tamura, Y. Kioi, T. Miki, S. Tsukiji, I. Hamachi, Fluorophore labeling of native fkbp12 by ligand-directed tosyl chemistry allows detection of its molecular interactions in vitro and in living cells. J. Am. Chem. Soc. 135, 6782–6785 (2013)CrossRefGoogle Scholar
  8. K.E. Beatty, D.A. Tirrell, Two-color labeling of temporally defined protein populations in mammalian cells. Bioorg. Med. Chem. Lett. 18, 5995–5999 (2008)CrossRefGoogle Scholar
  9. A. Hartmann, G. Krainer, M. Schlierf, Different fluorophore labeling strategies and designs affect millisecond kinetics of DNA hairpins. Molecules 19, 13735–13754 (2014)CrossRefGoogle Scholar
  10. C.G. Jones, V. Stavila, M.A. Conroy, P. Feng, B.V. Slaughter, C.E. Ashley, M.D. Allendorf, Versatile synthesis and fluorescent labeling of zif-90 nanoparticles for biomedical applications. ACS Appl. Mater. Interfaces 8, 7623–7630 (2016)CrossRefGoogle Scholar
  11. H. Sahoo, Fluorescent labeling techniques in biomolecules: a flashback. RSC Adv. 2, 7017–7029 (2012)CrossRefGoogle Scholar
  12. W. Nomura, Y. Tanabe, H. Tsutsumi, T. Tanaka, K. Ohba, N. Yamamoto, H. Tamamura, Fluorophore labeling enables imaging and evaluation of specific cxcr4− ligand interaction at the cell membrane for fluorescence-based screening. Bioconjug. Chem. 19, 1917–1920 (2008)CrossRefGoogle Scholar
  13. Z. Li, K. Munro, I.I. Ebralize, M.R. Narouz, J.D. Padmos, H. Hao, C.M. Crudden, J.H. Horton, N-heterocyclic carbene self-assembled monolayers on gold as surface plasmon resonance biosensors. Langmuir 33, 13936–13944 (2017)CrossRefGoogle Scholar
  14. S. Savas, A. Ersoy, Y. Gulmez, S. Kilic, B. Levent, Z. Altintas, Nanoparticle enhanced antibody and DNA biosensors for sensitive detection of salmonella. Materials 11, 1541 (2018)CrossRefGoogle Scholar
  15. L. Huang, Z. Li, Y. Lou, F. Cao, D. Zhang, X. Li, Recent advances in scanning electrochemical microscopy for biological applications. Materials 11, 1389 (2018)CrossRefGoogle Scholar
  16. J.G. Egan, N. Drossis, I.I. Ebralidze, H.M. Fruehwald, N.O. Laschuk, J. Poisson, H.W. de Haan, O.V. Zenkina, Hemoglobin-driven iron-directed assembly of gold nanoparticles. RSC Adv. 8, 15675–15686 (2018)CrossRefGoogle Scholar
  17. M. Salerno, S. Dante, Scanning kelvin probe microscopy: challenges and perspectives towards increased application on biomaterials and biological samples. Materials 11, 951 (2018)CrossRefGoogle Scholar
  18. X. Ji, K. Ji, V. Chittavong, R.E. Aghoghovbia, M. Zhu, B. Wang, Click and fluoresce: a bioorthogonally activated smart probe for wash-free fluorescent labeling of biomolecules. J. Org. Chem. 82, 1471–1476 (2017)CrossRefGoogle Scholar
  19. H. Nonaka, S.-h. Fujishima, S.-h. Uchinomiya, A. Ojida, I. Hamachi, Selective covalent labeling of tag-fused gpcr proteins on live cell surface with a synthetic probe for their functional analysis. J. Am. Chem. Soc. 132, 9301–9309 (2010)CrossRefGoogle Scholar
  20. V.C. DeRocco, T. Anderson, J. Piehler, D.A. Erie, K. Weninger, Four-color single molecule fluorescence with noncovalent dye labeling to monitor dynamic multimolecular complexes. Biotechniques 49, 807 (2010)CrossRefGoogle Scholar
  21. M. Rashidian, J.K. Dozier, M.D. Distefano, Enzymatic labeling of proteins: techniques and approaches. Bioconjug. Chem. 24, 1277–1294 (2013)CrossRefGoogle Scholar
  22. M.Z. Lin, L. Wang, Selective labeling of proteins with chemical probes in living cells. Physiology 23, 131–141 (2008)CrossRefGoogle Scholar
  23. Y. Yano, N. Furukawa, S. Ono, Y. Takeda, K. Matsuzaki, Selective amine labeling of cell surface proteins guided by coiled-coil assembly. Biopolymers 106, 484–490 (2016)CrossRefGoogle Scholar
  24. L.A. Montoya, M.D. Pluth, Hydrogen sulfide deactivates common nitrobenzofurazan-based fluorescent thiol labeling reagents. Anal. Chem. 86, 6032–6039 (2014)CrossRefGoogle Scholar
  25. M.H. Lauer, C. Vranken, J. Deen, W. Frederickx, W. Vanderlinden, N. Wand, V. Leen, M.H. Gehlen, J. Hofkens, R.K. Neely, Methyltransferase-directed covalent coupling of fluorophores to DNA. Chem. Sci. 8, 3804–3811 (2017)CrossRefGoogle Scholar
  26. Y. Suseela, N. Narayanaswamy, S. Pratihar, T. Govindaraju, Far-red fluorescent probes for canonical and non-canonical nucleic acid structures: current progress and future implications. Chem. Soc. Rev. 47, 1098–1131 (2018)CrossRefGoogle Scholar
  27. M. Schürmann, G. Cojoc, S. Girardo, E. Ulbricht, J. Guck, P. Müller, Three-dimensional correlative single-cell imaging utilizing fluorescence and refractive index tomography. J. Biophotonics 11, e201700145 (2018)CrossRefGoogle Scholar
  28. E.A. Specht, E. Braselmann, A.E. Palmer, A critical and comparative review of fluorescent tools for live-cell imaging. Annu. Rev. Physiol. 79, 93–117 (2017)CrossRefGoogle Scholar
  29. K.M. Piltti, B.J. Cummings, K. Carta, A. Manughian-Peter, C.L. Worne, K. Singh, D. Ong, Y. Maksymyuk, M. Khine, A.J. Anderson, Live-cell time-lapse imaging and single-cell tracking of in vitro cultured neural stem cells–tools for analyzing dynamics of cell cycle, migration, and lineage selection. Methods 133, 81–90 (2018)CrossRefGoogle Scholar
  30. S. Claveau, J.-R. Bertrand, F. Treussart, Fluorescent nanodiamond applications for cellular process sensing and cell tracking. Micromachines 9, 247 (2018)CrossRefGoogle Scholar
  31. N. Futai, M. Tamura, T. Ogawa, M. Tanaka, Microfluidic long-term gradient generator with axon separation prototyped by 185 nm diffused light photolithography of su-8 photoresist. Micromachines 10, 9 (2019)CrossRefGoogle Scholar
  32. M. Gallab, K. Tomita, S. Omata, F. Arai, Fabrication of 3d capillary vessel models with circulatory connection ports. Micromachines 9, 101 (2018)CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Mechanical Design Engineering, College of EngineeringChonbuk National UniversityJeonjuSouth Korea
  2. 2.Advanced Development GroupSamsung SDI Co.YonginSouth Korea
  3. 3.Department of Nano-Bio Mechanical System Engineering, College of EngineeringChonbuk National UniversityJeonjuSouth Korea

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