Physicochemical properties of new cyanine dye derivatives in DNA conjugates
https://doi.org/10.29235/1561-8331-2025-61-2-95-104
Abstract
Cyanine dyes are one of the most commonly used classes of fluorescent probes. All Cy5 fluoresce at ~ 660 nm, while Cy7 emit in the near-infrared range (700–900 nm), making them particularly suitable for biomedical applications due to reduced tissue autofluorescence in this spectral region. The fluorescence intensity of cyanine dyes typically increases upon conjugation with biomolecules such as nucleic acids. Furthermore, their fluorescence can be significantly modulated through duplex formation between dye-modified single-stranded DNA and its complementary sequence. In this study, we investigated physicochemical properties of a series of Cy5 and Cy7 derivatives with substituents of varying lengths at distinct molecular positions in both single-and double-stranded DNA conjugates.
Supporting agencies: This work has been performed with the financial support of Belarusian Republican Foundation for Fundamental Research (projects No. Ф24В-006 and Х23РНФ-041) and China Scholarship Council Foundation (No. 202008400011). The authors express their gratitude to M.R. Rebkovets and V.V. Kaminskaya for the synthesis of the studied oligonucleotides.
About the Authors
F. Fan
Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus
Belarus
Belarus
Fan Fan – Postgraduate Student, Institute of Physical-Organic Chemistry of the National Academy of Science of Belarus.
13, Surganov Str., 220072, Minsk
V. A. Povedailo
B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus
Belarus
Belarus
Vladimir A. Povedailo – Dr. Sc. (Physics and Mathematics), Chief Researcher, Institute of Physics of the National Academy of Science of Belarus.
68, Nezavisimosti Ave., 220072, Minsk
A. P. Kadutskii
Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus
Belarus
Belarus
Aleksey P. Kadutskii – Researcher, Institute of Physical-Organic Chemistry of the National Academy of Science of Belarus.
13, Surganov Str., 220072, Minsk
G. V. Maleev
Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences
Russian Federation
Russian Federation
Grigoriy V. Maleev – Senior Researcher, Institute of Physiologically Active Compounds at Federal Research Center of Problems of Chemical Physics and Medicinal Chemistry of Russian Academy of Sciences.
1, Academian Semenov Ave., Chernogolovka, Moscow region, 142432
V. V. Shmanai
Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus
Belarus
Belarus
Vadim V. Shmanai – Ph. D. (Chemistry), Associate Professor, Head of the Laboratory, Institute of Physical-Organic Chemistry of the National Academy of Science of Belarus.
13, Surganov Str., 220072, Minsk
References
1. Li X., Yin Y., Yang X., Zhi Z., Zhao X. Temperature dependence of interaction between double stranded DNA and Cy3 or Cy5. Chemical Physics Letters, 2011, vol. 513, no. 4–6, pp. 271–275. https://doi.org/10.1016/j.cplett.2011.08.017
2. Kurutos A., Ryzhova O., Trusova V., Gorbenko G., Gadjev N., Deligeorgiev T. Symmetric meso-chloro-substituted pentamethine cyanine dyes containing benzothiazolyl/benzoselenazolyl chromophores novel synthetic approach and studies on photophysical properties upon interaction with bio-objects. Journal of fluorescence, 2016, no. 26, no. 1, pp. 177–187. https://doi.org/10.1007/s10895-015-1700-4
3. Nanjunda R., Owens E. A., Mickelson L., Dost T. L., Stroeva E. M., Huynh H. T., Germann M. W., Henary M. M., Wilson W. D. Selective G-quadruplex DNA recognition by a new class of designed cyanines. Molecules, 2013, vol. 18, no. 11, pp. 13588–13607. https://doi.org/10.3390/molecules181113588
4. Yarmoluk S. M., Kovalska V. B., Losytskyy M. Y. Symmetric cyanine dyes for detecting nucleic acids. Biotechnic & Histochemistry, 2008, vol. 83, no. 3–4, pp. 131–145. https://doi.org/10.1080/10520290802383684
5. Kitamura A., Tornmalm J., Demirbay B., Piguet J., Kinjo M., Widengren J. Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells. Nucleic acids research, 2023, vol. 51, no. 5, pp. e27–e27. https://doi.org/10.1093/nar/gkac1255
6. Stennett E. M., Ciuba M. A., Lin S., Levitus M. Demystifying PIFE: the photophysics behind the protein-induced fluorescence enhancement phenomenon in Cy3. The Journal of Physical Chemistry Letters, 2015, vol. 6, no. 10, pp. 1819–1823. https://doi.org/10.1021/acs.jpclett.5b00613
7. Rashid F., Raducanu V. S., Zaher M. S., Tehseen M., Habuchi S., Hamdan S. M. Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation. Nature Communications, 2019, vol. 10, no. 1, pp. 2104. https://doi.org/10.1038/s41467-019-10137-9
8. Hwang H., Myong S. Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions. Chemical Society Reviews, 2014, vol. 43, no. 4, pp. 1221–1229. https://doi.org/10.1039/C3CS60201J
9. Cheng Y., Wang N., Ren Z., Xu C. Development of fluorescence-based nucleic acid blot hybridization method using Cy5. 5 labeled DNA probes. Journal of Microbiological Methods, 2022, vol. 197, pp. 106479. https://doi.org/10.1016/j.mimet.2022.106479
10. Zhang C., Liu T., Su Y., Luo S., Zhu Y., Tan X., Fan S., Zhang L., Zhou Y., Cheng T., Shi C. A near-infrared fluorescent heptamethine indocyanine dye with preferential tumor accumulation for in vivo imaging. Biomaterials, 2010, vol. 31, no. 25, pp. 6612–6617. https://doi.org/10.1016/j.biomaterials.2010.05.007
11. Fernandez-Fernandez A., Manchanda R., Lei T., Carvajal D. A., Tang Y., Kazmi S. Z. R., McGoron A. J. Comparative study of the optical and heat generation properties of IR820 and indocyanine green. Molecular Imaging, 2012, vol. 11, no. 2, pp. 99–113. https://doi.org/10.2310/7290.2011.00031
12. Ebert B., Riefke B., Sukowski U., Licha K. Cyanine dyes as contrast agents for near-infrared imaging in vivo: acute tolerance, pharmacokinetics, and fluorescence imaging. Journal of Biomedical Optics, 2011, vol. 16, no. 6, pp. 066003. https://doi.org/10.1117/1.3585678
13. Pronkin P., Tatikolov A. Isomerization and properties of isomers of carbocyanine dyes. Sci, 2019, vol. 1, no. 1, pp. 19. https://doi.org/10.3390/sci1010019
14. Cooper M., Ebner A., Briggs M., Burrows M., Gardner N., Richardson R., West R. Cy3B™: improving the performance of cyanine dyes. Journal of Fluorescence, 2004, vol. 14, no. 2, pp. 145–150. https://doi.org/10.1023/B:JOFL.0000016286.62641.59
15. Widengren J., Schwille P. Characterization of photoinduced isomerization and back-isomerization of the cyanine dye Cy5 by fluorescence correlation spectroscopy. The Journal of Physical Chemistry A, 2000, vol. 104, no. 27, pp. 6416–6428. https://doi.org/10.1021/jp000059s
16. Sanchez-Galvez A., Hunt P., Robb M. A., Olivucci M., Vreven T., Schlegel H. B. Ultrafast radiationless deactivation of organic dyes: evidence for a two-state two-mode pathway in polymethine cyanines. Journal of the American Chemical Society, 2000, vol. 122, no. 12, pp. 2911–2924. https://doi.org/10.1021/ja993985x
17. Fan F., Povedailo V. A., Lysenko I. L., Seviarynchyk T. P., Sharko O. L., Mazunin I. O., Shmanai V. V. Fluorescent properties of cyanine dyes as a matter of the environment. Journal of Fluorescence, 2024, vol. 34, no. 2, pp. 925–933. https://doi.org/10.1007/s10895-023-03321-0
18. Åkesson E., Hakkarainen A., Laitinen E., Helenius V., Gillbro T., Korppi-Tommola J., Sundström V. Analysis of microviscosity and reaction coordinate concepts in isomerization dynamics described by Kramers’ theory. The Journal of Chemical Physics, 1991, vol. 95, no. 9, pp. 6508–6523. https://doi.org/10.1063/1.461521
19. Sanborn M. E., Connolly B. K., Gurunathan K., Levitus M. Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. The Journal of Physical Chemistry B, 2007, vol. 111, no. 37, pp. 11064–11074. https://doi.org/10.1021/jp072912u
20. Williams R. J., Peralta J. M., Tsang V. C., Narayanan N., Casay G. A., Lipowska M., Strekowski L., Patonay G. Near-infrared heptamethine cyanine dyes: a new tracer for solid-phase immunoassays. Applied Spectroscopy, 1997, vol. 51, no. 6, pp. 836–843. https://doi.org/10.1366/0003702971941115
21. Yuan L., Lin W., Zheng K., He L., Huang W. Far-red to near infrared analyte-responsive fluorescent probes based on organic fluorophore platforms for fluorescence imaging. Chemical Society Reviews, 2013, vol. 42, no. 2, pp. 622–661. https://doi.org/10.1039/C2CS35313J
22. Feng L., Chen W., Ma X., Liu S., Yin J. Near-infrared heptamethine cyanines (Cy7): from structure, property to application. Organic & Biomolecular Chemistry, 2020, vol. 18, no. 46, pp. 9385–9397. https://doi.org/10.1039/D0OB01962C
23. Levitz A., Marmarchi F., Henary M. Introduction of various substitutions to the methine bridge of heptamethine cyanine dyes Via substituted dianil linkers. Photochemical & Photobiological Sciences, 2018, vol. 17, no. 10, pp. 1409–1416. https://doi.org/10.1039/c8pp00218e
24. Rostovtsev V. V., Green L. G., Fokin V. V., Sharpless K. B. A stepwise huisgen cycloaddition process: copper (I)‐ catalyzed regioselective “ligation” of azides and terminal alkynes. Angewandte Chemie, 2002, vol. 114, no. 14, pp. 2708–2711. https://doi.org/10.1002/1521-3773(20020715)41:14<2596::aid-anie2596>3.0.co;2-4
25. Tornøe C. W., Christensen C., Meldal M. Peptidotriazoles on solid phase [1,2,3]-triazoles by regiospecific copper (I)-catalyzed 1, 3-dipolar cycloadditions of terminal alkynes to azides. The Journal of Organic Chemistry, 2002, vol. 67, no. 9, pp. 3057–3064. https://doi.org/10.1021/jo011148j
26. Stackova L., Muchova E., Russo M., Slavicek P., Stacko P., Klán P. Deciphering the structure–property relations in substituted heptamethine cyanines. The Journal of Organic Chemistry, 2020, vol. 85, no 15, pp. 9776–9790. https://doi.org/10.1021/acs.joc.0c01104
27. Iqbal A., Wang L., Thompson K. C., Lilley D. M., Norman D. G. The structure of cyanine 5 terminally attached to double-stranded DNA: implications for FRET studies. Biochemistry, 2008, vol. 47, no 30, pp. 7857–7862. https://doi.org/10.1021/bi800773f
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