Skip to main content
SpringerLink
Log in

Fluorescent Properties of Cyanine Dyes As a Matter of the Environment

  • RESEARCH
  • Published:
Journal of Fluorescence Aims and scope Submit manuscript

Abstract

In non-viscous aqueous solutions, the cyanine fluorescent dyes Cy3 and Cy5 have rather low fluorescence efficiency (the fluorescence quantum yields of Cy3 and Cy5 are 0.04 and 0.3, respectively [1, 2]) and short excited state lifetimes due to their structural features. In this work, we investigated the effect of solubility and rotational degrees of freedom on the fluorescence efficiency of Cy3 and Cy5 in several ways. We compared the fluorescence efficiencies of two cyanine dyes sCy3 and sCy5 with the introduction of a sulfonyl substituent in the aromatic ring as well as covalently bound to T10 oligonucleotides. The results show that because of the different lengths of the polymethine chains between the aromatic rings of the dyes, cis–trans-isomerization has a much greater effect on the Cy3 molecule than on the Cy5 molecule, while the effect of aggregation is also significant.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

Availability of Data and Materials

Not applicable.

References

  1. Cooper M, Ebner A, Briggs M, Burrows M, Gardner N, Richardson R, West R (2004) Cy3B™: improving the performance of cyanine dyes. J Fluoresc 14:145–150. https://doi.org/10.1023/b:jofl.0000016286.62641.59

    Article  CAS  PubMed  Google Scholar 

  2. Wong KL, Bünzli JCG, Tanner PA (2020) Quantum yield and brightness. J Lumin 224:117256. https://doi.org/10.1016/j.jlumin.2020.117256

  3. Stennett EMS, Ciuba MA, Lin S, Levitus M (2015) Demystifying PIFE: The Photophysics Behind the Protein-Induced Fluorescence Enhancement Phenomenon in Cy3. J Phys Chem Lett 6(10):1819–1823. https://doi.org/10.1021/acs.jpclett.5b00613

    Article  CAS  PubMed  Google Scholar 

  4. Rashid F, Raducanu V-S, Zaher MS, Tehseen M, Habuchi S, Hamdan SM (2019) Initial state of DNA-Dye complex sets the stage for protein induced fluorescence modulation. Nat Commun 10(1):2104. https://doi.org/10.1038/s41467-019-10137-9

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  5. Jares-Erijman EA, Jovin TM (1996) Determination of DNA Helical Handedness by Fluorescence Resonance Energy Transfer. J Mol Biol 257(3):597–617. https://doi.org/10.1006/jmbi.1996.0188

    Article  CAS  PubMed  Google Scholar 

  6. Li X, Yin Y, Yang X, Zhi Z, Zhao XS (2011) Temperature dependence of interaction between double stranded DNA and Cy3 or Cy5. Chem Phys Lett 513(4–6):271–275. https://doi.org/10.1016/j.cplett.2011.08.017

    Article  ADS  CAS  Google Scholar 

  7. Kurutos A, Ryzhova O, Trusova V, Gorbenko G, Gadjev N, Deligeorgiev T (2016) Symmetric meso-chloro-substituted pentamethine cyanine dyes containing benzothiazolyl/benzoselenazolyl chromophores novel synthetic approach and studies on photophysical properties upon interaction with bio-objects. J Fluoresc 26:177–187. https://doi.org/10.1007/s10895-015-1700-4

    Article  CAS  PubMed  Google Scholar 

  8. Yarmoluk SM, Kovalska VB, Losytskyy M (2008) Symmetric cyanine dyes for detecting nucleic acids. Biotech Histochem 83(3–4):131–145. https://doi.org/10.1080/10520290802383684

    Article  CAS  PubMed  Google Scholar 

  9. Kurutos A, Orehovec I, Paić AT, Crnolatac I, Horvat L, Gadjev N, Deligeorgiev T (2018) New series of non-toxic DNA intercalators, mitochondria targeting fluorescent dyes. Dyes Pigm 148:452–459. https://doi.org/10.1016/j.dyepig.2017.09.049

  10. Kurutos A, Orehovec I, Saftić D, Horvat L, Crnolatac I, Piantanida I, Deligeorgiev T (2018) Cell penetrating, mitochondria targeting multiply charged DABCO-cyanine dyes. Dyes Pigm 158:517–525. https://doi.org/10.1016/j.dyepig.2018.05.035

    Article  CAS  Google Scholar 

  11. Constantin TP, Silva GL, Robertson KL, Hamilton TP, Fague K, Waggoner AS, Armitage BA (2008) Synthesis of new fluorogenic cyanine dyes and incorporation into RNA fluoromodules. Org Lett 10(8):1561–1564. https://doi.org/10.1021/ol702920e

    Article  CAS  PubMed  Google Scholar 

  12. Fegan A, Shirude PS, Balasubramanian S (2008) Rigid cyanine dye nucleic acid labels. Chem Commun 17:2004–2006. https://doi.org/10.1039/B801629A

    Article  Google Scholar 

  13. Kitamura A, Tornmalm J, Demirbay B, Piguet J, Kinjo M, Widengren J (2023) Trans-cis isomerization kinetics of cyanine dyes reports on the folding states of exogeneous RNA G-quadruplexes in live cells. Nucleic Acids Res. https://doi.org/10.1093/nar/gkac1255

    Article  PubMed  PubMed Central  Google Scholar 

  14. Norman DG, Grainger RJ, Uhrín D, Lilley DMJ (2000) Location of Cyanine-3 on Double-Stranded DNA: Importance for Fluorescence Resonance Energy Transfer Studies†. Biochemistry 39(21):6317–6324. https://doi.org/10.1021/bi992944a

    Article  CAS  PubMed  Google Scholar 

  15. Iqbal A, Wang L, Thompson KC, Lilley DMJ, Norman DG (2008) The Structure of Cyanine 5 Terminally Attached to Double-Stranded DNA: Implications for FRET Studies†. Biochemistry 47(30):7857–7862. https://doi.org/10.1021/bi800773f

    Article  CAS  PubMed  Google Scholar 

  16. Laib S, Seeger S (2004) FRET studies of the interaction of dimeric cyanine dyes with DNA. J Fluoresc 14:187–191. https://doi.org/10.1023/b:jofl.0000016290.34070.ee

    Article  CAS  PubMed  Google Scholar 

  17. Von der Haar M, Heuer C, Pähler M, Von der Haar K, Lindner P, Scheper T, Stahl F (2016) Optimization of cyanine dye stability and analysis of FRET interaction on DNA microarrays. Biology 5(4):47. https://doi.org/10.3390/biology5040047

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Guo X, Yang D, Sun R, Li Q, Du H, Tang Y, Sun H (2021) A cyanine dye supramolecular FRET switch driven by G-quadruplex to monitor mitophagy. Dyes Pigm 192:109429. https://doi.org/10.1016/j.dyepig.2021.109429

  19. Zhytniakivska O, Kurutos A, Shchuka M, Vus K, Tarabara U, Trusova V, Gorbenko G (2021) Fӧrster resonance energy transfer between Thioflavin T and unsymmetrical trimethine cyanine dyes on amyloid fibril scaffold. Chem Phys Lett 785:139127. https://doi.org/10.1016/j.cplett.2021.139127

  20. Főrster T (1959) 10th Spiers Memorial Lecture. Transfer mechanisms of electronic excitation. Discuss. Faraday Soc. 27(0):7–17. https://doi.org/10.1039/df9592700007

  21. Sanchez-Galvez A, Hunt P, Robb MA, Olivucci M, Vreven T, Schlegel HB (2000) Ultrafast Radiationless Deactivation of Organic Dyes: Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines. J Am Chem Soc 122(12):2911–2924. https://doi.org/10.1021/ja993985x

    Article  CAS  Google Scholar 

  22. Levitus M, Negri RM, Aramendia PF (1995) Rotational Relaxation of Carbocyanines. Comparative Study with the Isomerization Dynamics. J Phys Chem 99(39):14231–14239. https://doi.org/10.1021/j100039a008

  23. Rullière C (1976) Laser action and photoisomerisation of 3,3′-diethyl oxadicarbocyanine iodide (DODCI): Influence of temperature and concentration. Chem Phys Lett 43(2):303–308. https://doi.org/10.1016/0009-2614(76)85308-0

    Article  ADS  Google Scholar 

  24. Di Paolo RE, Scaffardi LB, Duchowicz R, Bilmes GM (1995) Photoisomerization Dynamics and Spectroscopy of the Polymethine Dye DTCI. J Phys Chem 99(38):13796–13799. https://doi.org/10.1021/j100038a008

    Article  Google Scholar 

  25. Scaffardi L, Di Paolo RE, Duchowicz R (1997) Simultaneous absorption and fluorescence analysis of the cyanine dye DOCI. J Photochem Photobiol, A 107(1–3):185–188. https://doi.org/10.1016/s1010-6030(97)00026-9

    Article  CAS  Google Scholar 

  26. Aramendia PF, Negri RM, Roman ES (1994) Temperature Dependence of Fluorescence and Photoisomerization in Symmetric Carbocyanines. Influence of Medium Viscosity and Molecular Structure. J Phys Chem 98(12):3165–3173. https://doi.org/10.1021/j100063a020

  27. Sczepan M, Rettig W, Bricks L, Y., Slominski, Y. L., & Tolmachev, A. I. (1999) Unsymmetric cyanines: chemical rigidization and photophysical properties. J Photochem Photobiol, A 124(1–2):75–84. https://doi.org/10.1016/s1010-6030(99)00045-3

    Article  CAS  Google Scholar 

  28. Sanborn ME, Connolly BK, Gurunathan K, Levitus M (2007) Fluorescence Properties and Photophysics of the Sulfoindocyanine Cy3 Linked Covalently to DNA. J Phys Chem B 111(37):11064–11074. https://doi.org/10.1021/jp072912u

    Article  CAS  PubMed  Google Scholar 

  29. Åkesson E, Hakkarainen A, Laitinen E, Helenius V, Gillbro T, Korppi-Tommola J, Sundström V (1991) Analysis of microviscosity and reaction coordinate concepts in isomerization dynamics described by Kramers’ theory. J Chem Phys 95(9):6508–6523. https://doi.org/10.1063/1.461521

    Article  ADS  Google Scholar 

  30. Kretschy N, Sack M, Somoza MM (2016) Sequence-Dependent Fluorescence of Cy3- and Cy5-Labeled Double-Stranded DNA. Bioconjug Chem 27(3):840–848. https://doi.org/10.1021/acs.bioconjchem.6b00053

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Pace NA, Hennelly SP, Goodwin PM (2021) Immobilization of cyanines in DNA produces systematic increases in fluorescence intensity. J Phys Chem Lett 12(37):8963–8971. https://doi.org/10.1021/acs.jpclett.1c02022

    Article  CAS  PubMed  Google Scholar 

  32. Stennett EM, Ma N, Van Der Vaart A, Levitus M (2014) Photophysical and dynamical properties of doubly linked Cy3–DNA constructs. J Phys Chem B 118(1):152–163. https://doi.org/10.1016/j.bpj.2013.11.448

    Article  CAS  PubMed  Google Scholar 

  33. Hall LM, Gerowska M, Brown T (2012) A highly fluorescent DNA toolkit: synthesis and properties of oligonucleotides containing new Cy3, Cy5 and Cy3B monomers. Nucleic Acids Res 40(14):e108–e108. https://doi.org/10.1093/nar/gks303

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Kurutos A, Crnolatac I, Orehovec I, Gadjev N, Piantanida I, Deligeorgiev T (2016) Novel synthetic approach to asymmetric monocationic trimethine cyanine dyes derived from N-ethyl quinolinum moiety. Combined fluorescent and ICD probes for AT-DNA labelling. J Lumin 174:70–76. https://doi.org/10.1016/j.jlumin.2016.01.035

    Article  CAS  Google Scholar 

  35. Kurutos A, Ryzhova O, Tarabara U, Trusova V, Gorbenko G, Gadjev N, Deligeorgiev T (2016) Novel synthetic approach to near-infrared heptamethine cyanine dyes and spectroscopic characterization in presence of biological molecules. J Photochem Photobiol A 328:87–96. https://doi.org/10.1016/j.jphotochem.2016.05.019

    Article  CAS  Google Scholar 

  36. Sun C, Li B, Zhao M, Wang S, Lei Z, Lu L, Zhang F (2019) J-aggregates of cyanine dye for NIR-II in vivo dynamic vascular imaging beyond 1500 nm. J Am Chem Soc 141(49):19221–19225. https://doi.org/10.1021/jacs.9b10043

  37. Wei K, Wu Y, Li P, Zheng X, Ji C, Yin M (2023) Modulating planarity of cyanine dye to construct highly stable H-aggregates for enhanced photothermal therapy. Nano Res 16(1):970–979. https://doi.org/10.1007/s12274-022-4818-0

    Article  ADS  CAS  Google Scholar 

  38. Zhytniakivska O, Kurutos A, Tarabara U, Vus K, Trusova V, Gorbenko G, Deligeorgiev T (2020) Probing the amyloid protein aggregates with unsymmetrical monocationic trimethine cyanine dyes. J Mol Liq 311:113287. https://doi.org/10.1016/j.molliq.2020.113287

  39. Kurutos A, Shindo Y, Hiruta Y, Oka K, Citterio D (2022) Organelle-selective near-infrared fluorescent probes for intracellular microenvironment labeling. Dyes Pigm 204:110424. https://doi.org/10.1016/j.dyepig.2022.110424

  40. Kolb HC, Finn MG, Sharpless KB (2001) Click chemistry: diverse chemical function from a few good reactions. Angew Chem Int Ed 40(11):2004–2021. https://doi.org/10.1002/1521-3773(20010601)40:11<2004::aid-anie2004>3.0.co;2-5

    Article  CAS  Google Scholar 

  41. Gadde S, Batchelor EK, Kaifer AE (2009) Controlling the formation of cyanine dye H‐and J‐aggregates with cucurbituril hosts in the presence of anionic polyelectrolytes. Chem Eur J 15(24):6025–6031. https://doi.org/10.1002/chem.200802546

  42. West W, Pearce S, Grum F (1967) Stereoisomerism in cyanine dyes–meso-substituted thiacarbocyanines. J Phys Chem 71(5):1316–1326. https://doi.org/10.1021/j100864a021

    Article  CAS  Google Scholar 

  43. Cho J, Oh S, Lee D, Han JW, Yoo J, Park D, Lee G (2021) Spectroscopic sensing and quantification of AP-endonucleases using fluorescence-enhancement by cis–trans isomerization of cyanine dyes. RSC Adv 11(19):11380–11386. https://doi.org/10.1039/D0RA08051A

    Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

  44. Segur JB, Oberstar HE (1951) Viscosity of glycerol and its aqueous solutions. Ind Eng Chem 43(9):2117–2120. https://doi.org/10.1021/ie50501a040

    Article  CAS  Google Scholar 

  45. Takamura K, Fischer H, Morrow NR (2012) Physical properties of aqueous glycerol solutions. J Petrol Sci Eng 98:50–60. https://doi.org/10.1016/j.petrol.2012.09.003

    Article  CAS  Google Scholar 

Download references

Funding

F.F. was supported by grant from The Fund of China Scholarship Council, 202008400011. I.L.L., T.P.S., O.L.S., V.V.S. were supported by grant from Belarusian Republican Foundation for Fundamental Research (BRFFR) X23RNF-041. I.O.M. was supported by grant from Russian Science Foundation No. 23–45-10010.

Author information

Authors and Affiliations

  1. Institute of Physical Organic Chemistry, National Academy of Sciences of Belarus, 13 Surganova str., 220072, Minsk, Belarus

    Fan Fan, Ivan L. Lysenko, Tatsiana P. Seviarynchyk, Olga L. Sharko & Vadim V. Shmanai

  2. B.I. Stepanov Institute of Physics, National Academy of Sciences of Belarus, 68 Nezavisimost′ Ave., 220072, Minsk, Belarus

    Vladimir A. Povedailo

  3. Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia

    Ilya O. Mazunin

Authors
  1. Fan Fan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Vladimir A. Povedailo
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ivan L. Lysenko
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Tatsiana P. Seviarynchyk
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Olga L. Sharko
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Ilya O. Mazunin
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Vadim V. Shmanai
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

I.L.L., T.P.S. synthesized the compounds. F.F., V.A.P. performed all spectrophotometric and spectrofluorimetric measurements and calculations, wrote the main manuscript text and prepared figures. V.V.S., O.L.S., I.O.M. designed the study, analysed data, and edited the main manuscript text. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Vadim V. Shmanai.

Ethics declarations

Ethical Approval

Not required for this research since it does not involve any animal or biological experiments.

Competing Interests

The authors declare that they have no conflict of interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fan, F., Povedailo, V.A., Lysenko, I.L. et al. Fluorescent Properties of Cyanine Dyes As a Matter of the Environment. J Fluoresc 34, 925–933 (2024). https://doi.org/10.1007/s10895-023-03321-0

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10895-023-03321-0

Keywords

Search

Navigation