Biopolym. Cell. 2025; 41(2):121.
http://dx.doi.org/10.7124/bc.000B16
Bioorganic Chemistry
Effect of DNA, RNA and HSA on the spectral-luminescent properties of several monomethine cyanine dyes
1Kazakov–Kravchenko O. S., 1Balanda A. O., 2Losytskyy M. Yu., 1Yarmoluk S. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143
  2. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01601

Abstract

Aim. This work was aimed at investigation of the effect of DNA, RNA, and HSA on the absorption and fluorescence spectra of 8 monomethine cyanine dyes, which are based on different chromophores and contain various affinity-modifying groups. Methods. UV-vis absorption and fluorescence spectroscopy. Results. Several dyes were found to have good fluorescent responses to the presence of DNA, RNA, and HSA. The dye fb128, which contains a charged group, was shown to increase its fluorescence intensity in the presence of DNA and RNA by 160 and 240 times, respectively, while the dye up385 increased its fluorescence intensity by almost 60 times in the presence of human serum albumin. Conclusions. The most promising dye fb128, as well as the dyes fb123, fb124 and fb131, can be further investigated as fluorescent probes sensitive to nucleic acids in various specific applications (PCR, fluorescent microscopy etc.).
Keywords: monomethine cyanine dyes, fluorescent probes, nucleic acids, human serum albumin
Full text: (PDF, in English)

References

[1] Molecular Probes Handbook, A Guide to Fluorescent Probes and Labeling Technologies, 11th Edition, Iain Johnson, Michelle T.Z. Spence [Eds.], 2010, Published by Life Technologies.
[2] Mackay J, Landt O. (2007). Real-Time PCR Fluorescent Chemistries. In: Hilario, E., Mackay, J. (eds) Protocols for Nucleic Acid Analysis by Nonradioactive Probes. Methods in Molecular Biology, vol 353. Humana Press.
[3] Okamoto A. Next-generation fluorescent nucleic acids probes for microscopic analysis of intracellular nucleic acids. Appl Microsc. 2019; 49(1):14.
[4] Yarmoluk SM, Kovalska VB, Volkova KD. (2011). Optimized Dyes for Protein and Nucleic Acid Detection. In: Demchenko, A. (eds) Advanced Fluorescence Reporters in Chemistry and Biology III. Springer Series on Fluorescence, vol 113. Springer, Berlin, Heidelberg.
[5] Seah D, Cheng Z, Vendrell M. Fluorescent Probes for Imaging in Humans: Where Are We Now? ACS Nano. 2023; 17(20):19478-90.
[6] Wang X, Ding Q, Groleau RR, Wu L, Mao Y, Che F, Kotova O, Scanlan EM, Lewis SE, Li P, Tang B, James TD, Gunnlaugsson T. Fluorescent Probes for Disease Diagnosis. Chem Rev. 2024; 124(11):7106-64.
[7] Guimarães DG, Santos VLA, Simplicio SS, Rolim LA, Gonsalves AA, Araújo CRM. Naphthoxazole and benzoxazole as fluorescent DNA probes - a systematic review. Biotechnol Res Innov. 2024; 8(1):e2024010.
[8] Aristova D, Kosach V, Chernii S, Slominsky Y, Balanda A, Filonenko V, Yarmoluk S, Rotaru A, Özkan HG, Mokhir A, Kovalska V. Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy. Methods Appl Fluoresc. 2021; 9(4):045002.
[9] Okshevsky M, Meyer RL. Evaluation of fluorescent stains for visualizing extracellular DNA in biofilms. J Microbiol Methods. 2014; 105:102-4.
[10] Kovalska VB, Tokar VP, Losytskyy MY, Deligeorgiev T, Vassilev A, Gadjev N, Drexhage KH, Yarmoluk SM. Studies of monomeric and homodimeric oxazolo[4,5-b]pyridinium cyanine dyes as fluorescent probes for nucleic acids visualization. J Biochem Biophys Methods. 2006; 68(3):155-65.
[11] Yarmoluk SM, Kovalska VB, Kryvorotenko DV, Balanda AO, Ogul'chansky TYu. Interaction of cyanine dyes with nucleic acids. XXV. Influence of affinity-modifying groups in the structure of benzothiazol-4-[2,6-dimethylpyridinium] dyes on the spectral properties of the dyes in the presence of nucleic acids. Spectrochim Acta A Mol Biomol Spectrosc. 2001; 57(7):1533-40.
[12] Lee LG, Chen CH, Chiu LA. Thiazole orange: a new dye for reticulocyte analysis. Cytometry. 1986; 7(6):508-17.
[13] Rye HS, Yue S, Wemmer DE, Quesada MA, Haugland RP, Mathies RA, Glazer AN. Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications. Nucleic Acids Res. 1992; 20(11):2803-12.
[14] Ogul'chansky TYu, Losytskyy MYu, Kovalska VB, Yashchuk VM, Yarmoluk SM. Interactions of cyanine dyes with nucleic acids. XXIV. Aggregation of monomethine cyanine dyes in presence of DNA and its manifestation in absorption and fluorescence spectra. Spectrochim Acta A Mol Biomol Spectrosc. 2001; 57(7):1525-32.
[15] Emerson ES, Conlin MA, Rosenoff AE, Norland KS, Rodriguez H, Chin D, Bird GR. Geometrical Structure and Absorption Spectrum of a Cyanine Dye Aggregate. J Phys Chem. 1967; 71(8):2396-403.
[16] West W, Pearce S. The Dimeric State of Cyanine Dyes. J Phys Chem. 1965; 69(6):1894-903.
[17] Herz AH. Dye-Dye Interactions of Cyanines in Solution and at AgBr Surfaces. Photogr Sci Eng. 1974; 18(3):323-35.
[18] Zipper H, Brunner H, Bernhagen J, Vitzthum F. Investigations on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. Nucleic Acids Res. 2004; 32(12):e103.
[19] Ogul'chansky TYu, Yashchuk VM, Losytskyy MYu, Kocheshev IO, Yarmoluk SM. Interaction of cyanine dyes with nucleic acids. XVII. Towards an aggregation of cyanine dyes in solutions as a factor facilitating nucleic acid detection. Spectrochim Acta A Mol Biomol Spectrosc. 2000; 56(4):805-14.