Biopolym. Cell. 2018; 34(5):374-386.
http://dx.doi.org/10.7124/bc.000987
Bioorganic Chemistry
N-alkylaryl styrylcyanine dyes as fluorescent probes for nucleic acids detection
1Kuperman M. V., 1Snihirova Y. V., 1Kryvorotenko D. V., 1Losytskyy M. Yu., 1Kovalska V. B., 1Yarmoluk S. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03143

Abstract

Aim. To synthesize and characterize a series of N-alkylaryl benzothiazole styrylcyanine dyes as potential fluorescent probes for nucleic acids (NA) detection. Methods. Synthesis, absorption and fluorescence spectroscopy, gel electrophoresis. Results. The modification of N-alkyl styrylcyanine by variation of aromatic moieties insignificantly affected its inherent fluorescent properties. Weakly fluorescent in an unbound state, the dyes noticeably increased their emission upon binding to dsDNA/RNA (up to 83-fold for the derivative with N-alkylbenzylamine group (Sbt1) complexed with dsDNA: with a binding constant (Kb) of 5.0×104 M–1, detection limit of dsDNA in solution of 6.2×10–7 Mbp (0.4 µg)). When bound to dsDNA, styrylcyanines have moderate quantum yields (up to ~22 %). The variation of structure of the terminal aromatic group allowed to discriminate between dsDNA and RNA: the fluorescence of the Sbt2 dye with the N-alkylphenantroline group increased 14 and 55-fold, respectively. A higher discernibility of post-electrophoretic staining at low DNA concentrations (3.6 ng/lane) by the Sbt3 dye with the N-alkyldipyridyl group was observed compared to the commonly used ethidium bromide. Conclusions. Due to the sensitivity of novel styrylcyanines to NA in solution and in gel electrophoresis, they could be proposed as photostable, low-toxic and inexpensive fluorescent probes for laboratory use.
Keywords: styrylcyanines, nucleic acids detection, fluorescent probes.
Full text: (PDF, in English)

References

[1] Deligeorgiev T, Kaloyanova S, Vaquero JJ. Intercalating cyanine dyes for nucleic acid detection. Rec Pat Mat Sci. 2009; 2(1): 1–26.
[2] Timtcheva I, Maximova V, Deligeorgiev T, Gadjev N, Drexhage KH, Petkova I. Homodimeric monomethine cyanine dyes as fluorescent probes of biopolymers. J Photochem Photobiol B. 2000;58(2-3):130-5.
[3] Hilal H, Taylor JA. Cyanine dyes for the detection of double stranded DNA. J Biochem Biophys Methods. 2008;70(6):1104-8.
[4] Kirsanov KI, Lesovaya EA, Yakubovskaya MG, Belitsky GA. SYBR Gold and SYBR Green II are not mutagenic in the Ames test. Mutat Res. 2010;699(1-2):1-4.
[5] Dragan AI, Pavlovic R, McGivney JB, Casas-Finet JR, Bishop ES, Strouse RJ, Schenerman MA, Geddes CD. SYBR Green I: fluorescence properties and interaction with DNA. J Fluoresc. 2012;22(4):1189-99.
[6] Potter AJ, Wener MH. Flow cytometric analysis of fluorescence in situ hybridization with dye dilution and DNA staining (flow-FISH-DDD) to determine telomere length dynamics in proliferating cells. Cytometry A. 2005;68(1):53-8.
[7] Bourzac KM, LaVine LJ, Rice MS. Analysis of DAPI and SYBR Green I as alternatives to ethidium bromide for nucleic acid staining in agarose gel electrophoresis. J Chem Educ. 2003; 80 (11): 1292.
[8] Albota M, Beljonne D, Brédas JL, Ehrlich JE, Fu JY, Heikal AA, Hess SE, Kogej T, Levin MD, Marder SR, McCord-Maughon D, Perry JW, Röckel H, Rumi M, Subramaniam G, Webb WW, Wu XL, Xu C. Design of organic molecules with large two-photon absorption cross sections. Science. 1998;281(5383):1653-6.
[9] Fujita H, Nakano M, Takahata M, Yamaguchi K. A new strategy of enhancing two-photon absorption in conjugated molecules: Introduction of charged defects. Chem Phys Lett. 2002; 358(5-6):435–41.
[10] Wu L-Z, Tang X-J, Jiang M-H, Tung C-H. Two-photon induced fluorescence of novel dyes. Chem Phys Lett. 1999; 315(5-6):379–82.
[11] Bohländer PR, Wagenknecht HA. Bright and photostable cyanine-styryl chromophores with green and red fluorescence colour for DNA staining. Methods Appl Fluoresc. 2015;3(4):044003.
[12] Deligeorgiev T, Vasilev A, Kaloyanova S, Vaquero JJ. Styryl dyes – synthesis and applications during the last 15 years. Color Tech. 2010; 126(2): 55–80.
[13] Kurutos A, Ryzhova O, Trusova V, Tarabara U, Gorbenko G, Gadjev N, Deligeorgiev T. Novel asymmetric monomethine cyanine dyes derived from sulfobetaine benzothiazolium moiety as potential fluorescent dyes for non-covalent labeling of DNA. Dyes Pigm. 2016; 130: 122–8.
[14] Tokar VP, Losytskyy MY, Kovalska VB, Kryvorotenko DV, Balanda AO, Prokopets VM, Galak MP, Dmytruk IM, Yashchuk VM, Yarmoluk SM. Fluorescence of styryl dyes-DNA complexes induced by single- and two-photon excitation. J Fluoresc. 2006;16(6):783-91.
[15] Balanda M, Rams M, Nayak SK, Tomkowicz Z, Haase W, Tomala K, Yakhmi JV. Slow magnetic relaxations in the anisotropic Heisenberg chain compound Mn(III) tetra(ortho-fluorophenyl)porphyrin-tetracyanoethylene. Phys Rev B. 2006; 74(22):224421.
[16] Kubin RF, Fletcher AN. Fluorescence quantum yields of some rhodamine dyes. J Lumin. 1982; 27(4): 455–62.
[17] McGhee JD, von Hippel PH. Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. J Mol Biol. 1974;86(2):469-89.
[18] 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.
[19] Dhebri A, Ellenbogen S, Arora P, Kishore M. Audit of Sentinel Node Biopsy (SNB): comparing with national standards. Eur J Surg Oncol. 2011; 37: S5–S6.
[20] Steinmeyer J, Rönicke F, Schepers U, Wagenknecht HA. Synthesis of Wavelength-Shifting Fluorescent DNA and RNA with Two Photostable Cyanine-Styryl Dyes as the Base Surrogate Pair. ChemistryOpen. 2017;6(4):514-518.
[21] Emerson ES, Conlin MA, Rosenoff AE, Norland KS, Rodriguez H, Chin D, Bird GR. The geometrical structure and absorption spectrum of a cyanine dye aggregate. J Phys Chem. 1967; 71(8): 2396–403.
[22] Jensen LK, Gotfredsen CH, Bondensgaard K, Jacobsen JP. Bis-Intercalation of homodimeric thiazole orange dyes in selective binding sites of DNA studied by 1H NMR spectroscopy. Acta Chem Scand. 1998; 52: 641–50.
[23] Petersen M, Hamed AA, Pedersen EB, Jacobsen JP. Bis-intercalation of homodimeric thiazole orange dye derivatives in DNA. Bioconjug Chem. 1999;10(1):66-74.
[24] Sovenyhazy KM, Bordelon JA, Petty JT. Spectroscopic studies of the multiple binding modes of a trimethine-bridged cyanine dye with DNA. Nucleic Acids Res. 2003;31(10):2561-9.
[25] 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.
[26] Kurutos A, Ryzhova O, Trusova V, Tarabara U, Gorbenko G, GadjevN, Deligeorgiev T. Novel asymmetric monomethine cyanine dyes derived from sulfobetaine benzothiazolium moiety as potential fluorescent dyes for noncovalent labeling of DNA. Dyes Pigm. 2016; 130: 122–8.
[27] Kovalska VB, Kryvorotenko DV, Balanda AO, Losytskyy MY, Tokar VP, Yarmoluk SM. Fluorescent homodimer styrylcyanines: synthesis and spectral-luminescent studies in nucleic acids and protein complexes. Dyes Pigm. 2005; 67(1): 47–54.
[28] Almaqwashi AA, Andersson J, Lincoln P, Rouzina I, Westerlund F, Williams MC. DNA intercalation optimized by two-step molecular lock mechanism. Sci Rep. 2016;6:37993.
[29] Ihmels H, Otto D. Intercalation of organic dye molecules into double-stranded DNA-general principles and recent developments. Supermolec Dye Chem. 2005; 161–204.
[30] Armitage BA. Cyanine dye–DNA interactions: intercalation, groove binding, and aggregation DNA. DNA Binders and Related Subjects. 2005; 253: 55–76.
[31] Peters AT, Freeman HS. Analytical chemistry of synthetic colorants. Advances in color chemistry series. The Netherlands : "Springer Science & Business Media", 1995; 2: 81 p.