Biopolym. Cell. 2020; 36(1):36-47.
Методи
Пряме мічення нуклеозидів 3-тіазолілкумариновими флуоресцентними барвниками
1Кузів Я. Б., 1Дубей І. Я.
  1. Інститут молекулярної біології і генетики НАН України
    Вул. Академіка Заболотного, 150, Київ, Україна, 03143

Abstract

Мета. Отримання й дослідження нуклеозидів, мічених флуорофорами на основі кумарину без попередньої функціоналізації. Методи. Органічний синтез, адсорбційна та флуоресцентна спектроскопія. Результати. Проведене пряме мічення 2’-дезоксинуклеозидів карбокси-модифікованими тіазолілкумаринами. Кон’югати отримано реакцією гідроксибензотріазольних активованих естерів барвників з 5’-гідроксилом нуклеозиду в присутності основи або з аміногрупою цитозину. Досліджено їхні оптичні властивості в метанолі й фосфатному буфері. Висновки. N- та O-ацилювання піримідинових нуклеозидів похідними кумаринів дозволило отримати кон’югати з яскравою блакитною емісією.
Keywords: кумарини, нуклеозиди, флуоресцентне мічення, активовані естери

References

[1] Gonçalves MST. Fluorescent labeling of biomolecules with organic probes. Chem. Rev. 2009; 109(1): 190-212.
[2] Li C, Tebo AG, Gautier A. Fluorogenic labeling strategies for biological imaging. Int J Mol Sci. 2017; 18: 1473.
[3] Wojczewski C, Stolze K, Engels JW. Fluorescent oligonucleotides - versatile tools as probes and primers for DNA and RNA analysis. Synlett 1999; 1999(10): 1667-78.
[4] Sinkeldam RW, Greco NJ, Tor Y. Fluorescent analogs of biomolecular building blocks: design, properties, and applications. Chem Rev. 2010; 110(5): 2579-2619.
[5] El-Sagheer AH, Brown T. Nucleic acid labeling, ligation, and modification. In: Chemoselective and Bioorthogonal Ligation Reactions. V. 2. Eds. by Algar WR, Dawson PE, Medintz IL. Wiley, Weinheim, 2017;335-62.
[6] Emmrich T, El-Tayeb A, Taha H, Seifert R, Müller CE, Link A. Synthesis of a hydrolytically stable, fluorescent-labeled ATP analog as a tool for probing adenylyl cyclases. Bioorg Med Chem. Lett 2010; 20(1): 232-5.
[7] Shinohara Y, Matsumoto K, Kugenuma K, Morii T, Saito Y, Saito I. Design of environmentally sensitive fluores-cent 2′-deoxyguanosine containing arylethynyl moieties: distinction of thymine base by base-discriminating fluo-rescent (BDF) probe. Bioorg Med Chem Lett. 2010; 20(9): 2817-20.
[8] Wilhelmsson LM. Fluorescent nucleic acid base analogues. Q Rev Biophys. 2010; 43(2): 159-83.
[9] Matsumoto K, Takahashi N, Suzuki A, Morii T, Saito Y, Saito I. Design and synthesis of highly solvatochromic fluorescent 2′-deoxyguanosine and 2′-deoxyadenosine analogs. Bioorg Med Chem Lett. 2011; 21(4): 1275-8.
[10] Suzuki A, Takahashi N, Okada Y, Saito I, Nemoto N, Saito Y. Naphthalene-based environmentally sensitive fluo-rescent 8-substituted 2′-deoxyadenosines: application to DNA detection. Bioorg Med Chem Lett. 2013; 23(3): 886-92.
[11] Goodwin KJ, Gangl E, Sarkar U, Pop-Damkov P, Jones N, Borodovsky A, Woessner R, Fretland AJ. Development of a quantification method for adenosine in tumors by LC-MS/MS with dansyl chloride derivatization. Anal Biochem. 2019; 568: 78-88.
[12] De Schutter C, Roy V, Favetta P, Pavageau C, Maisonneuve S, Bogliotti N, Xie J, Agrofoglio LA. Synthesis and characterization of various 5′-dye-labeled ribonucleosides. Org Biomol Chem. 2018; 16(35): 6552-63.
[13] Prykota TI, Pfleiderer W. Nucleotides part LXXX: Synthesis of 3'-O fluorescence labeled thymidine derivatives and their 5'-o-triphosphates. Nucleosides Nucleotides Nucleic Acids 2011; 30(7-8): 544-51.
[14] Katritzky AR, Ozcan S, Todadze E. Labeling of nucleosides with fluorescent 6-chloro-2,3-napthalimide. Bioorg Med Chem Lett. 2010; 20(17): 5326-8.
[15] Shaughnessy KH. Palladium-catalyzed modification of unprotected nucleosides, nucleotides, and oligonucleo-tides. Molecules 2015; 20: 9419-54
[16] Hata T, Kurihara T. The N4-benzoylation of deoxycytidilic and cytidylic acids by means of 2-chloromethyl-4-nitrophenyl benzoate. Chem Lett. 1973; 2(8): 859-62.
[17] Igolen J, Morin C. Rapid syntheses of protected 2'-deoxycytidine derivatives. J Org Chem. 1980; 45(23): 4802-4.
[18] Steinfeld AS, Naider F, Becker JM. A simple method for selective acylation of cytidines and cytosines under mild reaction conditions. J Chem Res (M). 1979: 1437-50.
[19] Yarmoluk SM, Kostenko AM, Kryvorotenko DV, Dubey IYa. Nucleoside N-acylation with active derivatives of amino acids. Biopolym Cell 1996; 12(5): 50-5.
[20] Otera J, Nishikido J. Esterification: Methods, Reactions, and Applications. 2nd Ed. Wiley, Weinheim, 2010. - 386 p.
[21] But TYS, Toy PH. The Mitsunobu reaction: origin, mechanism, improvements, and applications. Chem Asian J. 2007; 2(11): 1340-55.
[22] Holmberg K, Hansen B. Ester synthesis with dicyclohexylcarbodiimide improved by acid catalysts. Acta Chem Scand B 1979; 33: 410-2.
[23] Kim MH, Patel D V. "BOP" as a reagent for mild and efficient preparation of esters. Tetrahedron Lett. 1994; 35(31): 5603-6.
[24] Pon RT, Yu S, Sanghvi YS. Rapid esterification of nueleosides to solid-phase supports for oligonucleotide synthesis using uronium and phosphonium coupling reagents. Bioconjug Chem. 1999; 10(6): 1051-7.
[25] Klausner YS, Chorev M. Synthesis of depsipeptides by catalysis of active esters with 1-hydroxybenzotriazole. Chem Commun. 1975; (24): 973-4.
[26] Coste J, Campagne J-M. A propos de l'estérification des acides carboxyliques par le BOP ou le PyBOP. Tetrahe-dron Lett. 1995; 36(24): 4253-6.
[27] Subirós-Funosas R, Prohens R, Barbas R, El-Faham A, Albericio F. Oxyma: An efficient additive for peptide synthesis to replace the benzotriazole-based HOBt and HOAt with a lower risk of explosion. Chem Eur J. 2009; 15(37): 9394-403.
[28] Stawikowski M, Cudic P. Depsipeptide synthesis. Methods Mol Biol. 2007; 386: 321-39.
[29] Twibanire J d AK, Grindley TB. Polyester dendrimers: smart carriers for drug delivery. Polymers (Basel). 2014; 6(1): 179-213.
[30] Wang Y, Aleiwi BA, Wang Q, Kurosu M. Selective esterifications of primary alcohols in a water-containing sol-vent. Org Lett. 2012; 14(18): 4910-3.
[31] Bergmann F, Bannwarth W, Tam S. Solid phase synthesis of directly linked PNA-DNA-hybrids. Tetrahedron Lett. 1995; 36(38): 6823-6.
[32] Twibanire JDAK, Omran RP, Grindley TB. Facile synthesis of a library of lyme disease glycolipid antigens. Org Lett. 2012; 14(15): 3909-11.
[33] Chapleur Y, Castro B, Toubiana R. "Le BOP" reagent and imidazole for selective O-acylation of trehalose. J Chem Soc Perkin Trans 1. 1980: 1940-3.
[34] Dubey LV, Dubey IYa. Onium salts as coupling reagents in the preparation of silica polymer supports for oligo-nucleotide synthesis. Ukr Bioorg Acta. 2004; 1(1-2): 23-8.
[35] Kuziv IaB, Ishchenko VV, Khilya VP, Dubey IYa. Synthesis of reagents based on 7-substituted 3-thiazolylcoumarins for covalent labeling of oligonucleo-tides. Ukr Bioorg Acta. 2008; 6(1): 3-12.
[36] Kuziv IaB, Ishchenko VV, Khilya VP, Dubey IYa. Synthesis of carboxyalkyl derivatives of 3-furylcoumarins for the fluorescent labeling of biomolecules. Ukr Bioorg Acta. 2009; 7(2): 47-54.
[37] Gait MJ (Ed.). Oligonucleotide synthesis: a practical approach. IRL Press, Oxford, 1984. 218 p.
[38] Reynolds GA, Drexhage KH. New coumarin dyes with rigidized structure for flash amp-pumped dye lasers. Opt. Commun. 1975; 13(3): 222-5.
[39] Salgado LEV, Vargas-Hernández C. Spectrophotometric determination of the pKa, isosbestic point and equation of absorbance vs pH for a universal pH indicator. Am J Anal Chem. 2014; 05(17): 1290-301.
[40] Gryaznov SM, Letsinger RL. Synthesis of oligonucleotides via monomers with unprotected bases. J Am Chem Soc. 1991; 113(15): 5876-7.
[41] Fink DW, Koehler WR. pH effects on fluorescence of umbelliferone. Anal Chem. 1970; 42(9): 990-3.