Optimization of Synthesis Conditions of Chloramphenicol AptamerFunctionalized DNA Hydrogels

Abstract

Aptamer-functionalized DNA hydrogels are used in many fields due to their high specificity, stability and flexibility. In this study, the synthesis of chloramphenicol-specific aptamer sequence functionalized DNA hydrogel was performed and certain parameters for hydrogel stability were optimized. For the synthesis, the 5' ends of the acrydite modified chloramphenicol-specific aptamer and the partially conjugated DNA strand were attached to the polymer structure as a side branch and held together by hybridization of the complementary regions, hydrogel synthesis was carried out. The optimized parameters were the concentrations of acrydite-modified DNA sequences, the percentage of acrylamide, the molar ratios of linear polymer solutions containing chloramphenicol aptamer and DNA strand 1. In addition, the effects of reaction temperature and the length of the complementary region on gel stability were evaluated. As a result, aptamer-functionalized DNA hydrogel synthesis was completed at 25°C with aptamer and DNA strand solutions mixed in 1:1 molar ratio using 40% acrylamide stock solution from 60% linear polyacrylamideDNA conjugation for DNA hydrogel stability. In addition, it was concluded that the length of the conjugate region between the aptamer sequence and the DNA strand increases stability.

Keywords

• Aptamer
• DNA hydrogel
• chloramphenicol

Project Number

218Z125

Kloramfenikol Aptameri Fonksiyonlandırılmış DNA Hidrojellerinin Sentez Koşullarının Optimizasyonu

Abstract

Aptamer fonksiyonlandırılmış DNA hidrojelleri yüksek özgünlük, stabilite ve esneklik gibi özellikleri nedeniyle birçok alanda kullanılmaktadır. Bu çalışma kapsamında kloramfenikole özgü aptamer dizisi fonksiyonlandırılmış DNA hidrojeli sentezi gerçekleştirilmiş ve hidrojel stabilitesi için önemli parametreler optimize edilmiştir. Sentez için 5’ uçları akridit modifiyeli kloramfenikole özgü aptamer ile ona kısmen eşlenik DNA ipliği polimer yapıya yan dal olarak katılmış ve eşlenik bölgelerin hibridizasyonu ile bir arada tutularak hidrojel sentezi gerçekleştirilmiştir. Optimize edilmiş parametreler akridit modifiyeli DNA dizilerinin konsantrasyonları, akrilamid yüzdesi, kloramfenikol aptameri ve DNA iplik 1 içeren lineer polimer çözeltilerin molar oranlarıdır. Ayrıca, reaksiyon sıcaklığı ve eşlenik bölgenin uzunluğunun jel stabilitesine etkisi değerlendirilmiştir. Sonuç olarak, DNA hidrojel stabilitesi için %60’lık lineer poliakrilamid-DNA konjugasyonundan, %40 akrilamid stok çözeltisi kullanılarak 1:1 molar oranda karıştırılan aptamer ve DNA iplik çözeltileri ile 25°C’de aptamer fonksiyonlandırılmış DNA hidrojeli sentezi tamamlanmıştır. Bunlara ek olarak, aptamer dizisi ile DNA iplik arasındaki eşlenik bölgenin uzunluğunun stabiliteyi artırdığı sonucuna varılmıştır.

Keywords

• Aptamer
• DNA hidrojel
• kloramfenikol

Supporting Institution

Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (TÜBİTAK)

Project Number

218Z125

Thanks

Bu çalışma Türkiye Bilimsel ve Teknolojik Araştırma Kurumu (TÜBİTAK) tarafından desteklenmiştir. (Proje No: 218Z125).

References

1. Amaya-González, S., de-Los-Santos-Álvarez, N., Miranda-Ordieres, A.J., Lobo-Castañón, M.J. (2015). Sensitive gluten determination in gluten-free foods by an electrochemical aptamer-based assay. Anal Bioanal Chem., 407, 20, 6021-9.
2. Bai, W., Spivak, D. A. (2014). A Double‐Imprinted Diffraction‐Grating Sensor Based on a Virus‐Responsive Super‐Aptamer Hydrogel Derived from an Impure Extract. Angew. Chem., Int. Ed., 53, 2095–2098.
3. Bajpai, A.K., Shukla, S.K., Bhanu, S., Kankane, S. (2008). Responsive polymers in controlled drug delivery Prog. Polym. Sci., 33, 1088-1118.
4. Bayrac, A.T., Sefah, K., Parekh, P., Bayrac, C., Gulbakan, B., Oktem, H.A., Tan, W. (2011). In Vitro Selection of DNA Aptamers to Glioblastoma Multiforme. ACS Chem. Neurosci., 2, 3, 175–181.
5. Bayraç, C., Eyidoğan, F., Avni Öktem, H. (2017). DNA aptamer-based colorimetric detection platform for Salmonella Enteritidis, Biosensors and Bioelectronics, 98, 22-28.
6. Bruno, J.G., Carrillo, M.P., Philips, T. (2008). In vitro antibacterial effects of antilipopolysaccharide DNA aptamer-C1qrs complexes. Folia Microbiol (Praha), 53, 4, 295-302.
7. Castillo, G., Spinella, K., Poturnayová, A., Šnejdárková, M., Mosiello, L., Hianik, T. (2015). Detection of aflatoxin B1 by aptamer-based biosensor using PAMAM dendrimers as immobilization platform. Food Control, 52, 9-18.
8. Dasgupta, A. (2012). Chapter 3 - Advances in antibiotic measurement. Advances in Clinical Chemistry, Editör:. Makowski, G.S. 56, 75-104, Elsevier.

9. Dong, Z., Huang, G., Xu, S., Deng, C., Zhu, J, Chen, S., Yang, X. and Zhao, S. (2009). Real-time and label-free detection of chloramphenicol residues with specific molecular interaction, J. Microsc., 234, 255–261.
10. Duan Y, Gao Z, Wang L, Wang H, Zhang H, Li H. (2016). Selection and Identification of Chloramphenicol-Specific DNA Aptamers by Mag-SELEX. Appl Biochem Biotechnol. 180(8):1644-1656.
11. Dumont, V., Huet, A. C., Traynor, I., Elliot, C. and Delahaut, P. 2006. “A surface plasmon resonance biosensor assay for the simultaneous determination of thiamphenicol, florfenicol, florfenicol amine and chloramphenicol residues in shrimps”, Anal. Chim. Acta., 567, 2,179–183.
12. Ellington, A.D., Szostak, J.W. (1990). In vitro selection of RNA molecules that bind specific ligands. Nature, 346, 818–822.
13. Famulok, M. (1994). Molecular recognition of amino acids by RNA‐aptamers: an L‐citrulline RNA motif and its evolution into an L‐arginine binder, Journal of the American Chemical Society, 116, 1698–1706.
14. Ferguson, B. S., Hoggarth, D. A., Maliniak, D., Ploense, K., White, R. J., Woodward, N., Hsieh, K., Bonham, A.J., Eisenstein, M., Kippin T.E., Plaxco, K.W., Soh, H. T. (2013). Real-time, aptamer-based tracking of circulating therapeutic agents in living animals. Sci. Transl. Med. 5, 213ra165.
15. Guo, Y., Wang, X., Sun, X. (2015). A label-free Electrochemical Aptasensor Based on Electrodeposited Gold Nanoparticles and Methylene Blue for Tetracycline Detection, Int. J. Electrochem. Sci., 10, 3668-3679.
16. Huang, H., Qi, X., Chen, Y., Wu Z. (2019). Thermo-sensitive hydrogels for delivering biotherapeutic molecules: A review, Saudi Pharmaceutical Journal, 27, 7, 990-999
17. Istamboulié, G., Paniel, N., Zara, L., Reguillo Granados, L., Barthelmebs, L., Noguer, T. (2016). Development of an impedimetric aptasensor for the determination of aflatoxin M1 in milk. Talanta, 146, 464-9.
18. Jiang, H., Pan, V., Vivek, S., Weeks, E.R., Ke, Y. (2016). Programmable DNA HydrogelsAssembledfromMultidomain DNA Strands. ChemBioChem, 17, 1156 – 1162.
19. Kang, H., Trondoli, A.C., Zhu, G., Chen, Y., Chang, Y.J., Liu, H., Huang, Y.F., Zhang, X., Tan, W. (2011). Near-infrared light-responsive core-shell nanogels for targeted drug delivery, AcsNano., 5, 5094-5099.
20. Karaseva, N. A., Ermolaeva, T. N. (2012). A piezoelectric immunosensor for chloramphenicol detection in food. Talanta, 93, 44–48.
21. Li, J., Mo, L., Lu., C.H., Fu, T., Yang, H.H., Tan, W. (2016). Functional nucleic acid-based hydrogels for bioanalytical and biomedical applications. Chem Soc Rev., 45, 5, 1410–1431.
22. Liu, Y., Yan, K., Okoth, O. K., Zhang, J. (2015). A lebel-free photoelectrochemical aptasensor based on nitrogen-doped graphene quantum dots for chloramphenicol determination. Biosensors and Bioelectronics, 74, 1016-1021.
23. Liu , C., Han, J., Pei ,Y., Du, J. (2018). Aptamer Functionalized DNA Hydrogel for Wise-Stage Controlled Protein Release, Appl. Sci., 8, 1941. https://doi.org/10.3390/app8101941
24. Luo, C., Lei, Y., Yan , L., Yu, T., Li, Q., Zhang, D., Ding, S., Ju, H. (2012). A Rapid and Sensitive Aptamer‐Based Electrochemical Biosensor for Direct Detection of Escherichia Coli O111. Electroanalysis, 24, 5, 1186-1191.
25. Ma, X., Jiang, Y., Jia, F., Yu, Y., Chen, J., Wang, Z. (2014). An aptamer-based electrochemical biosensor for the detection of Salmonella. J Microbiol Methods, 98, 94-8.
26. Mamani, M. C. V., Reyes, F. G. R., Ratha, S. (2009). Multiresidue determination of tetracyclines, sulphonamides and chloramphenicol in bovine milk using HPLC-DAD. Food Chem., 117, 3, 545–552.
27. Mehta, J., Van Dorst, B., Rouah-Martin, E., Herrebout, W., Scippo, M. L., Blust, R. and Robbens, J. (2011). In vitro selection and characterization of DNA aptamers recognizing chloramphenicol, J. Biotechnol., 155, 361–369.
28. Miao, Y., Gan, N., Li, T., Zhang, H., Cao, Y., Jiang, Q. (2015). A colorimetric aptasensor for chloramphenicol in fish based on double-stranded DNA antibody labeled enzyme-linked polymer nanotracers for signal amplification. Sensors and Actuators, B: Chemical, 220, 679-687.
29. Miao, Y., Gan, N., Li, T., Cao, Y., Hu, F., Chen, Y. (2016). An ultrasensitive fluorescence aptasensor for chloramphenicol based on FRET between quantum dots as donor and the magnetic SiO2@Au NPs probe as acceptor with exonuclease-assisted target recycling. Sens. Actuators B: Chem., 222, 1066-1072.
30. Mishra, R.K., Hayat, A., Catanante, G., Ocaña, C., Marty, J.L. (2015). A label free aptasensor for Ochratoxin A detection in cocoa beans: An application to chocolate industries. Anal Chim Acta., 889,106-12.
31. Morya, V., Walia, S., Mandal, B.B., Ghoroi, C., Bhatia, D. (2020). Functional DNA Based Hydrogels: Development, Properties and Biological Applications. ACS Biomater. Sci. Eng., 6, 11, 6021–6035
32. Mottier, P., Parisod, V., Gremaud, E., Guy, P. A., Stadler, R. H. (2003). Determination of the antibiotic chloramphenicol in meat and seafood products by liquid chromatography – electrospray ionization tandem mass spectrometry. J. Chromatogr. A., 994, 1–2, 75–84.
33. Nagahara, S., Matsuda, T. (1996). Hydrogel formation via hybridization of oligonucleotides derivatized in water-soluble vinyl polymers. Polym. Gels Networks, 4, 111–127.
34. Neuhaus, B. K., Hurlbut, J. A., Hammack, W. (2002). LC/MS/MS analysis of chloramphenicol in shrimp. USFDA, 18, 20–31.
35. Ocaña, C., Hayat, A., Mishra, R., Vasilescu, A., del Valle, M., Marty, J.L. (2015). A novel electrochemical aptamer-antibody sandwich assay for lysozyme detection. Analyst, 140, 12, 4148-53.
36. Park, I. Kim D. (2006). Development of a chemiluminescent immunosensor for chloramphenicol. Anal. Chim. Acta, 578,19–24.
37. Pfenning, A. P., Roybal, J. E., Rupp, H. S., Turnipseed, S. B., Gonzales, S. A. and Hurlbut, J. A. (2000). Simultaneous determination of residues of chloramphenicol, florfenicol, florfenicol amine and thiamphenicol in shrimp tissue by gas chromatography with electron capture detection. J. AOAC Int., 83, 1, 26–30.
38. Robertson, D.L., Joyce, G.F. (1990). Selection in vitro of an RNA enzyme that specifically cleaves single‐stranded DNA. Nature,344, 6265, 467–468.
39. Rodziewicz, L., Zawadzka, I. (2007). Rapid determination of chloramphenicol residues in honey by liquid chromatography tandem mass spectrometry and the validation of method based on 2002/657/EC. APIACTA, 42, 25–30.
40. Sun, X., Li, F., Shen, G., Huang, J., Wang, X. (2014). Aptasensor based on the synergistic contributions of chitosan-gold nanoparticles, graphene-gold nanoparticles and multi-walled carbon nanotubes-cobalt phthalocyanine nanocomposites for kanamycin detection. Analyst, 139, 1, 299-308.
41. Tuerk, C., Gold, L. (1990). Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNApolymerase. Science, 249, 505–510.
42. Tajik, H., Malekinejad, H., Razavi-Rouhani, S.M., Pajouhi, M.R., Mahmoudi, R., Haghnazari, A. (2010). Chloramphenicol residues in chicken liver, kidney and muscle: A comparison among the antibacterial residues monitoring methods of four plate test, ELISA, and HPLC. Food & Chemical Toxicology, 48, 2464-2468.
43. Takahashi, M. (2018). Aptamers targeting cell surface proteins. Biochimie, 145, 63-72.
44. Trashin, S., de Jong, M., Breugelmans, T., Pilehvar, S., De Wael, K. (2015). Label‐Free Impedance Aptasensor for Major Peanut Allergen Ara h 1. Electroanalysis, 27, 1, 32-37.
45. van Bambeke, F., Mingeot-Leclercq, MP., Glupczynski, Y., Tulkens,P.M. 2017. 137 – Mechanisms of Action. Infectious Diseases, 4th edition. Editörler: Cohen, J., Powderly, W.G, Opal, S.M., 1162–1180.
46. Yadav, S.K., Agrawal, B., Chandra, P., Goyal, R.N. (2014). In vitro chloramphenicol detection in a Haemophilus influenza model using an aptamer-polymer based electrochemical biosensor. Biosensors and Bioelectronics, 55, 337-342.
47. Yan, L., Zhu, Z., Zou, Y., Huang, Y., Liu, D., Jia, S., Xu, D., Wu, M., Zhou, Y., Zhou, S., Yang C. J. (2013). Target-Responsive “Sweet” Hydrogel with Glucometer Readout for Portable and Quantitative Detection of Non-Glucose Targets. J. Am. Chem. Soc., 135, 3748–3751.
48. Yang, H., Liu, H., Kang, H., Tan W. (2008). Engineering Target-Responsive Hydrogels Based on Aptamer−Target Interactions. J. Am. Chem. Soc., 130, 6320–6321.
49. Yin, B.C., Ye, B.C., Wang, H., Zhu, Z., Tan, W. (2012). Colorimetric logic gates based on aptamer-crosslinked hydrogels. Chem Commun. 48, 1248–50.
50. Yuan, J., Oliver, R., Aguilar, M. I. and Wu, Y. (2008). Surface plasmon resonance assay for chloramphenicol. Anal. Chem., 80, 8329–8333.
51. Zadeh ,J. N., Steenberg, C. D., Bois, J. S., Wolfe, B. R., Pierce, M. B., Khan, A. R., Dirks, R. M., Pierce N. A. (2011). NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32:170–173
52. Zhao, L., Ball, C. H. (2009). Determination of Chloramphenicol, Florfenicol, and Thiamphenicol in Honey Using Agilent SampliQ OPT Solid-Phase Extraction Cartridges and Liquid Chromatography-Tandem Mass Spectrometry. Agilent LC/MS Newsletter.
53. Wilson, W.R., Cockerill, F.R. (1987). Tetracyclines, chloramphenicol, erythromycin, and clindamycin. Mayo Clin Proc., 62, 10, 906-15.