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Rapid and Specific Purification of RNA by PolyUracil Membranes

Year 2020, Volume 10, Issue 2, 466 - 482, 30.12.2020
https://doi.org/10.37094/adyujsci.780049

Abstract

Ribonucleic acid (RNA) plays a critically important role in cellular defense, deoxyribonucleic acid (DNA) replication, transcription, and gene expression for living organisms as well as, a lot of diseases such as cancer, immunodeficiency, tumors has been associated with RNA’s disruption. For this purpose, supermacropores membranes were designed to purify RNA using nucleotide-based ligand. In this study, polymerizable uracil monomer as uracil methacrylate (UraM) was synthesized, and 2-hydroxyethyl methacrylate (HEMA)-based membranes [poly(HEMA-UraM)] were prepared by bulk polymerization under partially frozen conditions by copolymerization of monomers, UraM, and HEMA. These membranes were characterized via swelling studies, Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy (SEM). To optimize separation conditions, effects of pH, initial RNA concentration, time, and temperature on RNA adsorption capacity were examined. Maximum adsorption of RNA on poly(HEMA-UraM) membrane was found to be 15.52 mg/g for 0.5 mg/mL RNA initial concentration at 25.0°C with an optimum pH of 7.0. After ten repetitive adsorption-desorption cycles, the RNA adsorption capacity decreased only 3.68%.

References

  • [[1] Sharp, P.A., The centrality of RNA, Cell, 136, 577-580, 2009.
  • [2] Perçin, I., İdil, N., Denizli, A., RNA purification from Escherichia coli cells using boronated nanoparticles, Colloids and Surfaces B: Biointerfaces, 162, 146-153, 2018.
  • [3] Martins, R., Queiroz, J., Sousa, F., Ribonucleic acid purification, Journal of Chromatography A, 1355, 1-14, 2014.
  • [4] Cooper, T.A., Wan, L., Dreyfuss, G., RNA and disease, Cell, 136, 777-793, 2009.
  • [5] Köse, K., Denizli, A., Poly (hydroxyethyl methacrylate) based magnetic nanoparticles for lysozyme purification from chicken egg white, Artificial cells, nanomedicine, and biotechnology, 41, 13-20, 2013.
  • [6] Yang, G., Lu, X., Yuan, L., LncRNA: a link between RNA and cancer, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1839, 1097-1109, 2014.
  • [7] Kim, I., Mckenna, S.A., Puglisi, E.V., Puglisi, J.D., Rapid purification of RNAs using fast performance liquid chromatography (FPLC), RNA, 13, 289-294, 2007.
  • [8] Martins, R., Queiroz, J.A., Sousa, F., Histidine affinity chromatography‐based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA, Biomedical Chromatography, 26, 781-788, 2012.
  • [9] McGinnis, A.C., Chen, B., Bartlett, M.G., Chromatographic methods for the determination of therapeutic oligonucleotides, Journal of Chromatography B, 883, 76-94, 2012.
  • [10] Romanovskaya, A., Sarin, L.P., Bamford, D.H., Poranen, M.M., High-throughput purification of double-stranded RNA molecules using convective interaction media monolithic anion exchange columns, Journal of Chromatography A, 1278, 54-60, 2013.
  • [11] Vomelova, I., Vaníčková, Z., Šedo, A., Technical note methods of RNA purification. All ways (should) lead to Rome, Folia Biologica (Praha), 55, 243-251, 2009.
  • [12] Warren, W.J., Vella, G., Principles and methods for the analysis and purification of synthetic deoxyribonucleotides by high-performance liquid chromatography, Molecular Biotechnology, 4, 179, 1995.
  • [13] Srivastava, A., Shakya, A.K., Kumar, A., Boronate affinity chromatography of cells and biomacromolecules using cryogel matrices, Enzyme and Microbial Technology, 51, 373-381, 2012.
  • [14] Uhlenbeck, O., Keeping RNA happy, RNA, 1, 4, 1995.
  • [15] Edwards, A.L., Garst, A.D., Batey, R.T., Determining structures of RNA aptamers and riboswitches by X-ray crystallography, Nucleic Acid and Peptide Aptamers, Springer2009, pp. 135-163.
  • [16] Garcia, F., Pires, E., Recovery processes for biological materials, Chromatography, Wiley, London, UK, 415-451, 1993.
  • [17] Scouten, W.H., Affinity chromatography; bioselective adsorption on inert matrices, Wiley, NewYork, 1981.
  • [18] Ayyar, B.V., Arora, S., Murphy, C., O’Kennedy, R., Affinity chromatography as a tool for antibody purification, Methods, 56, 116-129, 2012.
  • [19] Roque, A.C., Silva, C.S., Taipa, M.Â., Affinity-based methodologies and ligands for antibody purification: advances and perspectives, Journal of Chromatography A, 1160, 44-55, 2007.
  • [20] Andaç, M., Tamahkar, E., Denizli, A., Molecularly imprinted smart cryogels for selective nickel recognition in aqueous solutions, Journal of Applied Polymer Science, 49746.
  • [21] Emin Çorman, M., Bereli, N., Özkara, S., Uzun, L., Denizli, A., Hydrophobic cryogels for DNA adsorption: Effect of embedding of monosize microbeads into cryogel network on their adsorptive performances, Biomedical Chromatography, 27, 1524-1531, 2013.
  • [22] Bereli, N., Yavuz, H., Denizli, A., Protein chromatography by molecular imprinted cryogels, Journal of Liquid Chromatography & Related Technologies, 1-14, 2020.
  • [23] Öncel, P., Çetin, K., Topçu, A.A., Yavuz, H., Denizli, A., Molecularly imprinted cryogel membranes for mitomycin C delivery, Journal of Biomaterials Science Polymer Edition, 28, 519-531, 2017.
  • [24] Hur, D., Ekti, S.F., Say, R., N-Acylbenzotriazole mediated synthesis of some methacrylamido amino acids, Letters in Organic Chemistry, 4, 585-587, 2007.
  • [25] Armutcu, C., Çorman, M.E., Bayram, E., Uzun, L., Purification of Fab and Fc using papain immobilized cryogel bioreactor separator system, Journal of Chromatography B, 122396, 2020.
  • [26] Köse, K., Erol, K., Uzun, L., Denizli, A., PolyAdenine cryogels for fast and effective RNA purification, Colloids and Surfaces B: Biointerfaces, 146, 678-686, 2016.
  • [27] Köse, K., Uzun, L., PolyGuanine methacrylate cryogels for ribonucleic acid purification, Journal of Separation Science, 39, 1998-2005, 2016.
  • [28] Çorman, M.E., Poly-l-lysine modified cryogels for efficient bilirubin removal from human plasma, Colloids and Surfaces B: Biointerfaces, 167, 291-298, 2018.
  • [29] Daoud-Attieh, M., Chaib, H., Armutcu, C., Uzun, L., Elkak, A., Denizli, A., Immunoglobulin G purification from bovine serum with pseudo-specific supermacroporous cryogels, Separation and Purification Technology, 118, 816-822, 2013.
  • [30] Foo, K.Y., Hameed, B.H., Insights into the modeling of adsorption isotherm systems, Chemical engineering journal, 156, 2-10, 2010.
  • [31] Sarı, M.M., Armutcu, C., Bereli, N., Uzun, L., Denizli, A., Monosize microbeads for pseudo-affinity adsorption of human insulin, Colloids and Surfaces B: Biointerfaces, 84, 140-147, 2011.
  • [32] Erol, B., Erol, K., Gökmeşe, E., The effect of the chelator characteristics on insulin adsorption in immobilized metal affinity chromatography, Process Biochemistry, 83, 104-113, 2019.
  • [33] Ohale, P.E., Onu, C.E., Ohale, N.J., Obah, S.N., Adsorptive kinetics, isotherm and thermodynamic analysis of fishpond effluent coagulation using chitin derived coagulant from waste Brachyura shell, Chemical Engineering Journal Advances, 100036, 2020.
  • [34] Javadian, H., Ruiz, M., Taghvai, M., Sastre, A.M., Novel magnetic nanocomposite of calcium alginate carrying poly (pyrimidine-thiophene-amide) as a novel green synthesized polyamide for adsorption study of neodymium, terbium, and dysprosium rare-earth ions, Colloids and Surfaces A: Physicochemical and Engineering Aspects, 603, 125252, 2020.

PoliUrasil Membranlar ile Hızlı ve Spesifik RNA Saflaştırılması

Year 2020, Volume 10, Issue 2, 466 - 482, 30.12.2020
https://doi.org/10.37094/adyujsci.780049

Abstract

Ribonükleik asit (RNA), hücresel savunma, deoksiribonükleik asit (DNA) replikasyonu, transkripsiyon, canlı organizmalar için gen ekspresyonununda önemli bir rol oynar, bunun yanı sıra kanser, immün yetmezlik, tümör gibi birçok hastalık RNA'nın bozulmasıyla ilişkililendirilmiştir. Bu amaçla, RNA saflaştırmak için nükleotid bazlı ligand kullanılarak gözenekli membranlar tasarlanmıştır. Bu çalışmada, polimerize edilebilir urasil monomeri urasil metakrilat (UraM) olarak sentezlenmiş, 2-hidroksietil metakrilat (HEMA) bazlı membranlar [poli(HEMA-UraM)] UraM ve HEMA monomerlerinin kopolimerizasyonu ile kısmen dondurulmuş koşullar altında yığın polimerizasyonu ile hazırlanmıştır. Bu membranlar şişme çalışması, Fourier dönüşümlü kızılötesi spektroskopisi (FTIR) ve taramalı elektron mikroskobu (SEM) ile karakterize edilmiştir. Ayırma koşullarını optimize etmek için, pH, başlangıç RNA konsantrasyonu, süre ve sıcaklığın RNA adsorpsiyon kapasitesi üzerindeki etkileri incelenmiştir. Poli(HEMA-UraM) membranın maksimum RNA adsorpsiyonu 25.0 °C, pH 7.0, 0.5 mg/mL RNA başlangıç derişiminde 15.52 mg/g olduğu bulunmuştur. On tekrarlı adsorpsiyon-desorpsiyon döngüsünden sonra, RNA adsorpsiyon kapasitesi yalnızca %3.68 oranında azaldığı gözlenmiştir.Membran;

References

  • [[1] Sharp, P.A., The centrality of RNA, Cell, 136, 577-580, 2009.
  • [2] Perçin, I., İdil, N., Denizli, A., RNA purification from Escherichia coli cells using boronated nanoparticles, Colloids and Surfaces B: Biointerfaces, 162, 146-153, 2018.
  • [3] Martins, R., Queiroz, J., Sousa, F., Ribonucleic acid purification, Journal of Chromatography A, 1355, 1-14, 2014.
  • [4] Cooper, T.A., Wan, L., Dreyfuss, G., RNA and disease, Cell, 136, 777-793, 2009.
  • [5] Köse, K., Denizli, A., Poly (hydroxyethyl methacrylate) based magnetic nanoparticles for lysozyme purification from chicken egg white, Artificial cells, nanomedicine, and biotechnology, 41, 13-20, 2013.
  • [6] Yang, G., Lu, X., Yuan, L., LncRNA: a link between RNA and cancer, Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms, 1839, 1097-1109, 2014.
  • [7] Kim, I., Mckenna, S.A., Puglisi, E.V., Puglisi, J.D., Rapid purification of RNAs using fast performance liquid chromatography (FPLC), RNA, 13, 289-294, 2007.
  • [8] Martins, R., Queiroz, J.A., Sousa, F., Histidine affinity chromatography‐based methodology for the simultaneous isolation of Escherichia coli small and ribosomal RNA, Biomedical Chromatography, 26, 781-788, 2012.
  • [9] McGinnis, A.C., Chen, B., Bartlett, M.G., Chromatographic methods for the determination of therapeutic oligonucleotides, Journal of Chromatography B, 883, 76-94, 2012.
  • [10] Romanovskaya, A., Sarin, L.P., Bamford, D.H., Poranen, M.M., High-throughput purification of double-stranded RNA molecules using convective interaction media monolithic anion exchange columns, Journal of Chromatography A, 1278, 54-60, 2013.
  • [11] Vomelova, I., Vaníčková, Z., Šedo, A., Technical note methods of RNA purification. All ways (should) lead to Rome, Folia Biologica (Praha), 55, 243-251, 2009.
  • [12] Warren, W.J., Vella, G., Principles and methods for the analysis and purification of synthetic deoxyribonucleotides by high-performance liquid chromatography, Molecular Biotechnology, 4, 179, 1995.
  • [13] Srivastava, A., Shakya, A.K., Kumar, A., Boronate affinity chromatography of cells and biomacromolecules using cryogel matrices, Enzyme and Microbial Technology, 51, 373-381, 2012.
  • [14] Uhlenbeck, O., Keeping RNA happy, RNA, 1, 4, 1995.
  • [15] Edwards, A.L., Garst, A.D., Batey, R.T., Determining structures of RNA aptamers and riboswitches by X-ray crystallography, Nucleic Acid and Peptide Aptamers, Springer2009, pp. 135-163.
  • [16] Garcia, F., Pires, E., Recovery processes for biological materials, Chromatography, Wiley, London, UK, 415-451, 1993.
  • [17] Scouten, W.H., Affinity chromatography; bioselective adsorption on inert matrices, Wiley, NewYork, 1981.
  • [18] Ayyar, B.V., Arora, S., Murphy, C., O’Kennedy, R., Affinity chromatography as a tool for antibody purification, Methods, 56, 116-129, 2012.
  • [19] Roque, A.C., Silva, C.S., Taipa, M.Â., Affinity-based methodologies and ligands for antibody purification: advances and perspectives, Journal of Chromatography A, 1160, 44-55, 2007.
  • [20] Andaç, M., Tamahkar, E., Denizli, A., Molecularly imprinted smart cryogels for selective nickel recognition in aqueous solutions, Journal of Applied Polymer Science, 49746.
  • [21] Emin Çorman, M., Bereli, N., Özkara, S., Uzun, L., Denizli, A., Hydrophobic cryogels for DNA adsorption: Effect of embedding of monosize microbeads into cryogel network on their adsorptive performances, Biomedical Chromatography, 27, 1524-1531, 2013.
  • [22] Bereli, N., Yavuz, H., Denizli, A., Protein chromatography by molecular imprinted cryogels, Journal of Liquid Chromatography & Related Technologies, 1-14, 2020.
  • [23] Öncel, P., Çetin, K., Topçu, A.A., Yavuz, H., Denizli, A., Molecularly imprinted cryogel membranes for mitomycin C delivery, Journal of Biomaterials Science Polymer Edition, 28, 519-531, 2017.
  • [24] Hur, D., Ekti, S.F., Say, R., N-Acylbenzotriazole mediated synthesis of some methacrylamido amino acids, Letters in Organic Chemistry, 4, 585-587, 2007.
  • [25] Armutcu, C., Çorman, M.E., Bayram, E., Uzun, L., Purification of Fab and Fc using papain immobilized cryogel bioreactor separator system, Journal of Chromatography B, 122396, 2020.
  • [26] Köse, K., Erol, K., Uzun, L., Denizli, A., PolyAdenine cryogels for fast and effective RNA purification, Colloids and Surfaces B: Biointerfaces, 146, 678-686, 2016.
  • [27] Köse, K., Uzun, L., PolyGuanine methacrylate cryogels for ribonucleic acid purification, Journal of Separation Science, 39, 1998-2005, 2016.
  • [28] Çorman, M.E., Poly-l-lysine modified cryogels for efficient bilirubin removal from human plasma, Colloids and Surfaces B: Biointerfaces, 167, 291-298, 2018.
  • [29] Daoud-Attieh, M., Chaib, H., Armutcu, C., Uzun, L., Elkak, A., Denizli, A., Immunoglobulin G purification from bovine serum with pseudo-specific supermacroporous cryogels, Separation and Purification Technology, 118, 816-822, 2013.
  • [30] Foo, K.Y., Hameed, B.H., Insights into the modeling of adsorption isotherm systems, Chemical engineering journal, 156, 2-10, 2010.
  • [31] Sarı, M.M., Armutcu, C., Bereli, N., Uzun, L., Denizli, A., Monosize microbeads for pseudo-affinity adsorption of human insulin, Colloids and Surfaces B: Biointerfaces, 84, 140-147, 2011.
  • [32] Erol, B., Erol, K., Gökmeşe, E., The effect of the chelator characteristics on insulin adsorption in immobilized metal affinity chromatography, Process Biochemistry, 83, 104-113, 2019.
  • [33] Ohale, P.E., Onu, C.E., Ohale, N.J., Obah, S.N., Adsorptive kinetics, isotherm and thermodynamic analysis of fishpond effluent coagulation using chitin derived coagulant from waste Brachyura shell, Chemical Engineering Journal Advances, 100036, 2020.
  • [34] Javadian, H., Ruiz, M., Taghvai, M., Sastre, A.M., Novel magnetic nanocomposite of calcium alginate carrying poly (pyrimidine-thiophene-amide) as a novel green synthesized polyamide for adsorption study of neodymium, terbium, and dysprosium rare-earth ions, Colloids and Surfaces A: Physicochemical and Engineering Aspects, 603, 125252, 2020.

Details

Primary Language English
Subjects Chemistry, Multidisciplinary
Published Date December 2020
Journal Section Chemistry
Authors

Canan ARMUTCU (Primary Author)
HACETTEPE UNIVERSITY
0000-0002-0920-2843
Türkiye

Thanks C. Armutcu thanks Sena Piskin, Mirac Tuysuz and Dr. E. Ozgur for their valuable help during the study.
Publication Date December 30, 2020
Application Date August 13, 2020
Acceptance Date December 10, 2020
Published in Issue Year 2020, Volume 10, Issue 2

Cite

Bibtex @research article { adyujsci780049, journal = {Adıyaman University Journal of Science}, issn = {2147-1630}, eissn = {2146-586X}, address = {}, publisher = {Adıyaman University}, year = {2020}, volume = {10}, pages = {466 - 482}, doi = {10.37094/adyujsci.780049}, title = {Rapid and Specific Purification of RNA by PolyUracil Membranes}, key = {cite}, author = {Armutcu, Canan} }
APA Armutcu, C. (2020). Rapid and Specific Purification of RNA by PolyUracil Membranes . Adıyaman University Journal of Science , 10 (2) , 466-482 . DOI: 10.37094/adyujsci.780049
MLA Armutcu, C. "Rapid and Specific Purification of RNA by PolyUracil Membranes" . Adıyaman University Journal of Science 10 (2020 ): 466-482 <https://dergipark.org.tr/en/pub/adyujsci/issue/58660/780049>
Chicago Armutcu, C. "Rapid and Specific Purification of RNA by PolyUracil Membranes". Adıyaman University Journal of Science 10 (2020 ): 466-482
RIS TY - JOUR T1 - Rapid and Specific Purification of RNA by PolyUracil Membranes AU - Canan Armutcu Y1 - 2020 PY - 2020 N1 - doi: 10.37094/adyujsci.780049 DO - 10.37094/adyujsci.780049 T2 - Adıyaman University Journal of Science JF - Journal JO - JOR SP - 466 EP - 482 VL - 10 IS - 2 SN - 2147-1630-2146-586X M3 - doi: 10.37094/adyujsci.780049 UR - https://doi.org/10.37094/adyujsci.780049 Y2 - 2020 ER -
EndNote %0 Adıyaman University Journal of Science Rapid and Specific Purification of RNA by PolyUracil Membranes %A Canan Armutcu %T Rapid and Specific Purification of RNA by PolyUracil Membranes %D 2020 %J Adıyaman University Journal of Science %P 2147-1630-2146-586X %V 10 %N 2 %R doi: 10.37094/adyujsci.780049 %U 10.37094/adyujsci.780049
ISNAD Armutcu, Canan . "Rapid and Specific Purification of RNA by PolyUracil Membranes". Adıyaman University Journal of Science 10 / 2 (December 2020): 466-482 . https://doi.org/10.37094/adyujsci.780049
AMA Armutcu C. Rapid and Specific Purification of RNA by PolyUracil Membranes. ADYU J SCI. 2020; 10(2): 466-482.
Vancouver Armutcu C. Rapid and Specific Purification of RNA by PolyUracil Membranes. Adıyaman University Journal of Science. 2020; 10(2): 466-482.
IEEE C. Armutcu , "Rapid and Specific Purification of RNA by PolyUracil Membranes", Adıyaman University Journal of Science, vol. 10, no. 2, pp. 466-482, Dec. 2021, doi:10.37094/adyujsci.780049

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