Optimization of oligonucleotides characteristics with topsis

Simple item page
dc.citation.epage47
dc.citation.issue3
dc.citation.journalTitleУкраїнський журнал із машинобудування і матеріалознавства
dc.citation.spage40
dc.contributor.affiliationConcordia University
dc.contributor.authorJavanbakht, Taraneh
dc.coverage.placenameЛьвів
dc.coverage.placenameLviv
dc.date.accessioned2024-04-03T07:37:00Z
dc.date.available2024-04-03T07:37:00Z
dc.date.created2023-02-28
dc.date.issued2023-02-28
dc.description.abstractThis paper focused on a new application of the TOPSIS method for the prediction and optimization of the oligonucleotides characteristics. This method has been used for these purposes as it has shown its efficacy for these analyses. This is the first time that it has been applied to the investigation of these biomolecules. The hypothesis in this paper was that the characteristics of these biomaterials would be optimized according to their structural differences. The obtained results showed that the stabilization of oligonucleotides would affect their ranking with TOPSIS when the stability of these biomolecules increased against enzymes in their structure. In other words, the oligonucleotides with less enzymatic degradation were ranked better with this method. This study showed the first application of this algorithm for the prediction and optimization of the oligonucleotides’ characteristics. The results in this work revealed that the ranks of candidates depended on their distances from their ideal solutions. This showed that TOPSIS could be used as an appropriate method in the optimization of oligonucleotides as the rankings with this method would coincide with the data that concern the stability of these biomolecules against enzymatic degradation. The results of this work could be applied for the preparation of novel materials with applications in science and engineering.
dc.format.extent40-47
dc.format.pages8
dc.identifier.citationJavanbakht T. Optimization of oligonucleotides characteristics with topsis / Taraneh Javanbakht // Ukrainian Journal of Mechanical Engineering and Materials Science. — Lviv : Lviv Politechnic Publishing House, 2023. — Vol 9. — No 3. — P. 40–47.
dc.identifier.citationenJavanbakht T. Optimization of oligonucleotides characteristics with topsis / Taraneh Javanbakht // Ukrainian Journal of Mechanical Engineering and Materials Science. — Lviv : Lviv Politechnic Publishing House, 2023. — Vol 9. — No 3. — P. 40–47.
dc.identifier.doidoi.org/10.23939/ujmems2023.03.040
dc.identifier.issn2411-8001
dc.identifier.urihttps://ena.lpnu.ua/handle/ntb/61639
dc.language.isoen
dc.publisherВидавництво Львівської політехніки
dc.publisherLviv Politechnic Publishing House
dc.relation.ispartofУкраїнський журнал із машинобудування і матеріалознавства, 3 (9), 2023
dc.relation.ispartofUkrainian Journal of Mechanical Engineering and Materials Science, 3 (9), 2023
dc.relation.references[1] Binder, H., Preibisch, S. Specific and nonspecific hybridization of oligonucleotide probes on microarrays, Biophys. J., vol. 89, pp. 337-352, 2005. https://doi.org/10.1529/biophysj.104.055343
dc.relation.references[2] Iyer, M. et al. Accelerated hybridization of oligonucleotides to duplex DNA, J. Biol. Chem., vol. 270, pp. 14712-14717, 1995. https://doi.org/10.1074/jbc.270.24.14712
dc.relation.references[3] Juskowiak, B., Nucleic acid-based fluorescent probes and their analytical potential, Anal. Bioanal. Chem., vol. 399, pp. 3157-3176, 2011. https://doi.org/10.1007/s00216-010-4304-5
dc.relation.references[4] Waminal, N.E. et al., Rapid and efficient FISH using pre-labeled oligomer probes, Scientific Reports, 8224, 2018. https://doi.org/10.1038/s41598-018-26667-z
dc.relation.references[5] Rukov, J.L. et al. Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs, Nucleic Acids Res., vol. 43, pp. 8476-8487, 2015. https://doi.org/10.1093/nar/gkv759
dc.relation.references[6] Lai, F., et al. Directed RNase H cleavage of nascent transcripts causes transcription termination, Molecular Cell, vol. 77, pp. 1032-1043, 2020. https://doi.org/10.1016/j.molcel.2019.12.029
dc.relation.references[7] Vickers, T.A., Crooke, S.T. Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms, Plos One, 2014. https://doi.org/10.1371/journal.pone.0108625
dc.relation.references[8] Lee, J.E. et al. RNase H-mediated degradation of toxic RNA in myotonic dystrophy type 1, Proceedings of the National Academy of Sciences, vol. 109, pp. 4221-4226, 2012. https://doi.org/10.1073/pnas.1117019109
dc.relation.references[9] Dallavalle, S. et al. Improvement of conventional anti-cancer drugs as new tools against multidrug resistant tumors, Drug Resistance Uptakes, vol. 50, 100682, 2020. https://doi.org/10.1016/j.drup.2020.100682
dc.relation.references[10] Emran, T.B. et al. Multidrug resistance in cancer: Understanding molecular mechanisms, immunoprevention and therapeutic approaches, Frontiers, Sec. Pharmacology of Anti-Cancer Drugs, 2022. https://doi.org/10.3389/fonc.2022.891652
dc.relation.references[11] Vaidya, F.U. et al. Molecular and cellular paradigms of multidrug resistance in cancer, Cancer Reports, e1291, 2020. https://doi.org/10.1002/cnr2.1291
dc.relation.references[12] Fojo, A.T. et al. Expression of a multidrug-resistance gene in human tumors and tissues, Proc. Natl. Acad. Sci., vol. 84, pp. 265-269, 1987. https://doi.org/10.1073/pnas.84.1.265
dc.relation.references[13] Roninson, I.B. The role of MDR1 (P-glycoprotein) gene in multidrug resistance in vitro and in vivo, Biochem. Pharmacol., vol. 43, pp. 95-102, 1992. https://doi.org/10.1016/0006-2952(92)90666-7
dc.relation.references[14] Ling, V. P-glycoprotein and resistance to anticancer drugs, Cancer, vol. 69, pp. 2603-2609, 1992. https://doi.org/10.1002/1097-0142(19920515)69:10<2603::AID-CNCR2820691034>3.0.CO;2-E
dc.relation.references[15] Choong, E. The permeability P-glycoprotein: a focus on enantioselectivity and brain distribution, Expert Opin. Drug Metab. Toxicol., vol. 6, pp. 953-65, 2010. https://doi.org/10.1517/17425251003789394
dc.relation.references[16] Djavanbakht Samani, T., Jolles, B., Laigle, A. Best minimally modified antisense oligonucleotides according to cell nuclease activity, Antisense and Nucleic Acid Drug Development, vol. 11, pp. 129-136 2001. https://doi.org/10.1089/108729001300338654
dc.relation.references[17] Brigui, I., Djavanbakht Samani, T., Jollès, B., Laigle, A. Minimally modified phosphodiester antisense oligodeoxyribonucleotide directed against the multidrug resistance gene mdr1, Biochem. Pharmacol., vol. 65, pp. 747-54, 2003. https://doi.org/10.1016/S0006-2952(02)01558-7
dc.relation.references[18] Whitesell, L. et al. Stability, clearance, and disposition of intraventricularly administered oligodeoxynucleotides: Implications for therapeutic application within the central nervous system, Proc. Natl. Acad. Sci., vol. 90, pp. 4665-4669, 1993. https://doi.org/10.1073/pnas.90.10.4665
dc.relation.references[19] Culman, J. Antisense oligonucleotides in the study of central mechanisms of the cardiovascular regulation, Exp.Physiol., vol. 85, pp. 757-767, 2000. https://doi.org/10.1111/j.1469-445X.2000.02143.x
dc.relation.references[20] Wojcik, M. et al. Nucleotide pyrophosphatase/phosphodiesterase 1 Is responsible for degradation of antisense phosphorothioate oligonucleotides, Oligonucleotides, vol. 17, pp. 134-45, 2007. https://doi.org/10.1089/oli.2007.0021
dc.relation.references[21] Kanazaki, M. et al. Highly nuclease-resistant phosphodiester-type oligodeoxynucleotides containing 4'α-C-aminoalkylthymidines form thermally stable duplexes with DNA and RNA. A candidate for potent antisense molecules, J. Am. Chem. Soc., vol. 122, pp. 2422-2432, 2000. https://doi.org/10.1021/ja9934706
dc.relation.references[22] Jahrsdörfer, B. et al. Phosphorothyoate oligodeoxynucleotides block nonspecific binding of Cy5 conjugates to monocytes, J. Immunol. Methods., vol. 297, pp. 259-263, 2005. https://doi.org/10.1016/j.jim.2004.11.023
dc.relation.references[23] Hatta, T. et al. Phosphorothioate oligonucleotides block reverse transcription by the RNase-H activity associated with the HIV-1 polymerase, Biochemical and Biophysical Research Communications, vol. 211, pp. 1041-1046, 1995. https://doi.org/10.1006/bbrc.1995.1916
dc.relation.references[24] Javanbakht, T., Chakravorty, S. Prediction of human behavior with TOPSIS. Fuzzy Extension and Applications, vol. 3, pp. 109-125.
dc.relation.references[25] Javanbakht, T., Chakravorty, S. Optimization of machine learning algorithms for proteomic analysis using TOPSIS, Journal of Engineering Sciences, vol. 9, pp. E7-E12, 2022. https://doi.org/10.21272/jes.2022.9(2).e2
dc.relation.references[26] Balioti, V., Tzimopoulos, C., Evangelides, C. Multi-criteria decision making using TOPSIS method under fuzzy environment. Application in spillway selection, Proceedings, vol. 2, 637, 2018. https://doi.org/10.3390/proceedings2110637
dc.relation.references[27] Bulgurcu, B. Application of TOPSIS technique for financial performance evaluation of technology firms in Istanbul stock exchange market, Procedia, vol. 62, pp. 1033-1040, 2012. https://doi.org/10.1016/j.sbspro.2012.09.176
dc.relation.references[28] Wang, J. et al. Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials, Langmuir, 38, vol. 11, pp. 3553-3560, 2022. https://doi.org/10.1021/acs.langmuir.2c00108
dc.relation.references[29] Kim, J. et al. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides, Theranostics, vol. 9, 3191-3212, 2019. https://doi.org/10.7150/thno.33921
dc.relation.references[30] Sahle, F.F., Lowe, T.L. Design strategies for programmable oligonucleotide nanotherapeutics, Drug Discov Today, vol. 25, 73-88, 2020. https://doi.org/10.1016/j.drudis.2019.09.006
dc.relation.references[31] Wei, M. et al. Polyvalent immunostimulatory nanoagents with self-assembled CpG oligonucleotide-conjugated gold nanoparticle, Angewandte Chemie, vol. 51, pp. 1202-1206, 2011. https://doi.org/10.1002/anie.201105187
dc.relation.references[32] Maccullock, T. et al. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterialsm, Organic and Biomolecular Chemistry, vol. 17, pp. 1668-1682, 2019. https://doi.org/10.1039/C8OB02436G
dc.relation.references[33] Javanbakht, T. et al. Correlation between physicochemical properties of superparamagnetic iron oxide nanoparticles and their reactivity with hydrogen peroxide, Canadian Journal of Chemistry, vol. 98, pp. 601-608, 2020. https://doi.org/10.1139/cjc-2020-0087
dc.relation.references[34] Javanbakht, T. Ghane-Motlagh, B., Sawan, M. Comparative study of antibiofilm activity and physicochemical properties of microelectrode arrays, Microelectronic Engineering, vol. 229, 111305, 2020. https://doi.org/10.1016/j.mee.2020.111305
dc.relation.references[35] Da Pieve, F. Physicochemical properties and complexity of amino acids beyond our biosphere: Analysis of the isoleucine group from meteorites, ACS Earth Space Chem., vol. 3, pp. 1955-1965, 2019. https://doi.org/10.1021/acsearthspacechem.9b00131
dc.relation.references[36] Djavanbakht, T. et al. Effets d'un chauffage thermique sur les performances de miroirs multicouches Mo/Si, Mo/C et Ni/C pour le rayonnement X mou, J. Phys. IV France, vol. 10, pp. 281-287, 2000. https://doi.org/10.1051/jp4:20001031
dc.relation.references[37] Gatoo, M.A. et al. Physicochemical properties of nanomaterials: Implication in associated toxic manifestations, BioMed Research International, vol. 2014, 498420, 2014. https://doi.org/10.1155/2014/498420
dc.relation.references[38] Javanbakht, T., David, E. Rheological and physical properties of a nanocomposite of graphene oxide nanoribbons with polyvinyl alcohol, Journal of Thermoplastic Composite Materials, vol. 35, pp. 651-664, 2020. https://doi.org/10.1177/0892705720912767
dc.relation.references[39] Javanbakht, T. Investigation of rheological properties of graphene oxide and its nanocomposite with polyvinyl alcohol, Ukrainian Journal of Mechanical Engineering and Materials Science, vol. 7, pp. 23-32, 2021. https://doi.org/10.23939/ujmems2021.01-02.023
dc.relation.references[40] Javanbakht, T. et al. Related physicochemical, rheological, and dielectric properties of nanocomposites of superparamagnetic iron oxide nanoparticles with polyethyleneglycol, Journal of Applied Polymer Science, vol. 136, 48280-48290, 2019. https://doi.org/10.1002/app.48280
dc.relation.references[41] Farooq, F. et al. Experimental investigation of hybrid carbon nanotubes and graphite nanoplatelets on rheology, shrinkage, mechanical, and microstructure of SCCM, Materials, vol. 13, 230, 2020. https://doi.org/10.3390/ma13010230
dc.relation.references[42] Javanbakht, T., Sokolowski, W. Thiol-ene/acrylate systems for biomedical shape-memory polymers, Shape Memory Polymers for Biomedical Applications, pp. 157-166, 2015. https://doi.org/10.1016/B978-0-85709-698-2.00008-8
dc.relation.references[43] Patil-Sen, Y. Advances in nano-biomaterials and their applications in biomedicine, Emerg Top Life Sci., vol. 14, pp. 169-176, 2021. https://doi.org/10.1042/ETLS20200333
dc.relation.references[44] Feng, J.-J. et al. Biocompatible functional nanomaterials: Synthesis, properties, and applications, Journal of Nanomaterials, vol. 2013, 385939, 2013. https://doi.org/10.1155/2013/385939
dc.relation.references[45] Javanbakht, T., Hadian, H., Wilkinson, K.J. Comparative study of physicochemical properties and antibiofilm activity of graphene oxide nanoribbons, Journal of Engineering Sciences, wol. 7, pp. C1-C8, 2020. https://doi.org/10.21272/jes.2020.7(1).c1
dc.relation.references[46] Bezerra, D.M., Assaf, E.M. Influence of the preparation method on the structural properties of mixed metal oxides, Science and Technology of Materials, vol. 30, pp. 166-173, 2018. https://doi.org/10.1016/j.stmat.2018.07.001
dc.relation.references[47] Ishihara, K. et al. Preparation of phospholipid polymers and their properties as polymer hydrogel membranes, Polymer Journal, vol. 22, pp. 355-360, 1990. https://doi.org/10.1295/polymj.22.355
dc.relation.references[48] Jadhav, P.S. et al. Study of the preparation and properties of polyvinyl chloride/nitrocellulose polymer blends, Polymer International, vol. 71, 1009-1021, 2022. https://doi.org/10.1002/pi.6385
dc.relation.references[49] Saini K; Preparation method, Properties and Crosslinking of hydrogel: A review, Pharma Tutor, vol. 5, pp. 27-36, 2017.
dc.relation.references[50] Al-Muhtaseb, S.A., Ritter, J.A. Preparation and properties of resorcinol-formaldehyde organic and carbon gels, Advanced Materials, vol. 15, pp. 101-114, 2003. https://doi.org/10.1002/adma.200390020
dc.relation.references[51] Varatharajulu, M. et al. Multi criteria decision making through TOPSIS and COPRAS on drilling parameters of magnesium AZ91, Journal of Magnesium and Alloys, Vol. 10, pp. 2857-2874, 2022. https://doi.org/10.1016/j.jma.2021.05.006
dc.relation.references[52] Shukla, A. et al. Applications of TOPSIS algorithm on various manufacturing processes: A review, Materials Today: Proceedings, vol. 4, pp. 5320-5329, 2017. https://doi.org/10.1016/j.matpr.2017.05.042
dc.relation.references[53] Kazi, F.M. et al. Multi-objective optimization of the aluminum powder-mixed EDM process using the GRA and TOPSIS techniques based on the fuzzy AHP approach, Journal of applied research and technology, vol. 19, 2022. https://doi.org/10.22201/icat.24486736e.2021.19.5.1133
dc.relation.references[54] Hanine, M. et al. Application of an integrated multi-criteria decision making AHP-TOPSIS methodology for ETL software selection, Springer Plus, 263, 2016. https://doi.org/10.1186/s40064-016-1888-z
dc.relation.references[55] Javanbakht, T. A novel automated decision-making process for analysis of ions and organic materials in drinking water, J. Eng. Sci., vol. 10, pp. H1-H7, 2023. https://doi.org/10.21272/jes.2023.10(1).h1
dc.relation.references[56] Darji, V.P., Rao, R.V. Application of AHP/EVAMIX method for decision making in the industrial environment, American Journal of Operations Research, vol.3, 39747, 2013. https://doi.org/10.4236/ajor.2013.36053
dc.relation.references[57] Rafiee, R. et al. The optimum support selection by using fuzzy analytical hierarchy process method for Beheshtabad water transporting tunnel in Naien, Iranian Journal of Fuzzy Systems, vol. 10, pp. 39-51, 2013.
dc.relation.references[58] Li, Y. et al. The research of applying TOPSIS combined with grey relational analysis approach for building energy consumption evaluation, Proceedings of the 8th International Symposium on Heating, Ventilation and Air Conditioning, pp. 611-619, 2013. https://doi.org/10.1007/978-3-642-39578-9_64
dc.relation.references[59] Magableh, G.M., Mistarihi, M.Z. Applications of MCDM approach (ANP-TOPSIS) to evaluate supply chain solutions in the context of COVID-19, Heliyon, vol. 8, e09062, 2022. https://doi.org/10.1016/j.heliyon.2022.e09062
dc.relation.references[60] ArunRamnath, R., Thyla, P.R. Measurement and optimization of multi-attribute characteristics in milling epoxy granite composites using rsm and combined ahp-topsis, Surface Topography: Metrology and Properties, vol. 10, 025023, 2022. https://doi.org/10.1088/2051-672X/ac4566
dc.relation.references[61] Huang, J. et al. Research on supply quantity transportation and ordering method based on TOPSIS and support vector regression, Academic Journal of Business and Management, vol. 3, pp. 51-55, 2021. https://doi.org/10.25236/AJBM.2021.031010
dc.relation.references[62] Yang, H. et al. Evaluation of DDOS attack degree based on GRA-TOPSIS model, International Conference on Smart Grid and Electrical Automation (ICSGEA), 2019. https://doi.org/10.1109/ICSGEA.2019.00129
dc.relation.referencesen[1] Binder, H., Preibisch, S. Specific and nonspecific hybridization of oligonucleotide probes on microarrays, Biophys. J., vol. 89, pp. 337-352, 2005. https://doi.org/10.1529/biophysj.104.055343
dc.relation.referencesen[2] Iyer, M. et al. Accelerated hybridization of oligonucleotides to duplex DNA, J. Biol. Chem., vol. 270, pp. 14712-14717, 1995. https://doi.org/10.1074/jbc.270.24.14712
dc.relation.referencesen[3] Juskowiak, B., Nucleic acid-based fluorescent probes and their analytical potential, Anal. Bioanal. Chem., vol. 399, pp. 3157-3176, 2011. https://doi.org/10.1007/s00216-010-4304-5
dc.relation.referencesen[4] Waminal, N.E. et al., Rapid and efficient FISH using pre-labeled oligomer probes, Scientific Reports, 8224, 2018. https://doi.org/10.1038/s41598-018-26667-z
dc.relation.referencesen[5] Rukov, J.L. et al. Dissecting the target specificity of RNase H recruiting oligonucleotides using massively parallel reporter analysis of short RNA motifs, Nucleic Acids Res., vol. 43, pp. 8476-8487, 2015. https://doi.org/10.1093/nar/gkv759
dc.relation.referencesen[6] Lai, F., et al. Directed RNase H cleavage of nascent transcripts causes transcription termination, Molecular Cell, vol. 77, pp. 1032-1043, 2020. https://doi.org/10.1016/j.molcel.2019.12.029
dc.relation.referencesen[7] Vickers, T.A., Crooke, S.T. Antisense oligonucleotides capable of promoting specific target mRNA reduction via competing RNase H1-dependent and independent mechanisms, Plos One, 2014. https://doi.org/10.1371/journal.pone.0108625
dc.relation.referencesen[8] Lee, J.E. et al. RNase H-mediated degradation of toxic RNA in myotonic dystrophy type 1, Proceedings of the National Academy of Sciences, vol. 109, pp. 4221-4226, 2012. https://doi.org/10.1073/pnas.1117019109
dc.relation.referencesen[9] Dallavalle, S. et al. Improvement of conventional anti-cancer drugs as new tools against multidrug resistant tumors, Drug Resistance Uptakes, vol. 50, 100682, 2020. https://doi.org/10.1016/j.drup.2020.100682
dc.relation.referencesen[10] Emran, T.B. et al. Multidrug resistance in cancer: Understanding molecular mechanisms, immunoprevention and therapeutic approaches, Frontiers, Sec. Pharmacology of Anti-Cancer Drugs, 2022. https://doi.org/10.3389/fonc.2022.891652
dc.relation.referencesen[11] Vaidya, F.U. et al. Molecular and cellular paradigms of multidrug resistance in cancer, Cancer Reports, e1291, 2020. https://doi.org/10.1002/cnr2.1291
dc.relation.referencesen[12] Fojo, A.T. et al. Expression of a multidrug-resistance gene in human tumors and tissues, Proc. Natl. Acad. Sci., vol. 84, pp. 265-269, 1987. https://doi.org/10.1073/pnas.84.1.265
dc.relation.referencesen[13] Roninson, I.B. The role of MDR1 (P-glycoprotein) gene in multidrug resistance in vitro and in vivo, Biochem. Pharmacol., vol. 43, pp. 95-102, 1992. https://doi.org/10.1016/0006-2952(92)90666-7
dc.relation.referencesen[14] Ling, V. P-glycoprotein and resistance to anticancer drugs, Cancer, vol. 69, pp. 2603-2609, 1992. https://doi.org/10.1002/1097-0142(19920515)69:10<2603::AID-CNCR2820691034>3.0.CO;2-E
dc.relation.referencesen[15] Choong, E. The permeability P-glycoprotein: a focus on enantioselectivity and brain distribution, Expert Opin. Drug Metab. Toxicol., vol. 6, pp. 953-65, 2010. https://doi.org/10.1517/17425251003789394
dc.relation.referencesen[16] Djavanbakht Samani, T., Jolles, B., Laigle, A. Best minimally modified antisense oligonucleotides according to cell nuclease activity, Antisense and Nucleic Acid Drug Development, vol. 11, pp. 129-136 2001. https://doi.org/10.1089/108729001300338654
dc.relation.referencesen[17] Brigui, I., Djavanbakht Samani, T., Jollès, B., Laigle, A. Minimally modified phosphodiester antisense oligodeoxyribonucleotide directed against the multidrug resistance gene mdr1, Biochem. Pharmacol., vol. 65, pp. 747-54, 2003. https://doi.org/10.1016/S0006-2952(02)01558-7
dc.relation.referencesen[18] Whitesell, L. et al. Stability, clearance, and disposition of intraventricularly administered oligodeoxynucleotides: Implications for therapeutic application within the central nervous system, Proc. Natl. Acad. Sci., vol. 90, pp. 4665-4669, 1993. https://doi.org/10.1073/pnas.90.10.4665
dc.relation.referencesen[19] Culman, J. Antisense oligonucleotides in the study of central mechanisms of the cardiovascular regulation, Exp.Physiol., vol. 85, pp. 757-767, 2000. https://doi.org/10.1111/j.1469-445X.2000.02143.x
dc.relation.referencesen[20] Wojcik, M. et al. Nucleotide pyrophosphatase/phosphodiesterase 1 Is responsible for degradation of antisense phosphorothioate oligonucleotides, Oligonucleotides, vol. 17, pp. 134-45, 2007. https://doi.org/10.1089/oli.2007.0021
dc.relation.referencesen[21] Kanazaki, M. et al. Highly nuclease-resistant phosphodiester-type oligodeoxynucleotides containing 4'α-C-aminoalkylthymidines form thermally stable duplexes with DNA and RNA. A candidate for potent antisense molecules, J. Am. Chem. Soc., vol. 122, pp. 2422-2432, 2000. https://doi.org/10.1021/ja9934706
dc.relation.referencesen[22] Jahrsdörfer, B. et al. Phosphorothyoate oligodeoxynucleotides block nonspecific binding of Cy5 conjugates to monocytes, J. Immunol. Methods., vol. 297, pp. 259-263, 2005. https://doi.org/10.1016/j.jim.2004.11.023
dc.relation.referencesen[23] Hatta, T. et al. Phosphorothioate oligonucleotides block reverse transcription by the RNase-H activity associated with the HIV-1 polymerase, Biochemical and Biophysical Research Communications, vol. 211, pp. 1041-1046, 1995. https://doi.org/10.1006/bbrc.1995.1916
dc.relation.referencesen[24] Javanbakht, T., Chakravorty, S. Prediction of human behavior with TOPSIS. Fuzzy Extension and Applications, vol. 3, pp. 109-125.
dc.relation.referencesen[25] Javanbakht, T., Chakravorty, S. Optimization of machine learning algorithms for proteomic analysis using TOPSIS, Journal of Engineering Sciences, vol. 9, pp. E7-E12, 2022. https://doi.org/10.21272/jes.2022.9(2).e2
dc.relation.referencesen[26] Balioti, V., Tzimopoulos, C., Evangelides, C. Multi-criteria decision making using TOPSIS method under fuzzy environment. Application in spillway selection, Proceedings, vol. 2, 637, 2018. https://doi.org/10.3390/proceedings2110637
dc.relation.referencesen[27] Bulgurcu, B. Application of TOPSIS technique for financial performance evaluation of technology firms in Istanbul stock exchange market, Procedia, vol. 62, pp. 1033-1040, 2012. https://doi.org/10.1016/j.sbspro.2012.09.176
dc.relation.referencesen[28] Wang, J. et al. Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials, Langmuir, 38, vol. 11, pp. 3553-3560, 2022. https://doi.org/10.1021/acs.langmuir.2c00108
dc.relation.referencesen[29] Kim, J. et al. Advances in intracellular delivery through supramolecular self-assembly of oligonucleotides and peptides, Theranostics, vol. 9, 3191-3212, 2019. https://doi.org/10.7150/thno.33921
dc.relation.referencesen[30] Sahle, F.F., Lowe, T.L. Design strategies for programmable oligonucleotide nanotherapeutics, Drug Discov Today, vol. 25, 73-88, 2020. https://doi.org/10.1016/j.drudis.2019.09.006
dc.relation.referencesen[31] Wei, M. et al. Polyvalent immunostimulatory nanoagents with self-assembled CpG oligonucleotide-conjugated gold nanoparticle, Angewandte Chemie, vol. 51, pp. 1202-1206, 2011. https://doi.org/10.1002/anie.201105187
dc.relation.referencesen[32] Maccullock, T. et al. Emerging applications of peptide-oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterialsm, Organic and Biomolecular Chemistry, vol. 17, pp. 1668-1682, 2019. https://doi.org/10.1039/P.8OB02436G
dc.relation.referencesen[33] Javanbakht, T. et al. Correlation between physicochemical properties of superparamagnetic iron oxide nanoparticles and their reactivity with hydrogen peroxide, Canadian Journal of Chemistry, vol. 98, pp. 601-608, 2020. https://doi.org/10.1139/cjc-2020-0087
dc.relation.referencesen[34] Javanbakht, T. Ghane-Motlagh, B., Sawan, M. Comparative study of antibiofilm activity and physicochemical properties of microelectrode arrays, Microelectronic Engineering, vol. 229, 111305, 2020. https://doi.org/10.1016/j.mee.2020.111305
dc.relation.referencesen[35] Da Pieve, F. Physicochemical properties and complexity of amino acids beyond our biosphere: Analysis of the isoleucine group from meteorites, ACS Earth Space Chem., vol. 3, pp. 1955-1965, 2019. https://doi.org/10.1021/acsearthspacechem.9b00131
dc.relation.referencesen[36] Djavanbakht, T. et al. Effets d'un chauffage thermique sur les performances de miroirs multicouches Mo/Si, Mo/C et Ni/C pour le rayonnement X mou, J. Phys. IV France, vol. 10, pp. 281-287, 2000. https://doi.org/10.1051/jp4:20001031
dc.relation.referencesen[37] Gatoo, M.A. et al. Physicochemical properties of nanomaterials: Implication in associated toxic manifestations, BioMed Research International, vol. 2014, 498420, 2014. https://doi.org/10.1155/2014/498420
dc.relation.referencesen[38] Javanbakht, T., David, E. Rheological and physical properties of a nanocomposite of graphene oxide nanoribbons with polyvinyl alcohol, Journal of Thermoplastic Composite Materials, vol. 35, pp. 651-664, 2020. https://doi.org/10.1177/0892705720912767
dc.relation.referencesen[39] Javanbakht, T. Investigation of rheological properties of graphene oxide and its nanocomposite with polyvinyl alcohol, Ukrainian Journal of Mechanical Engineering and Materials Science, vol. 7, pp. 23-32, 2021. https://doi.org/10.23939/ujmems2021.01-02.023
dc.relation.referencesen[40] Javanbakht, T. et al. Related physicochemical, rheological, and dielectric properties of nanocomposites of superparamagnetic iron oxide nanoparticles with polyethyleneglycol, Journal of Applied Polymer Science, vol. 136, 48280-48290, 2019. https://doi.org/10.1002/app.48280
dc.relation.referencesen[41] Farooq, F. et al. Experimental investigation of hybrid carbon nanotubes and graphite nanoplatelets on rheology, shrinkage, mechanical, and microstructure of SCCM, Materials, vol. 13, 230, 2020. https://doi.org/10.3390/ma13010230
dc.relation.referencesen[42] Javanbakht, T., Sokolowski, W. Thiol-ene/acrylate systems for biomedical shape-memory polymers, Shape Memory Polymers for Biomedical Applications, pp. 157-166, 2015. https://doi.org/10.1016/B978-0-85709-698-2.00008-8
dc.relation.referencesen[43] Patil-Sen, Y. Advances in nano-biomaterials and their applications in biomedicine, Emerg Top Life Sci., vol. 14, pp. 169-176, 2021. https://doi.org/10.1042/ETLS20200333
dc.relation.referencesen[44] Feng, J.-J. et al. Biocompatible functional nanomaterials: Synthesis, properties, and applications, Journal of Nanomaterials, vol. 2013, 385939, 2013. https://doi.org/10.1155/2013/385939
dc.relation.referencesen[45] Javanbakht, T., Hadian, H., Wilkinson, K.J. Comparative study of physicochemical properties and antibiofilm activity of graphene oxide nanoribbons, Journal of Engineering Sciences, wol. 7, pp. P.1-P.8, 2020. https://doi.org/10.21272/jes.2020.7(1).P.1
dc.relation.referencesen[46] Bezerra, D.M., Assaf, E.M. Influence of the preparation method on the structural properties of mixed metal oxides, Science and Technology of Materials, vol. 30, pp. 166-173, 2018. https://doi.org/10.1016/j.stmat.2018.07.001
dc.relation.referencesen[47] Ishihara, K. et al. Preparation of phospholipid polymers and their properties as polymer hydrogel membranes, Polymer Journal, vol. 22, pp. 355-360, 1990. https://doi.org/10.1295/polymj.22.355
dc.relation.referencesen[48] Jadhav, P.S. et al. Study of the preparation and properties of polyvinyl chloride/nitrocellulose polymer blends, Polymer International, vol. 71, 1009-1021, 2022. https://doi.org/10.1002/pi.6385
dc.relation.referencesen[49] Saini K; Preparation method, Properties and Crosslinking of hydrogel: A review, Pharma Tutor, vol. 5, pp. 27-36, 2017.
dc.relation.referencesen[50] Al-Muhtaseb, S.A., Ritter, J.A. Preparation and properties of resorcinol-formaldehyde organic and carbon gels, Advanced Materials, vol. 15, pp. 101-114, 2003. https://doi.org/10.1002/adma.200390020
dc.relation.referencesen[51] Varatharajulu, M. et al. Multi criteria decision making through TOPSIS and COPRAS on drilling parameters of magnesium AZ91, Journal of Magnesium and Alloys, Vol. 10, pp. 2857-2874, 2022. https://doi.org/10.1016/j.jma.2021.05.006
dc.relation.referencesen[52] Shukla, A. et al. Applications of TOPSIS algorithm on various manufacturing processes: A review, Materials Today: Proceedings, vol. 4, pp. 5320-5329, 2017. https://doi.org/10.1016/j.matpr.2017.05.042
dc.relation.referencesen[53] Kazi, F.M. et al. Multi-objective optimization of the aluminum powder-mixed EDM process using the GRA and TOPSIS techniques based on the fuzzy AHP approach, Journal of applied research and technology, vol. 19, 2022. https://doi.org/10.22201/icat.24486736e.2021.19.5.1133
dc.relation.referencesen[54] Hanine, M. et al. Application of an integrated multi-criteria decision making AHP-TOPSIS methodology for ETL software selection, Springer Plus, 263, 2016. https://doi.org/10.1186/s40064-016-1888-z
dc.relation.referencesen[55] Javanbakht, T. A novel automated decision-making process for analysis of ions and organic materials in drinking water, J. Eng. Sci., vol. 10, pp. H1-H7, 2023. https://doi.org/10.21272/jes.2023.10(1).h1
dc.relation.referencesen[56] Darji, V.P., Rao, R.V. Application of AHP/EVAMIX method for decision making in the industrial environment, American Journal of Operations Research, vol.3, 39747, 2013. https://doi.org/10.4236/ajor.2013.36053
dc.relation.referencesen[57] Rafiee, R. et al. The optimum support selection by using fuzzy analytical hierarchy process method for Beheshtabad water transporting tunnel in Naien, Iranian Journal of Fuzzy Systems, vol. 10, pp. 39-51, 2013.
dc.relation.referencesen[58] Li, Y. et al. The research of applying TOPSIS combined with grey relational analysis approach for building energy consumption evaluation, Proceedings of the 8th International Symposium on Heating, Ventilation and Air Conditioning, pp. 611-619, 2013. https://doi.org/10.1007/978-3-642-39578-9_64
dc.relation.referencesen[59] Magableh, G.M., Mistarihi, M.Z. Applications of MCDM approach (ANP-TOPSIS) to evaluate supply chain solutions in the context of COVID-19, Heliyon, vol. 8, e09062, 2022. https://doi.org/10.1016/j.heliyon.2022.e09062
dc.relation.referencesen[60] ArunRamnath, R., Thyla, P.R. Measurement and optimization of multi-attribute characteristics in milling epoxy granite composites using rsm and combined ahp-topsis, Surface Topography: Metrology and Properties, vol. 10, 025023, 2022. https://doi.org/10.1088/2051-672X/ac4566
dc.relation.referencesen[61] Huang, J. et al. Research on supply quantity transportation and ordering method based on TOPSIS and support vector regression, Academic Journal of Business and Management, vol. 3, pp. 51-55, 2021. https://doi.org/10.25236/AJBM.2021.031010
dc.relation.referencesen[62] Yang, H. et al. Evaluation of DDOS attack degree based on GRA-TOPSIS model, International Conference on Smart Grid and Electrical Automation (ICSGEA), 2019. https://doi.org/10.1109/ICSGEA.2019.00129
dc.relation.urihttps://doi.org/10.1529/biophysj.104.055343
dc.relation.urihttps://doi.org/10.1074/jbc.270.24.14712
dc.relation.urihttps://doi.org/10.1007/s00216-010-4304-5
dc.relation.urihttps://doi.org/10.1038/s41598-018-26667-z
dc.relation.urihttps://doi.org/10.1093/nar/gkv759
dc.relation.urihttps://doi.org/10.1016/j.molcel.2019.12.029
dc.relation.urihttps://doi.org/10.1371/journal.pone.0108625
dc.relation.urihttps://doi.org/10.1073/pnas.1117019109
dc.relation.urihttps://doi.org/10.1016/j.drup.2020.100682
dc.relation.urihttps://doi.org/10.3389/fonc.2022.891652
dc.relation.urihttps://doi.org/10.1002/cnr2.1291
dc.relation.urihttps://doi.org/10.1073/pnas.84.1.265
dc.relation.urihttps://doi.org/10.1016/0006-2952(92)90666-7
dc.relation.urihttps://doi.org/10.1002/1097-0142(19920515)69:10<2603::AID-CNCR2820691034>3.0.CO;2-E
dc.relation.urihttps://doi.org/10.1517/17425251003789394
dc.relation.urihttps://doi.org/10.1089/108729001300338654
dc.relation.urihttps://doi.org/10.1016/S0006-2952(02)01558-7
dc.relation.urihttps://doi.org/10.1073/pnas.90.10.4665
dc.relation.urihttps://doi.org/10.1111/j.1469-445X.2000.02143.x
dc.relation.urihttps://doi.org/10.1089/oli.2007.0021
dc.relation.urihttps://doi.org/10.1021/ja9934706
dc.relation.urihttps://doi.org/10.1016/j.jim.2004.11.023
dc.relation.urihttps://doi.org/10.1006/bbrc.1995.1916
dc.relation.urihttps://doi.org/10.21272/jes.2022.9(2).e2
dc.relation.urihttps://doi.org/10.3390/proceedings2110637
dc.relation.urihttps://doi.org/10.1016/j.sbspro.2012.09.176
dc.relation.urihttps://doi.org/10.1021/acs.langmuir.2c00108
dc.relation.urihttps://doi.org/10.7150/thno.33921
dc.relation.urihttps://doi.org/10.1016/j.drudis.2019.09.006
dc.relation.urihttps://doi.org/10.1002/anie.201105187
dc.relation.urihttps://doi.org/10.1039/C8OB02436G
dc.relation.urihttps://doi.org/10.1139/cjc-2020-0087
dc.relation.urihttps://doi.org/10.1016/j.mee.2020.111305
dc.relation.urihttps://doi.org/10.1021/acsearthspacechem.9b00131
dc.relation.urihttps://doi.org/10.1051/jp4:20001031
dc.relation.urihttps://doi.org/10.1155/2014/498420
dc.relation.urihttps://doi.org/10.1177/0892705720912767
dc.relation.urihttps://doi.org/10.23939/ujmems2021.01-02.023
dc.relation.urihttps://doi.org/10.1002/app.48280
dc.relation.urihttps://doi.org/10.3390/ma13010230
dc.relation.urihttps://doi.org/10.1016/B978-0-85709-698-2.00008-8
dc.relation.urihttps://doi.org/10.1042/ETLS20200333
dc.relation.urihttps://doi.org/10.1155/2013/385939
dc.relation.urihttps://doi.org/10.21272/jes.2020.7(1).c1
dc.relation.urihttps://doi.org/10.1016/j.stmat.2018.07.001
dc.relation.urihttps://doi.org/10.1295/polymj.22.355
dc.relation.urihttps://doi.org/10.1002/pi.6385
dc.relation.urihttps://doi.org/10.1002/adma.200390020
dc.relation.urihttps://doi.org/10.1016/j.jma.2021.05.006
dc.relation.urihttps://doi.org/10.1016/j.matpr.2017.05.042
dc.relation.urihttps://doi.org/10.22201/icat.24486736e.2021.19.5.1133
dc.relation.urihttps://doi.org/10.1186/s40064-016-1888-z
dc.relation.urihttps://doi.org/10.21272/jes.2023.10(1).h1
dc.relation.urihttps://doi.org/10.4236/ajor.2013.36053
dc.relation.urihttps://doi.org/10.1007/978-3-642-39578-9_64
dc.relation.urihttps://doi.org/10.1016/j.heliyon.2022.e09062
dc.relation.urihttps://doi.org/10.1088/2051-672X/ac4566
dc.relation.urihttps://doi.org/10.25236/AJBM.2021.031010
dc.relation.urihttps://doi.org/10.1109/ICSGEA.2019.00129
dc.rights.holder© Національний університет “Львівська політехніка”, 2023
dc.rights.holder© Javanbakht T., 2023
dc.subjectoligonucleotides
dc.subjectbiomolecule materials
dc.subjectTOPSIS
dc.subjectprediction
dc.subjectdecision-making process
dc.titleOptimization of oligonucleotides characteristics with topsis
dc.typeArticle

Files

Original bundle

Now showing 1 - 2 of 2
Thumbnail Image
Name:
2023v9n3_Javanbakht_T-Optimization_of_oligonucleotides_40-47.pdf
Size:
201.17 KB
Format:
Adobe Portable Document Format
Download
Thumbnail Image
Name:
2023v9n3_Javanbakht_T-Optimization_of_oligonucleotides_40-47__COVER.png
Size:
462.6 KB
Format:
Portable Network Graphics
Download

License bundle

Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.75 KB
Format:
Plain Text
Description:
Download

Collections

Ukrainian Journal of Mechanical Engineering and Materials Science. – 2023. – Vol. 9, No. 3