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Nucleobase-Modified Microgels Synthesized via Microfabrication Technology for DNA Adsorption

Year 2023, Volume: 10 Issue: 4, 309 - 315, 31.12.2023

Kemal Çetin

https://doi.org/10.17350/HJSE19030000320

Abstract

DNA isolation is a crucial procedure since DNA-based assays have great importance in molecular biology, biochemistry and biomedical applications. The objective of this study is to fabricate micron-sized hydrogels as adsorbents for DNA. Poly(2-hydroxyethyl methacrylate-co-glycidyl methacrylate) microgels were synthesized by free radical polymerization in the presence of N,N'-methylenebisacrylamide as a crosslinker, in the microholes of a microstencil array chip. Then, adenine was immobilized to microgels through the epoxy groups of glycidyl methacrylate. Scanning electron microscopy and Fourier transform infrared spectroscopy were employed to investigate the chemical and morphological characterizations of the microgels. The findings of the experiments demonstrate that the microgels had a cylindrical shape, were of uniform size, and had a height and diameter of around 500 μm. Observation of aromatic C=C peak confirmed the existence of adenine ligand in the microgel structure. Adsorption studies were carried out to determine the optimal conditions for DNA adsorption of nucleobase-immobilized microgels. After initially increasing, the quantity of DNA adsorbed onto the microgels reached a saturation level at a DNA concentration of around 2.0 mg/mL. The maximum adsorption was 38.54 mg/g microgels for an initial DNA concentration of 2.0 mg/mL in the optimum medium pH and temperature. DNA adsorption capabilities are shown to not significantly decline in recurrent adsorption-desorption cycles. As a result of the findings, adenine-immobilized microgels were demonstrated to be a viable option for DNA adsorption. Additionally, as a reference for future research, this study highlights the benefits of microfabrication technology, such as its simplicity of use in fabricating adsorption materials with the desired size, shape, and uniformity.

Keywords

Adsorption DNA Hydrogels Microfabrication Microgels Nucleobase

References

  • 1. Chen XW, Mao QX, Liu JW, Wang JH. Isolation/separation of plasmid DNA using hemoglobin modified magnetic nanocomposites as solid-phase adsorbent. Talanta 2012;100:107–12.
  • 2. Fakurpur Shirejini S, Dehnavi SM, Jahanfar M. Potential of superparamagnetic iron oxide nanoparticles coated with carbon dots as a magnetic nanoadsorbent for DNA isolation. Chem Eng Res Des 2023;190:580–9.
  • 3. Türkcan C, Akgöl S, Denizli A. Silanized polymeric nanoparticles for DNA isolation. Mater Sci Eng C 2013;33:4498–503.
  • 4. Akrami M, Dehnavi SM, Barjasteh M, Jahanfar M. Synthesis and characterization of iron oxide/functionalized graphene oxide nanocomposites for highly efficient DNA isolation. Mater Sci Eng B 2023;292:116401.
  • 5. Erol K. DNA adsorption via Co(II) immobilized cryogels. J Macromol Sci Part A 2016;53:629–35.
  • 6. Akgönüllü S, Denizli A. Recent advances in optical biosensing approaches for biomarkers detection. Biosens Bioelectron X 2022;12:100269.
  • 7. Köse K. Nucleotide incorporated magnetic microparticles for isolation of DNA. Process Biochem 2016;51:1644–9.
  • 8. Çetin K. Metal-Ion Assisted Imprinted Hydrogels For Recognition Of Lysozyme. Duzce Univ J Sci Technol 2021;9:545–55.
  • 9. Şarkaya K, Yildirim M, Alli A. One-step preparation of poly(NIPAM-pyrrole) electroconductive composite hydrogel and its dielectric properties. J Appl Polym Sci 2021;138:50527.
  • 10. Gopinathan J, Noh I. Click Chemistry-Based Injectable Hydrogels and Bioprinting Inks for Tissue Engineering Applications. Tissue Eng Regen Med 2018 155 2018;15:531–46.
  • 11. Rizzo F, Kehr NS. Recent Advances in Injectable Hydrogels for Controlled and Local Drug Delivery. Adv Healthc Mater 2021;10:2001341.
  • 12. Yang YJ, Mai DJ, Dursch TJ, Olsen BD. Nucleopore-Inspired Polymer Hydrogels for Selective Biomolecular Transport. Biomacromolecules 2018;19:3905–16.
  • 13. Grayson ACR, Shawgo RS, Johnson AM, Flynn NT, Li Y, Cima MJ, vd. A BioMEMS review: MEMS technology for physiologically integrated devices. Proc IEEE 2004;92:6–21.
  • 14. Chován T, Guttman A. Microfabricated devices in biotechnology and biochemical processing. Trends Biotechnol 2002;20:116–22.
  • 15. Sohn LL, Schwille P, Hierlemann A, Tay S, Samitier J, Fu J, vd. How Can Microfluidic and Microfabrication Approaches Make Experiments More Physiologically Relevant Cell Syst 2020;11:209
  • 16. Chung BG, Lee KH, Khademhosseini A, Lee SH. Microfluidic fabrication of microengineered hydrogels and their application in tissue engineering. Lab Chip 2011;12:45–59.
  • 17. Yanagawa F, Sugiura S, Kanamori T. Hydrogel microfabrication technology toward three dimensional tissue engineering. Regen Ther 2016;3:45–57.
  • 18. Coutinho DF, Sant S, Shakiba M, Wang B, Gomes ME, Neves NM, vd. Microfabricated photocrosslinkable polyelectrolytecomplex of chitosan and methacrylated gellan gum. J Mater Chem 2012;22:17262–71.
  • 19. Robert Walker T, Wu L, Patel K, Zandieh M, Liu J. Promotion of DNA Adsorption onto Microplastics by Transition Metal Ions. Microplastics 2023, Vol 2, Pages 158-167 2023;2:158–67.
  • 20. Wang X, Fei W, Zhou Z, Zhu M, Chang Y, Guo Q, vd. Immobilization of Multivalent Titanium Cations on Magnetic Composite Microspheres for Highly Efficient DNA Extraction and Amplification. ACS Appl Mater Interfaces 2023;15:42170–81.
  • 21. Çorman ME, 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. Biomed Chromatogr 2013;27:1524–31.
  • 22. Zandieh M, Patel K, Liu J. Adsorption of Linear and Spherical DNA Oligonucleotides onto Microplastics. Langmuir 2022;38:1915–22.
  • 23. Wang J, Wang Z, Huang PJJ, Bai F, Liu J. Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials. Langmuir 2022;38:3553–60.
  • 24. Meng Y, Liu P, Zhou W, Ding J, Liu J. Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells. ACS Nano 2018;12:9070–80.
  • 25. Muñoz ADO, Escobedo-Morales A, Skakerzadeh E, Anota EC. Effect of homonuclear boron bonds in the adsorption of DNA nucleobases on boron nitride nanosheets. J Mol Liq 2021;322:114951.
  • 26. Memmedova T, Armutcu C, Uzun L, Denizli A. Polyglycidyl methacrylate based immunoaffinity cryogels for insulin adsorption. Mater Sci Eng C 2015;52:178–85.
  • 27. Yoshikawa T, Umeno D, Saito K, Sugo T. High-performance collection of palladium ions in acidic media using nucleic-acidbase- immobilized porous hollow-fiber membranes. J Memb Sci 2008;307:82–7.
  • 28. Çetin K, Denizli A. Polyethylenimine-functionalized microcryogels for controlled release of diclofenac sodium. React Funct Polym 2022;170:105125.
  • 29. Zhang D, Domke KF, Pettinger B, Zhang D, Domke KF, Pettinger B. Tip-Enhanced Raman Spectroscopic Studies of the Hydrogen Bonding between Adenine and Thymine Adsorbed on Au (111). ChemPhysChem 2010;11:1662–5.
  • 30. Ullah F, Othman MBH, Javed F, Ahmad Z, Akil HM. Classification, processing and application of hydrogels: A review. Mater Sci Eng C 2015;57:414–33.
  • 31. Üzek R, Uzun L, Şenel S, Denizli A. Nanospines incorporation into the structure of the hydrophobic cryogels via novel cryogelation method: An alternative sorbent for plasmid DNA purification. Colloids Surfaces B Biointerfaces 2013;102:243–50.
  • 32. Zandieh M, Liu J. Transition Metal-Mediated DNA Adsorption on Polydopamine Nanoparticles. Langmuir 2020;36:3260–7.
  • 33. Tanaka T, Sakai R, Kobayashi R, Hatakeyama K, Matsunaga T. Contributions of phosphate to DNA adsorption/desorption behaviors on aminosilane-modified magnetic nanoparticles. Langmuir 2009;25:2956–61.
  • 34. Zhang HP, Bai S, Xu L, Sun Y. Fabrication of mono-sized magnetic anion exchange beads for plasmid DNA purification. J Chromatogr B 2009;877:127–33.
  • 35. Perçin I, Sağlar E, Yavuz H, Aksöz E, Denizli A. Poly(hydroxyethyl methacrylate) based affinity cryogel for plasmid DNA purification. Int J Biol Macromol 2011;48:577–82.
  • 36. Chiang CL, Sung CS, Chen CY. Application of silica–magnetite nanocomposites to the isolation of ultrapure plasmid DNA from bacterial cells. J Magn Magn Mater 2006;305:483–90.
  • 37. Ongkudon CM, Danquah MK. Anion exchange chromatography of 4.2 kbp plasmid based vaccine (pcDNA3F) from alkaline lysed E. coli lysate using amino functionalised polymethacrylate conical monolith. Sep Purif Technol 2011;78:303–10.
  • 38. Çimen D, Yilmaz F, Perçin I, Türkmen D, Denizli A. Dye affinity cryogels for plasmid DNA purification. Mater Sci Eng C 2015;56:318–24.
  • 39. Saraji M, Yousefi S, Talebi M. Plasmid DNA purification by zirconia magnetic nanocomposite. Anal Biochem 2017;539:33–8.
  • 40. Medina-Llamas JC, Chávez-Guajardo AE, Andrade CAS, Alves KGB, de Melo CP. Use of magnetic polyaniline/maghemite nanocomposite for DNA retrieval from aqueous solutions. J Colloid Interface Sci 2014;434:167–74.
  • 41. Önal B, Odabaşı M. Design and application of a newly generated bio/synthetic cryogel column for DNA capturing. Polym Bull 2021;78:6011–28.
  • 42. Ceylan Ş, Kalburcu T, Gedikli M, Odabaşı M. Application of Cu2+- attached Magnetite Nanoparticles Embedded Supermacroporous Monolithic Composite Cryogels for DNA Adsorption. Hacettepe J Biol Chem 2011;39:163–72.
  • 43. Han Y, Forde GM. Single step purification of plasmid DNA using peptide ligand affinity chromatography. J Chromatogr B 2008;874:21–6.
  • 44. Liu B, Liu J. DNA adsorption by indium tin oxide nanoparticles. Langmuir 2015;31:371–7.
  • 45. Li X, Zhang J, Gu H. Adsorption and desorption behaviors of DNA with magnetic mesoporous silica nanoparticles. Langmuir 2011;27:6099–106.
  • 46. Çetin K. Magnetic nanoparticles embedded microcryogels for bilirubin removal. Process Biochem 2022;112:203–8.
  • 47. Altaf R, Lin X, Zhuang W qin, Lu H, Rout PR, Liu D. Nitrilotrismethylenephosphonate sorption from wastewater on zirconium-lanthanum modified magnetite: Reusability and mechanism study. J Clean Prod 2021;314:128045.
  • 48. Suresh Kumar P, Ejerssa WW, Wegener CC, Korving L, Dugulan AI, Temmink H, vd. Understanding and improving the reusability of phosphate adsorbents for wastewater effluent polishing. Water Res 2018;145:365–74.
  • 49. Bhar R, Kanwar R, Mehta SK. Surface engineering of nanoparticles anchored meso-macroporous silica heterostructure: An efficient adsorbent for DNA. Mater Chem Phys 2020;255:123541.

Year 2023, Volume: 10 Issue: 4, 309 - 315, 31.12.2023

Kemal Çetin

https://doi.org/10.17350/HJSE19030000320

Abstract

References

  • 1. Chen XW, Mao QX, Liu JW, Wang JH. Isolation/separation of plasmid DNA using hemoglobin modified magnetic nanocomposites as solid-phase adsorbent. Talanta 2012;100:107–12.
  • 2. Fakurpur Shirejini S, Dehnavi SM, Jahanfar M. Potential of superparamagnetic iron oxide nanoparticles coated with carbon dots as a magnetic nanoadsorbent for DNA isolation. Chem Eng Res Des 2023;190:580–9.
  • 3. Türkcan C, Akgöl S, Denizli A. Silanized polymeric nanoparticles for DNA isolation. Mater Sci Eng C 2013;33:4498–503.
  • 4. Akrami M, Dehnavi SM, Barjasteh M, Jahanfar M. Synthesis and characterization of iron oxide/functionalized graphene oxide nanocomposites for highly efficient DNA isolation. Mater Sci Eng B 2023;292:116401.
  • 5. Erol K. DNA adsorption via Co(II) immobilized cryogels. J Macromol Sci Part A 2016;53:629–35.
  • 6. Akgönüllü S, Denizli A. Recent advances in optical biosensing approaches for biomarkers detection. Biosens Bioelectron X 2022;12:100269.
  • 7. Köse K. Nucleotide incorporated magnetic microparticles for isolation of DNA. Process Biochem 2016;51:1644–9.
  • 8. Çetin K. Metal-Ion Assisted Imprinted Hydrogels For Recognition Of Lysozyme. Duzce Univ J Sci Technol 2021;9:545–55.
  • 9. Şarkaya K, Yildirim M, Alli A. One-step preparation of poly(NIPAM-pyrrole) electroconductive composite hydrogel and its dielectric properties. J Appl Polym Sci 2021;138:50527.
  • 10. Gopinathan J, Noh I. Click Chemistry-Based Injectable Hydrogels and Bioprinting Inks for Tissue Engineering Applications. Tissue Eng Regen Med 2018 155 2018;15:531–46.
  • 11. Rizzo F, Kehr NS. Recent Advances in Injectable Hydrogels for Controlled and Local Drug Delivery. Adv Healthc Mater 2021;10:2001341.
  • 12. Yang YJ, Mai DJ, Dursch TJ, Olsen BD. Nucleopore-Inspired Polymer Hydrogels for Selective Biomolecular Transport. Biomacromolecules 2018;19:3905–16.
  • 13. Grayson ACR, Shawgo RS, Johnson AM, Flynn NT, Li Y, Cima MJ, vd. A BioMEMS review: MEMS technology for physiologically integrated devices. Proc IEEE 2004;92:6–21.
  • 14. Chován T, Guttman A. Microfabricated devices in biotechnology and biochemical processing. Trends Biotechnol 2002;20:116–22.
  • 15. Sohn LL, Schwille P, Hierlemann A, Tay S, Samitier J, Fu J, vd. How Can Microfluidic and Microfabrication Approaches Make Experiments More Physiologically Relevant Cell Syst 2020;11:209
  • 16. Chung BG, Lee KH, Khademhosseini A, Lee SH. Microfluidic fabrication of microengineered hydrogels and their application in tissue engineering. Lab Chip 2011;12:45–59.
  • 17. Yanagawa F, Sugiura S, Kanamori T. Hydrogel microfabrication technology toward three dimensional tissue engineering. Regen Ther 2016;3:45–57.
  • 18. Coutinho DF, Sant S, Shakiba M, Wang B, Gomes ME, Neves NM, vd. Microfabricated photocrosslinkable polyelectrolytecomplex of chitosan and methacrylated gellan gum. J Mater Chem 2012;22:17262–71.
  • 19. Robert Walker T, Wu L, Patel K, Zandieh M, Liu J. Promotion of DNA Adsorption onto Microplastics by Transition Metal Ions. Microplastics 2023, Vol 2, Pages 158-167 2023;2:158–67.
  • 20. Wang X, Fei W, Zhou Z, Zhu M, Chang Y, Guo Q, vd. Immobilization of Multivalent Titanium Cations on Magnetic Composite Microspheres for Highly Efficient DNA Extraction and Amplification. ACS Appl Mater Interfaces 2023;15:42170–81.
  • 21. Çorman ME, 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. Biomed Chromatogr 2013;27:1524–31.
  • 22. Zandieh M, Patel K, Liu J. Adsorption of Linear and Spherical DNA Oligonucleotides onto Microplastics. Langmuir 2022;38:1915–22.
  • 23. Wang J, Wang Z, Huang PJJ, Bai F, Liu J. Adsorption of DNA Oligonucleotides by Self-Assembled Metalloporphyrin Nanomaterials. Langmuir 2022;38:3553–60.
  • 24. Meng Y, Liu P, Zhou W, Ding J, Liu J. Bioorthogonal DNA Adsorption on Polydopamine Nanoparticles Mediated by Metal Coordination for Highly Robust Sensing in Serum and Living Cells. ACS Nano 2018;12:9070–80.
  • 25. Muñoz ADO, Escobedo-Morales A, Skakerzadeh E, Anota EC. Effect of homonuclear boron bonds in the adsorption of DNA nucleobases on boron nitride nanosheets. J Mol Liq 2021;322:114951.
  • 26. Memmedova T, Armutcu C, Uzun L, Denizli A. Polyglycidyl methacrylate based immunoaffinity cryogels for insulin adsorption. Mater Sci Eng C 2015;52:178–85.
  • 27. Yoshikawa T, Umeno D, Saito K, Sugo T. High-performance collection of palladium ions in acidic media using nucleic-acidbase- immobilized porous hollow-fiber membranes. J Memb Sci 2008;307:82–7.
  • 28. Çetin K, Denizli A. Polyethylenimine-functionalized microcryogels for controlled release of diclofenac sodium. React Funct Polym 2022;170:105125.
  • 29. Zhang D, Domke KF, Pettinger B, Zhang D, Domke KF, Pettinger B. Tip-Enhanced Raman Spectroscopic Studies of the Hydrogen Bonding between Adenine and Thymine Adsorbed on Au (111). ChemPhysChem 2010;11:1662–5.
  • 30. Ullah F, Othman MBH, Javed F, Ahmad Z, Akil HM. Classification, processing and application of hydrogels: A review. Mater Sci Eng C 2015;57:414–33.
  • 31. Üzek R, Uzun L, Şenel S, Denizli A. Nanospines incorporation into the structure of the hydrophobic cryogels via novel cryogelation method: An alternative sorbent for plasmid DNA purification. Colloids Surfaces B Biointerfaces 2013;102:243–50.
  • 32. Zandieh M, Liu J. Transition Metal-Mediated DNA Adsorption on Polydopamine Nanoparticles. Langmuir 2020;36:3260–7.
  • 33. Tanaka T, Sakai R, Kobayashi R, Hatakeyama K, Matsunaga T. Contributions of phosphate to DNA adsorption/desorption behaviors on aminosilane-modified magnetic nanoparticles. Langmuir 2009;25:2956–61.
  • 34. Zhang HP, Bai S, Xu L, Sun Y. Fabrication of mono-sized magnetic anion exchange beads for plasmid DNA purification. J Chromatogr B 2009;877:127–33.
  • 35. Perçin I, Sağlar E, Yavuz H, Aksöz E, Denizli A. Poly(hydroxyethyl methacrylate) based affinity cryogel for plasmid DNA purification. Int J Biol Macromol 2011;48:577–82.
  • 36. Chiang CL, Sung CS, Chen CY. Application of silica–magnetite nanocomposites to the isolation of ultrapure plasmid DNA from bacterial cells. J Magn Magn Mater 2006;305:483–90.
  • 37. Ongkudon CM, Danquah MK. Anion exchange chromatography of 4.2 kbp plasmid based vaccine (pcDNA3F) from alkaline lysed E. coli lysate using amino functionalised polymethacrylate conical monolith. Sep Purif Technol 2011;78:303–10.
  • 38. Çimen D, Yilmaz F, Perçin I, Türkmen D, Denizli A. Dye affinity cryogels for plasmid DNA purification. Mater Sci Eng C 2015;56:318–24.
  • 39. Saraji M, Yousefi S, Talebi M. Plasmid DNA purification by zirconia magnetic nanocomposite. Anal Biochem 2017;539:33–8.
  • 40. Medina-Llamas JC, Chávez-Guajardo AE, Andrade CAS, Alves KGB, de Melo CP. Use of magnetic polyaniline/maghemite nanocomposite for DNA retrieval from aqueous solutions. J Colloid Interface Sci 2014;434:167–74.
  • 41. Önal B, Odabaşı M. Design and application of a newly generated bio/synthetic cryogel column for DNA capturing. Polym Bull 2021;78:6011–28.
  • 42. Ceylan Ş, Kalburcu T, Gedikli M, Odabaşı M. Application of Cu2+- attached Magnetite Nanoparticles Embedded Supermacroporous Monolithic Composite Cryogels for DNA Adsorption. Hacettepe J Biol Chem 2011;39:163–72.
  • 43. Han Y, Forde GM. Single step purification of plasmid DNA using peptide ligand affinity chromatography. J Chromatogr B 2008;874:21–6.
  • 44. Liu B, Liu J. DNA adsorption by indium tin oxide nanoparticles. Langmuir 2015;31:371–7.
  • 45. Li X, Zhang J, Gu H. Adsorption and desorption behaviors of DNA with magnetic mesoporous silica nanoparticles. Langmuir 2011;27:6099–106.
  • 46. Çetin K. Magnetic nanoparticles embedded microcryogels for bilirubin removal. Process Biochem 2022;112:203–8.
  • 47. Altaf R, Lin X, Zhuang W qin, Lu H, Rout PR, Liu D. Nitrilotrismethylenephosphonate sorption from wastewater on zirconium-lanthanum modified magnetite: Reusability and mechanism study. J Clean Prod 2021;314:128045.
  • 48. Suresh Kumar P, Ejerssa WW, Wegener CC, Korving L, Dugulan AI, Temmink H, vd. Understanding and improving the reusability of phosphate adsorbents for wastewater effluent polishing. Water Res 2018;145:365–74.
  • 49. Bhar R, Kanwar R, Mehta SK. Surface engineering of nanoparticles anchored meso-macroporous silica heterostructure: An efficient adsorbent for DNA. Mater Chem Phys 2020;255:123541.
There are 49 citations in total.

Details

Primary Language English
Subjects Biofabrication, Biomedical Sciences and Technology
Journal Section Research Articles
Authors

Kemal Çetin 0000-0002-7393-7377

Publication Date December 31, 2023
Submission Date June 6, 2023
Published in Issue Year 2023 Volume: 10 Issue: 4

Cite

Vancouver Çetin K. Nucleobase-Modified Microgels Synthesized via Microfabrication Technology for DNA Adsorption. Hittite J Sci Eng. 2023;10(4):309-15.
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