Vegetos
(An International Journal of Plant Research & Biotechnology)
Characterization of iron oxide magnetic nanoparticles for extraction of harar coffee (coffea arabica L.) genomic DNA
Research Articles | Published: 07 June, 2024
First Page: 182
Last Page: 196
Views: 1843
Keywords: Magnetic nanoparticles, Genomic DNA extraction, Coffee leaf, Adsorption, Desorption
Abstract
DNA extraction using magnetic nanoparticles (MNPs) has gained significant consideration due to their simple manipulation, cost-effectiveness, and less time-consuming. Even though magnetic separation has been extensively studied for different biological samples, there is a need for efficient methods to extract DNA from woody plants. The present study was aimed to synthesize iron oxide (Fe3O4) MNPs coated with Salicylic Acid (SA) for genomic DNA (gDNA) extraction from Harar coffee leaves. The Fe3O4 MNPs were synthesized from available iron salts under alkaline conditions followed by coating with SA. The synthesized material was characterized by ultraviolet-visible (UV-Vis), X-Ray Diffraction (XRD), Fourier-Transform Infrared (FTIR) spectroscopy, and Scanning Electron Microscopy (SEM). Point of zero charges were determined using the pH drift method. The synthesized Iron oxide magnetic nanoparticles coated with salicylic acid (Fe3O4/SA MNPs) were used for gDNA extraction from coffee leaves. The result of FTIR analysis indicated that, the carboxylic functional group was found in Fe3O4/SA MNPs that indicates successful surface modification. XRD analysis showed that the crystallite phase size of Fe3O4 and Fe3O4/SA MNPs with 14.35 and 10.44 nm respectively. The extraction results revealed that the quality and quantity of extracted gDNA using Fe3O4/SA MNPs were higher than that of the uncoated Fe3O4 and CTAB methods. The PCR assay indicated the amplification of extracted gDNA. The synthesized MNPs indicated respective values of 80% and 67% adsorption and desorption efficiency. The obtained results revealed the effectiveness and convenience of the synthesized Fe3O4/SA MNPs in gDNA extraction from plant leaf samples.
References
Abdel-Latif A, Osman G (2017) Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods 13:1–9
Abdurahman Y, Bekana D, Temesgen A, Bussa N, Aschale M, Teju E, Amde M (2023) Magnetic coffee residue biosorbent for selective extraction of zinc oxide nanoparticles in water samples. Bull Chem Soc Ethiop 37(4):859–873
Aboul-Maaty NAF, Oraby HAS (2019) Extraction of high-quality genomic DNA from different plant orders applying a modified CTAB-based method. Bull Natl Res Centre 43(1):1–10
Agre P, Nwachukwu C, Olasanmi B, Obidiegwu J, Nwachukwu E, Adebola P, Koeyer DD, Asrat A (2020) Sample preservation and plant sex prediction in white Guinea yam (Dioscorea rotundata). Journal of Applied Biotechnology Reports
Al-Alawy AF, Al-Abodi EE, Kadhim RM (2018) Synthesis and characterization of magnetic iron oxide nanoparticles by co-precipitation method at different conditions. J Eng 24(10):60–72
Ali A, Zafar H, Zia M, ul-Haq I, Phull AR, Ali JS, Hussain A (2016) Synthesis, characterization, applications, and challenges of iron oxide nanoparticles. Nanatechnol Sci Appl, 49–67
Ali N, Rampazzo RDCP, Costa ADT, Krieger MA (2017) Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics. BioMed Research International, 2017
Allen GC, Flores-Vergara MA, Krasynanski S, Kumar S, Thompson F (2006) Modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide. Nat Protoc 1(5):2320–2325
Ayoib A, Hashim U, Gopinath SC, Arshad MK (2017) DNA extraction on bio-chip: history and preeminence over conventional and solid-phase extraction methods. Appl Microbiol Biotechnol 101(22):8077–8088
Bai Y, Roncancio D, Suo Y, Shao Y, Zhang D, Zhou C (2019) A method based on amino-modified magnetic nanoparticles to extract DNA for PCR-based analysis. Colloids Surf B 179:87–93
Brescia P, Banks P (2009) Multi-Volume Analysis of Nucleic Acids Using the Epoch/Take3 Spectrophotometer System, BioTek Instruments, Inc. Application note, 2009
Chattopadhyay D, Sarkar K (2018) Purification of quality DNA from citrus plant using iron oxide nanoparticle as solid based support. J Plant Dev Sci 10(3):149–156
Chen Y, Liu Y, Shi Y, Ping J, Wu J, Chen H (2020) Magnetic particles for integrated nucleic acid purification, amplification and detection without pipetting. Trends Anal Chem 127:115912
Chiong KT, Damaj MB, Padilla CS, Avila CA, Pant SR, Mandadi KK, Mirkov TE (2017) Reproducible genomic DNA preparation from diverse crop species for molecular genetics applications. Plant Methods 13(1):1–11
Danthanarayana AN, Manatunga DC, De Silva RM, Chandrasekharan NV, De Silva N, KM (2018) Magnetofection and isolation of DNA using polyethyleneimine functionalized magnetic iron oxide nanoparticles. Royal Soc Open Sci 5(12):181369
Dauphin LA, Stephens KW, Eufinger SC, Bowen MD (2010) Comparison of five commercial DNA extraction kits for the recovery of Yersinia pestis DNA from bacterial suspensions and spiked environmental samples. J Appl Microbiol 108(1):163–172
De Angelis MM, Wang DG, Hawkins TL (1995) Solid-phase reversible immobilization for the isolation of PCR products. Nucleic Acids Res 23:22
Devi KD, Punyarani K, Singh S, Devi HS (2013) An efficient protocol for total DNA extraction from the members of order Zingiberales - suitable for diverse PCR based downstream applications. Springer Plus 2:669. https://doi.org/10.1186/2193-180-2-669
Edwards K, Johnstone C, Thompson C (1991) A simple and rapid method for the preparation of plant genomic DNA for PCR analysis. Nucleic Acids Res 19(6):1349–1349
Farhanian D, De Crescenzo G, Tavares JR (2018) Large-scale encapsulation of magnetic iron oxide nanoparticles via syngas photo-initiated chemical vapor deposition. Sci Rep 8(1):1–11
Firoozeh F, Neshan A, Khaledi A, Zibaei M, Amiri A, Sobhani A, Badmasti F, Nikbin VS (2022) Evaluation of the effect of magnetic nanoparticles on extraction of genomic DNA of Escherichia coli. Polym Bull 80(3):3153–3163
Gatabi MP, Moghaddam HM, Ghorbani M (2016) Point of zero charge of maghemite decorated multiwalled carbon nanotubes fabricated by chemical precipitation method. J Mol Liq 216:117–125
Ghaemi M, Absalan G (2014) Study on the adsorption of DNA on Fe3O4 nanoparticles and ionic liquid-modified Fe3O4 nanoparticles. Microchim Acta 181(1):45–53
Indira TK, Lakshmi PK (2010) Magnetic nanoparticles: a review. Int J Pharm Sci Nanatechnol 3(3):1035–1042
Je HH, Noh S, Hong SG, Ju Y, Kim J, Hwang DS (2017) Cellulose nanofibers for magnetically-separable and highly loaded enzyme immobilization. Chem Eng J 323:425–433
Kang K, Choi J, Nam JH, Chang H (2009) Preparation and characterization of chemically functionalized silica coated magnetic nanoparticles as a DNA separator. J Phys Chem 113(2):536–543
Kumar A, Gayakwad A, Panse U, Khasdeo K, Narayanan C, Ansari SA, Lazarus AD (2013) Optimization of DNA extraction methods for some important forest tree species. Int J Adv Biotechnol Res 4(3):364–371
Li P, Li M, Yuan Z, Jiang X, Yue D, Ye B, Zhao Z, Jiang J, Fan Q, Zhou Z, Chen H (2021) 3D printed integrated separator with hybrid micro-structures for high throughput and magnetic-free nucleic acid separation from organism samples. Sep Purif Technol 271:118881
Mahmood T, Saddique MT, Mustafa S, Alum A (2011) Comparison of different methods for the point of zero charge determination of nickel oxide. Ind Eng Chem Res 50(17):10017–10023
Manalastas-Cantos K, Konarev PV, Hajizadeh NR, Kikhney AG, Petoukhov MV, Molodenskiy DS, Panjkovich A, Mertens HD, Gruzinov A, Borges C, Jeffries CM (2021) ATSAS 3.0: expanded functionality and new tools for small-angle scattering data analysis. J Appl Crystallogr 54(1):343–355
McDonagh BH, Chinga-Carrasco G (2020) Characterization of porous structures of cellulose nanofibrils loaded with salicylic acid. Polymers 12(11):2538
Mikelashvili V, Kekutia S, Markhulia J, Kriechbaum M, Almasy L (2023) Synthesis and characterization of citric acid modified iron oxide nanoparticles prepared with electrohydraulic discharge treatment. Materials 16(2):746
Min JH, Woo MK, Yoon HY, Jang JW, Wu JH, Lim CS, Kim YK (2014) Isolation of DNA using magnetic nanoparticles coated with dimercaptosuccinic acid. Anal Biochem 447:114–118
Mohammed L, Goma HG, Ragab D, Zhu J (2017) Magnetic nanoparticles for environmental and biomedical applications. Particuology 30:1–14
Moreira PA, Oliveira DA (2011) Leaf age affects the quality of DNA extracted from Dimorphandra Mollis (Fabaceae), a tropical tree species from the Cerrado region of Brazil. Genet Mol Res 10(1):353–358
Oberacker P, Stepper P, Bond DM, Höhn S, Focken J, Meyer V, Jurkowski TP (2019) Bio-on-magnetic-beads (BOMB): open platform for high-throughput nucleic acid extraction and manipulation. PLoS Biol 17(1):e3000107
Paterson AH, Brubaker CL, Wendel JF (1993) A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis. Plant Mol Biol Rep 11:122
Pershina AG, Sazonov AE, Filimonov VD (2014) Magnetic nanoparticles–DNA interactions: design and applications of nanobiohybrid systems. Rus Chem Rev 83(4):299
Prodělalová J, Rittich B, Španová A, Petrová K, Beneš MJ (2004) Isolation of genomic DNA using magnetic cobalt ferrite and silica particles. J Chromatogr A 1056(1–2):43–48
Psifidi A, Dovas CI, Bramis G, Lazou T, Russel CL, Arsenos G, Banos G (2015) Comparison of eleven methods for genomic DNA extraction suitable for large-scale whole-genome genotyping and long-term DNA banking using blood samples. PLoS ONE 10(1):e0115960
Rahnama H, Sattarzadeh A, Kazemi F, Ahmadi N, Sanjarian F (2016) Comparative study of three magnetic nanoparticles (FeSO4, FeSO4/SiO2, FeSO4/SiO2/TiO2) in plasmid DNA extraction. Anal Biochem 513:68–76
Rostami H, Firoozeh F, Zibaei M, Salahshoorifar I (2020) Evaluation of genomic DNA extraction using monolayer and bilayer magnetic nanoparticles. Int J Enteric Pathogens 8(2):51–54
Santos ALF, Oliveira CQP, Arruda GNPN, John Martins JK (2018) Comparison of DNA extraction using proteinase K and extraction kit: analysis of the quality of the genetic material. J Bras Patol Med Lab 54(2):70–75
Sosa-Acosta JR, Silva JA, Fernández-Izquierdo L, Díaz-Castañón S, Ortiz M, Zuaznabar-Gardona JC, Díaz-García AM (2018) Iron oxide nanoparticles with potential applications in plasmid DNA isolation. Colloids Surfaces: Physicochemical Eng Aspects 545:167–178
Sun N, Deng C, Ge G, Xia Q (2015) Application of carboxyphenylboronic acid functionalized magnetic nanoparticles for extracting nucleic acid from seeds. Biotechnol Lett 37:211–218
Unal B, Durmus Z, Kavas H, Baykal A, Toprak MS (2010) Synthesis, conductivity and dielectric characterization of salicylic acid–Fe3O4 nanocomposite. Mater Chem Phys 123:184–190
Vanyorek L, Ilosvai ÁM, Szőri-Dorogházi E et al (2019) Synthesis of iron oxide nanoparticles for DNA purification. J Dispers Sci Technol 1–8. https://doi.org/10.1080/01932691.2019.1708380
Wang J, Ali Z, Wang N, Liang W, Liu H, Li F, Yang H, He L, Nie L, He N, Li Z (2015) Simultaneous extraction of DNA and RNA from Escherichia coli BL 21 based on silica-coated magnetic nanoparticles. Sci China Chem 58:1774–1778
Wilson K, Walker J (2005) Principles and techniques of biochemistry and molecular biology. University, Cambridge
Wilson K, Walker J (2010) Principles and Techniques of Biochemistry and Molecular Biology, 7th edition. Cambridge University press,New York, USA
Wu W, Wu Z, Yu T, Jiang C, Kim WS (2015) Recent progress on magnetic iron oxide nanoparticles: synthesis, surface functional strategies and biomedical applications. Sci Technol Adv Mater 16(2):e023501
Xin Z, Velten JP, Oliver MJ, Burke JJ (2003) High-throughput DNA extraction method suitable for PCR. Biotechniques 34(4):820–826
Yew YP, Shameli K, Miyake M, Kuwano N, Ahmad Khairudin NB, Mohamad SE, Lee KX (2016) Green synthesis of magnetite nanoparticles using seaweed (Kappaphycus alvarezii) extract. Nanoscale Res Lett 11(1):1–7
Yıldırım E, Arıkan B, Yücel O, Çakır O, Kara NT, İyim TB, Gürdağ G, Emik S (2022) Synthesis and characterization of amino functional poly (acrylamide) coated Fe3O4 nanoparticles and investigation of their potential usage in DNA isolation. Chem Pap 76(9):5747–5759
Zhou Z, Kadam U, Irudayaraj J (2013) One-stop genomic DNA extraction by salicylic acid coated magnetic nanoparticles. Anal Biochem 442(2):249–252
Author Information
Department of Biology, Wollega University, Wollega, Ethiopia