Abstract
Nano-PCR is a potential tool for the early detection of plant viruses. In the current study, different concentrations of silver nanoparticles (20 nm) and magnesium oxide nanoparticles (50 nm) were included in the PCR mixture to improve the sensitivity of PCR for the detection of tomato leaf curl virus. The inclusion of nanoparticles in single or combination in PCR mixture has resulted in improvement of PCR sensitivity. Four-fold improvement was exhibited by the inclusion of 3 ng/µL silver nanoparticles, whereas the combination of silver and magnesium oxide nanoparticles (3 ng/µL and 200 ng/µL, respectively), resulted in a 4.5-fold improvement. The inclusion of 200 ng/µL of magnesium oxide nanoparticles in the PCR mixture exhibited a 7.6-fold increase in PCR sensitivity. Replacement of magnesium chloride with a combination of silver and magnesium oxide nanoparticles (3 ng/µL and 275 ng/µL, respectively) resulted in a 12-fold increase. A 13-fold improvement in PCR sensitivity was observed by the replacement of magnesium chloride in PCR buffer with 275 ng/µL of magnesium oxide nanoparticles. This could also produce detectable amplicon in PCR with a minimum of 25 cycles, resulting in a 26.5% reduction in the duration of PCR. This is the first report on the use of magnesium oxide nanoparticles in PCR for the early detection and better management of tomato leaf curl virus.
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References
Amadeh A, Ghazimirsaeed E, Shamloo A, Dizani M (2021) Improving the performance of a photonic PCR system using TiO2 nanoparticles. J Ind Eng Chem 9:195–204. https://doi.org/10.1016/j.jiec.2020.10.036
Arkel AV, Flood EA, Bright NF (1953) The electrical conductivity of molten oxides. Can J Chem 31(11):1009–1019. https://doi.org/10.1139/v53-133
Bansod S, Bonde S, Tiwari V, Bawaskar M, Deshmukh S, Gaikwad S, Gade A, Rai M (2013) Bioconjugation of gold and silver nanoparticles synthesized by Fusarium oxysporum and their use in rapid identification of Candida species by using bioconjugate-nano-polymerase chain reaction. J Biomed Nanotech 9(12):1962–1971. https://doi.org/10.1166/jbn.2013.1727
Birnboim HC, Doly J (1979) A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucl Acids Res 7(6):1513–1523
Caruso AG, Bertacca S, Parrella G, Rizzo R, Davino S, Panno S (2022) Tomato brown rugose fruit virus: a pathogen that is changing the tomato production worldwide. Ann Appl Biol 181(3):258–274. https://doi.org/10.1111/aab.12788
Chen ZJ, Ou XM, Tang FQ, Jiang L (1996) Effect of nanometer particles on the adsorbability and enzymatic activity of glucose oxidase. Colloids Surf B 7(3–4):173–179. https://doi.org/10.1016/0927-7765(96)01291-X
Chen C, Wang L, Li R, Jiang G, Yu H, Chen T (2007) Effect of silver nanowires on electrical conductance of system composed of silver particles. J Mater Sci 42:3172–3176. https://doi.org/10.1007/s10853-007-1594-x
Deng D, McGrath PF, Robinson DJ, Harrison BD (1994) Detection and differentiation of whitefly-transmitted geminiviruses in plants and vector insects by the polymerase chain reaction with degenerate primers. Ann Appl Biol 125(2):327–336. https://doi.org/10.1111/j.1744-7348.1994.tb04973.x
FAO, 2022. FAOSTAT. Food and Agriculture Organization of the United Nations, Rome
Fiallo-Olivé E, Lett JM, Martin DP, Roumagnac P, Varsani A, Zerbini FM, Navas-Castillo J (2021) ICTV Report Consortium. ICTV virus taxonomy profile: geminiviridae (2021). J Gen Virol 102:1696. https://doi.org/10.1099/jgv.0.000738
Fu-Ming S, Xin L, Jia L (2017) Development of nano-polymerase chain reaction and its application. Chin J Anal Chem 45(11):1745–1753. https://doi.org/10.1016/S1872-2040(17)61051-X
Haber AL, Griffiths KR, Jamting ÅK, Emslie KR (2008) Addition of gold nanoparticles to real-time PCR: effect on PCR profile and SYBR Green I fluorescence. Anal Bioanal Chem 392(5):887–896. https://doi.org/10.1007/s00216-008-2358-4
Hemanta MR, Varsha K (2014) Enhancement in efficiency of polymerase chain reaction by silver nano-particles. Int Res J Biol Sci 3(2):30–33
Kadu P, Pandey S, Neekhra S, Kumar R, Gadhe L, Srivastava R, Sastry M, Maji SK (2020) Machine-free polymerase chain reaction with triangular gold and silver nanoparticles. J Phys Chem Lett 11(24):10489–10496. https://doi.org/10.1021/acs.jpclett.0c02708
Kambli P, Kelkar-Mane V (2016) Nanosized Fe3O4 an efficient PCR yield enhancer—comparative study with Au, Ag nanoparticles. Colloids Surf B Biointerfaces 141:546–552. https://doi.org/10.1016/j.colsurfb.2016.02.024
Karunanathie H, Kee PS, Ng SF, Kennedy MA, Chua EW (2022) PCR enhancers: types, mechanisms, and applications in long-range PCR. Biochimie 197:130–143. https://doi.org/10.1016/j.biochi.2022.02.009
Knowles TJ, Finka R, Smith C, Lin YP, Dafforn T, Overduin M (2009) Membrane proteins solubilized intact in lipid containing nanoparticles bounded by styrene maleic acid copolymer. J Am Chem Soc 131(22):7484–7485. https://doi.org/10.1021/ja810046q
Kumar M, Tomar M, Bhuyan DJ, Punia S, Grasso S, Sa AGA, Carciofi BAM, Arrutia F, Changan S, Singh S, Dhumal S (2021) Tomato (Solanum lycopersicum L.) seed: a review on bioactives and biomedical activities. Biomed Pharmacother. https://doi.org/10.1016/j.biopha.2021.112018
Kumari S, Krishnan N, Dubey V, Pandey KK, Singh J (2020) Characterization of recombinant tomato leaf curl Palampur virus causing leaf curl disease of Basella alba L. in India. J Plant Pathol 102:523–527. https://doi.org/10.1007/s42161-019-00464-7
Li M, Lin YC, Wu CC, Liu HS (2005) Enhancing the efficiency of a PCR using gold nanoparticles. Nucl Acids Res 33(21):184–184. https://doi.org/10.1093/nar/gni183
Lou X, Zhang Y (2013) Mechanism studies on nano-PCR and applications of gold nanoparticles in genetic analysis. ACS Appl Mater Interfaces 5(13):6276–6284. https://doi.org/10.1021/am4013209
Murray MG, Thompson W (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8(19):4321–4326. https://doi.org/10.1093/nar/8.19.4321
Nurliyana MR, Sahdan MZ, Wibowo KM, Muslihati A, Saim H, Ahmad SA, Sari Y, Mansor Z (2018) The detection method of Escherichia coli in water resources: a review. J Phys Conf Ser IOP Publ 995(1):012065. https://doi.org/10.1088/1742-6596/995/1/012065
Pan D, Wen Y, Mi L, Fan C, Hu J (2011) Nanomaterials-based polymerase chain reactions for DNA detection. Curr Org Chem 15(4):486–497. https://doi.org/10.2174/138527211794474447
Rajkumari N, Alex S, Soni KB, Anith KN, Viji MM, Kiran AG (2021) Silver nanoparticles for biolistic transformation in Nicotiana tabacum L. 3 Biotech 11:1–7. https://doi.org/10.1007/s13205-021-03043-9
Ramesh L, Viswanathan A (2021) Detection of Begomovirus in chilli and tomato plants using functionalized gold nanoparticles. Sci Rep 11(1):1–13. https://doi.org/10.1038/s41598-021-93615-9
Rojas MR, Macedo MA, Maliano MR, Soto-Aguilar M, Souza JO, Briddon RW, Kenyon L, Rivera Bustamante RF, Zerbini FM, Adkins S, Legg JP (2018) World management of geminiviruses. Annu Rev Phytopathol 56:637–677. https://doi.org/10.1146/annurev-phyto-080615-100327
Schmidt G, Stiverson J, Angen Ø, Yu Z (2014) Number of PCR cycles and magnesium chloride concentration affect detection of tet genes encoding ribosomal protection proteins in Swine manure. Adv Microbiol. https://doi.org/10.4236/aim.2014.412086
Simonovic A, Trifunovic-Momcilov M, Raspor M, Cingel A, Bogdanovic M, Dragicevic M, Subotic A (2012) Dimethyl sulfoxide improves sensitivity and specificity of RT-PCR and qRT-PCR amplification of low-expressed transgenes. Arch Biol Sci 64(3):865–876. https://doi.org/10.2298/ABS1203865S
Singh VK, Singh AK, Kumar A (2017) Disease management of tomato through PGPB: current trends and future perspective. 3 Biotech 7:1–10. https://doi.org/10.1007/s13205-017-0896-1
Stael S, Miller LP, Fernandez-Fernandez AD, Van Breusegem F (2022) Detection of damage-activated metacaspase activity activities by Western blot in plants. In: Plant proteases and plant cell death: methods and protocols. Springer US, New York, pp 127–137. https://doi.org/10.1007/978-1-0716-2079-3_11
Talebpour Z, Haghighi F, Taheri M, Hosseinzadeh M, Gharavi S, Habibi F, Aliahmadi A, Sadr AS, Azad J (2019) Binding interaction of spherical silver nanoparticles and calf thymus DNA: comprehensive multispectroscopic, molecular docking, and RAPD PCR studies. J Mol Liq 289:111185. https://doi.org/10.1016/j.molliq.2019.111185
Vasudeva RS, Samraj J (1948) A leaf curl disease of tomato. Phytopathol 38:364–359
Vunsh RON, Rosner A, Stein A (1990) The use of the polymerase chain reaction (PCR) for the detection of bean yellow mosaic virus in gladiolus. Ann Appl Biol 117(3):561–569
Wan W, Yeow JT, Van Dyke MI (2009) Effect of silver and titanium dioxide nanoparticles on PCR efficiency. In: 9th IEEE Confon Nanotechnol, pp 458–461
Wang Q, Li J, Cao X (2007) Silver nanoparticles enhance the specificity of repeated long PCR amplification. Tianjin Keji Daxue Xuebao 22(2):1
Yuce M, Kurt H, Mokkapati VR, Budak H (2014) Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR. Rscadv 4(69):36800–36814. https://doi.org/10.1039/C4RA06144F
Zheng G, Feng X, Chen J (2007) Effect of nano-TiO2 on the conformation transition of silk fibroin films. J Funct Polym 19(4):405. https://doi.org/10.1163/156856207782246786
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Devika, P.P., Alex, S., Soni, K.B. et al. Nano-PCR for the early detection of tomato leaf curl virus. 3 Biotech 14, 5 (2024). https://doi.org/10.1007/s13205-023-03842-2
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DOI: https://doi.org/10.1007/s13205-023-03842-2