DNA Probe as Biosensor Candidate for Clavibacter michiganensis subsp. michiganensis on Tomato Plants

  • Muslihah Nur Hidayati Applied Research Institute of Agricultural Quarantine
  • Suranto Sebelas Maret University, Surakarta 57126
  • Ari Susilowati Sebelas Maret University, Surakarta 57126
Keywords: digoxigenin, dot blot, hybridization, non-radioactive, tomA gene

Abstract

The study was conducted to evaluate gene detection technique using a specific DNA probe to detect tomA gene in Clavibacter michiganensis subsp. michiganensis, a bacteria causing cancer in tomatoes. The probe was designed using Primer3Plus program, labeled with the non-radioactive molecule digoxigenin (DIG) and used in the hybridization method with the dot blot technique. The test samples consisted of two types, i.e. genomic DNA samples from pure bacterial cultures and from artificially infected tomato seeds with C. michiganensis subsp. michiganensis. Samples derived from pure bacterial cultures showed positive hybridization results at all levels of DNA concentration; while samples from tomato seeds only showed positive reactions at concentrations of 10, 8, 6, and 4 g L-1. This study concludes that the designed probe has the potential to be used in the development of biosensor-based detection methods for C. michiganensis subsp. michiganensis in tomato seeds and is quite specific because there is no cross-reaction with non-target bacterial groups.

Downloads

Download data is not yet available.

References

Albuquerque P, Ribeiro N, Almeida A, Panschin I, Porfirio A, Vales M, Diniz, Madeira H, Tavares F. 2017. Application of a dot blot hybridization platform to assess Streptococcus uberis population structure in dairy herds. Frontiers in Microbiology. 54(8):1–11. DOI: https://doi.org/10.3389/fmicb.2017.00054.

Arlai D, Sirinarumitr T, Lertwatcharasarakul P, Viriyarumpa S, Phatthanakunanan S. 2021. Comparative of conventional dot blot hybridization and CARD dot blot hybridization for Salmonella detection in pork. Interdisciplinary Research Review. 16(4):9–15. https://ph02.tci-thaijo.org/index.php/jtir/article/view/244269.

Hartati YW, Yohan Y, Nurmalasari R, Gaffar S. 2016. Deteksi urutan oligonukleotida Mycobacterium tuberculosis secara voltammetri menggunakan screen printed carbon electrode (SPCE). Chimica et Natura Acta. 4(2):79–83. DOI: https://doi.org/10.24198/cna.v4.n2.10674.

Hendling M, Barisic I. 2019. In-silico design of DNA oligonucleotides: challenges and approaches. Computational and Structural Biotechnology Journal. 17:1056–1065. DOI: https://doi.org/10.1016/j.csbj.2019.07.008.

Huang J, Wu J, Li Z. 2015. Biosensing using hairpin DNA probe. Reviews in Analytical Chemistry. 34(1–2):1–27. DOI: https://doi.org/10.1515/revac-2015-0010.

Koopaee HK, Rezaei V, Esmailizadeh A, Sabahi F. 2020. DNA biosensors techniques and their applications in food safety, environmental protection and biomedical research: a mini-review. Journal of Cell and Developmental Biology. 3(1):28–35. DOI: https://doi.org/10.36959/596/446.

Lai TP, Wright WE, Shay JW. 2016. Generation of digoxigeninin corporated probes to enhance DNA detection sensitivity. Bio Techniques. 60(6):306–309. DOI: https://doi.org/10.2144/000114427.

Mishra N, Rai N, Singhai A. 2018. DNA probe labelling detection method and their application in medical research: a review. International Journal of Pharmacy & Pharmaceutical Research. 11(4):66–79.

Mohan V, Ananda HV. 2019. Biosensor: an emerging analytical tool. Journal of Biosensors & Bioelectronics. 10(2):1–3.

Nandi M, Macdonald J, Liu P, Weselowski B, Yuan Z. 2018. Clavibacter michiganensis ssp. michiganensis: Bacterial canker of tomato, molecular interactions and disease management. Molecular Plant Pathology. 19(8):2036–2050. DOI: https://doi.org/10.1111/mpp.12678.

Nuhantoro I, Mutaqin KH, Hidayat SH. 2018. Use of DNA probe for detection of Papaya ringspot virus using nucleic acid hybridization method. Jurnal Fitopatologi Indonesia. 14(3):89–96. DOI: https://doi.org/10.14692/jfi.14.3.89.

Nursista A. 2018. Pengembangan metode deteksi Clavibacter michiganensis subsp. michiganensis pada benih tomat [skripsi]. Bogor (ID): Institut Pertanian Bogor.

Rahmaryani IGAA, Ariani NK, Dewi DSW, Ani NKS, Sundari AA, Hartati KWY, Yowani SC. 2017. DNA probe design for detection mutation at codon 315 in katG gene of Mycobacterium tuberculosis to real-time polymerase chain reaction. Journal of Health Sciences and Medicine. 1(2):31–41. DOI: https://doi.org/10.24843/JHSM.2017.v01.i02.p08.

Shanion MH, Basu C. 2009. Optimization of a digoxigenin-based immunoassay system for gene detection in Arabidopsis thaliana. Journal of Biomolecular Techniques. 20:96–100. PMID: 19503620; PMCID: PMC2685603.

Teles FRR, Fonseca LP. 2008. Trends in DNA biosensors. Talanta. 77(2):606–623. DOI: https://doi.org/10.1016/j.talanta.2008.07.024.

Trianom B, Arwiyanto T, Joko T. 2018. Perancangan primer spesifik subspesies berbasis gen endoglukanase untuk deteksi Ralstonia syzygii subsp. syzygii. Jurnal Perlindungan Tanaman Indonesia. 22(2): 124−131. DOI: https://doi.org/10.22146/jpti.32217.

Viterbo D, Marchal A, Mosbach V, Poggi L, Vaysse W, Richard G. 2018. A fast, sensitive and cost-effective method for nucleic acid detection using non-radioactive probes. Biology Methods and Protocols. 3(1):1–6. DOI: https://doi.org/10.1093/biomethods/bpy006.

Vizzini P, Lacumin L, Comi G, Manzano M. 2017. Development and application of DNA molecular probes. AIMS Bioengineering. 4(1):113–132. DOI: https://doi.org/10.3934/bioeng.2017.1.113.

Wu J, Huang Y, Bian X, Li D, Cheng Q, Ding S. 2016. Biosensing of BCR/ABL fusion gene using an intensityinterrogation surface plasmon resonance imaging system. Optics Communications. 377:24–32. DOI: https://doi.org/10.1016/j.optcom.2016.05.035.

Wu Q, Zhang Y, Yang Q, Yuan N, Zhang W. 2019. Review of electrochemical DNA biosensors for detecting food borne pathogens. Sensors. 19(22):1–32. DOI: https://doi.org/10.3390/s19224916.

Published
2022-09-26
How to Cite
HidayatiM. N., Suranto, & SusilowatiA. (2022). DNA Probe as Biosensor Candidate for Clavibacter michiganensis subsp. michiganensis on Tomato Plants . Jurnal Fitopatologi Indonesia, 18(3), 125-133. https://doi.org/10.14692/jfi.18.3.125-133
Section
Articles
##plugins.generic.relatedArticle.noArticleFound##