IN SILICO OLIGONUCLEOTIDE PRIMER DESIGN FOR Campylobacter jejuni cytolethal distending toxin B GENE AMPLIFICATION

Rian Ka Praja

Abstract


Cytolethal distending toxin B (cdtB) is a genotoxinexpressed by Campylobacter jejuni. cdtB is a DNasethatinduces DNA double-strand breaks (DSB) in the nucleus causing cell cycle arrest at the G2/M phase and apoptosis. This study aimed to design and analyze in silico primer pairs to amplify cdtB gene ofC. jejuni.The cdtB gene sequence with accession number AY445094.1was retrieved from GenBank NCBI and primer pairs were designed by using Primer-BLAST. Further analysis of primer quality such asself dimer, hairpin, repeats, and runwere done by NetPrimer. The results showed that forward primer pair 3 (5’-AGCAAGTGGAGTGTTAGCGT-3’) and reverse primer pair 3 (5’- TTGGAGTGGCTGTTCTTGGT-3’) met requirements as an ideal primer set to amplify cdtB gene in the term of primer length, Tm and GC% with a product length of 103 bp.In addition, based on NetPrimer analysis results, this primer pair had no self dimer, hairpin, repeats, and run. It can be concluded that a primer set to amplify cdtB gene of C. jejunihas been successfully designed.However, a wet experiment is needed to run this primer set in the laboratory setting.

 

Keywords: Campylobacter jejuni, cdtB gene, in silico, primer.


Full Text:

PDF

References


MM Hassan W. Review on some virulence factors associated with Campylobacter colonization and infection in poultry and human. Am J Biomed Sci Res. 2019;3(5):460–3.

Khoshbakht R, Tabatabaei M, Shirzad Aski H, Hosseinzadeh S. Occurrence of virulence genes and strain diversity of thermophilic campylobacters isolated from cattle and sheep faecal samples. Iran J Vet Res. 2014;15(2):138–44.

de Carvalho AF, de Silva DM, Azevedo SS, Piatti RM, Genovez ME, Scarcelli E. Detection of CDT toxin genes in Campylobacter spp. strains isolated from broiler carcasses and vegetables in São Paulo, Brazil. Brazilian J Microbiol. 2013;44(3):693–9.

Silva J, Leite D, Fernandes M, Mena C, Gibbs PA, Teixeira P. Campylobacter spp.as a foodborne pathogen: A review. Vol. 2, Frontiers in Microbiology. Frontiers Research Foundation; 2011.

Modi S, Brahmbhatt MN, Chatur YA, Nayak JB. Prevalence of Campylobacter species in milk and milk products, their virulence gene profile and antibiogram. Vet World. 2015 Jan 2;8(1):1–8.

Lai CK, Chen YA, Lin CJ, Lin HJ, Kao MC, Huang MZ, et al. Molecular mechanisms and potential clinical applications of Campylobacter jejuni cytolethal distending toxin. Front Cell Infect Microbiol. 2016;6(FEB):1–8.

Méndez-Olvera ET, Bustos-Martínez JA, López-Vidal Y, Verdugo-Rodríguez A, Martínez-Gómez D. Cytolethal distending toxin from Campylobacter jejuni requires the cytoskeleton for toxic activity. Jundishapur J Microbiol. 2016;9(10).

Rahman MT, Uddin MS, Sultana R, Moue A, Setu M. Polymerase chain reaction (PCR): A short review. Anwer Khan Mod Med Coll J. 2013;4(1):30–6.

Valones MAA, Guimarães RL, Brandão LAC, De Souza PRE, De Albuquerque Tavares Carvalho A, Crovela S. Principles and applications of polymerase chain reaction in medical diagnostic fields: A review. Brazilian J Microbiol. 2009;40(1):1–11.

Garibyan L, Avashia N. Polymerase chain reaction. J Invest Dermatol. 2013;133(3):1–4.

Burpo FJ. A critical review of PCR primer design algorithms and crosshybridization case study. Biochemistry. 2001;86:1–12.

Sint D, Raso L, Traugott M. Advances in multiplex PCR: Balancing primer efficiencies and improving detection success. Methods Ecol Evol. 2012 Oct;3(5):898–905.

Suparman, Ahmad H, Ahmad Z. Desain primer PCR secara in silico untuk amplifikasi gen coi pada kupu-kupu Papilio ulysses linnaeus dari Pulau Bacan. J Pendidik Mat dan IPA. 2016;7(1):14.

Sari EN, Dewi RW, Dewi VR, Yowani SC, Yustiantara PS. Desain primer untuk amplifikasi regio promoter gen inha isolat p016 multidrug resistance Mycobacterium tuberculosis dengan metode polymerase chain reaction. J Farm Udayana. 2018;7(1):34.

Pradnyaniti D., Wirajana I., Yowani, S C. Desain primer secara in silico untuk amplifikasi fragmen gen rpoB Mycobacterium tuberculosis dengan polymerase chain reaction (PCR). J Farm Udayana. 2013;124–30.

Saraswati H, Wahyuni FD, Seprianto S. Desain primer secara in silico untuk amplifikasi gen cryIII dari Bacillus thuringiensisisolat lokal. Indones J Biotechnol Biodivers. 2019;3(1):33–8.




DOI: http://dx.doi.org/10.30649/obj.v4i1.88

Refbacks

  • There are currently no refbacks.


Copyright (c) 2021 Rian Arinta Kusuma Praja

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

 

ACCREDITED : SINTA 4 (S4)
Abstracting and Indexing: GARUDA, Neliti, ISJD-LIPI, Google Scholar, CrossRef, ROAD, PKP Index, Microsoft Academic (articles only) and SciLit.
 
Indexing:
sinta-logo
garuda
google
crossref
 
 
 Dimensions | The Next Evolution in Linked Scholarly Information
 
 
DOI Prefix:  10.30649

Template of the Manuscript: click the icon below, click menu bar FILE, choose and click Download, click Microsoft Wordocx)

Image result for google document


 

TURNITIN plagiarism check | Shopee Indonesia

 Zotero

Published by: Universitas Hang Tuah, Surabaya, Jawa Timur, Indonesia

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.