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Journal : Aceh Journal of Animal Science

In silico SYBR® green-based qPCR primer design for virulent protein C gene of Edwardsiella tarda Rian Ka Praja; Reny Rosalina
Aceh Journal of Animal Science Vol 6, No 3 (2021): November 2021
Publisher : Syiah Kuala University

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.13170/ajas.6.3.19989

Abstract

Edwardsiella tarda infection in fish results in economic losses in aquaculture industries worldwide. Besides, this pathogen is also a zoonotic agent causing gastrointestinal disease in humans. Detection of virulence factors expressed by E. tarda is a key for molecular diagnosis. This study aimed to design SYBR®Green-based quantitative PCR (qPCR) primer for E. tarda virulent protein C (EvpC) gene. A sequence of EvpC with accession number AY424360.4:6500-6991 obtained from GenBank NCBI was selected as the basis for qPCR primer design. qPCR primers were designed using Primer3 online software. Further analysis related to the secondary structure of each primer was carried out using Beacon Designer Free Edition. Five pairs of qPCR primers were successfully designed with Primer3. Based on the results of Primer3 and Beacon Designer analysis, F primer pair 1 (5'-GAATCCACCGACGATAAGCACAAA-3') and R primer pair 1 (5'-GACACGCAGCACCGACATCA-3') were the most favorable primer set since this primer met the criteria in terms of length, melting temperature, GC content, and self complementarity. In addition, this primer set had the highest (closest to zero) -ΔG value of cross dimer, self dimer, and hairpin. It can be concluded that SYBR® Green-based qPCR primer set for EvpC has been successfully designed. However, laboratory optimization experiments are essential for this designed primer set.
Co-Authors Akmal, Rizqy Fajar Syaikhul Amanda, Nadia Keisha Angeline Novia Toemon, Angeline Novia Anggita Ratri Pusporini Anugerahny, Margaretha Yayu Indah Anwar, Muhammad Naufa Arif Rahman Jabal Arini Ratnasari Auliazar, Tarra Austin Bertilova Carmelita, Austin Bertilova Balyas, Abi Bakring Bustomi, Qonita Sari Cristin, Mery Enjelica Decenly, Decenly Dwi Putri Safnurbaiti Dwijayanti, Rts. Sherly Elsa Trinovita Ewaldo, Cereymo Frethernety, Agnes Furtuna, Dewi Klarita Habib, Yusril Hanasia Hanasia, Hanasia Harianja, Henrigen Hartoyo, Riccardo Hasan, Muhamad Umar Muhtar Hermayantiningsih, Dwi I Dewa Gede Sandhikarana I Dewa Made Sukrama I Wayan Muda Suta Arta I Wayan Suardana Kahanjak, Donna Novina Karamo, Beatrice Benita Komang Januartha Putra Pinatih Kurniawan, Mutiara Lavefolia, Raissa Amanda Ledyani, Estilia Maretha, Lauren Muhammad Naufa Anwar Muhammad Ricko Fahrizal Nadia Kesiha Amanda Br Ginting Natalia Sri Martani Nawan Nawan, Nawan Nazhifah, Annida Kholifatun Ni Nengah Dwi Fatmawati Ni Nengah Dwi Fatmawati Ni Nyoman Sri Yuliani Nuha, Alya Firyal Permatasari, Silvani Purba, Yohana Catherine Debyola Putri, Nadiah Romadhona Rahmadina, Nasywa Putri Ranintha br Surbakti Ranti, Dalia Reny Rosalina Reny Rosalina Reny Rosalina, Reny Riccardo Hartoyo Rizki Rachmad Saputra Salsabila, Ivah Sandhikarana, I Dewa Gede Saputra, Rizky Rachmad Saputri, Astrid Ekklesia Sensia, Cici Meyriliani Simamora, Marta Monika Simanungkalit, Lusi Ulina Suharis, Jessica Elisabeth Sulistina, Dinda Ananda Suma, Joy Angel Aria Teresa, Astrid Trisia, Adelgrit Turnip, Oktaviani Naulita Utami, Nur Khalifah Putri Valerie, Sintice Dhea Wahyu Hidayati Widayati, Ratna Widhiyanto, Hendrykus Theo Damar Widiarti, Astri Yan Antonio Ysrafil, Ysrafil Zhofiroh, Nabilatul