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Journal : Innovative: Journal Of Social Science Research

Desain Primer Secara In Silico untuk Amplifikasi Mutagenesis GLY349→GLU349 pada Gen Glikoprotein Virus Rabies Strain GD-SH-01 sebagai Kandidat Marker Attenuasi Devi, Ni Wayan Antika Sri; Yowani, Sagung Chandra
Innovative: Journal Of Social Science Research Vol. 5 No. 4 (2025): Innovative: Journal Of Social Science Research
Publisher : Universitas Pahlawan Tuanku Tambusai

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31004/innovative.v5i4.19727

Abstract

Rabies is a fatal zoonotic disease caused by the rabies virus (RABV) with a case mortality rate almost 100% after the onset of symptoms. The Gly349→Glu349 mutation in the glycoprotein gene (G gene) of the rabies virus strain GD-SH-01 has been identified as a potential molecular marker for attenuation in the development of live attenuated vaccines. This study aims to design in silico primer pairs specific to the Gly349→Glu349 mutation to enable amplification of the target segment using Polymerase Chain Reaction (PCR). Primer design was carried out using the Primer3Plus software with parameters of primer length between 18–28 bases, melting temperature (Tm) of 55–65 °C, and GC content of 40–60%. Candidate primers were evaluated based on thermodynamic properties and secondary structure formation, and their specificity was analyzed using PrimerBLAST based on the mutated sequence. Five candidate primer pairs were generated, among which the third pair was selected as the best, producing a 175 bp PCR product with the Gly349→Glu349 mutation located at the center of the amplicon and demonstrating high specificity to the target sequence. The designed in silico primer pair shows strong potential for specific amplification of the Gly349→Glu349 mutation in the rabies virus glycoprotein gene. This design provides a scientific foundation for further molecular studies and the development of genetic analysis methods and rabies vaccines based on genetic engineering technology.
Desain Primer PCR Secara In Silico untuk Deteksi Gen NS1 DENV-2 Strain New Guinea C (NGC) sebagai Diagnosis Dini Demam Berdarah Dengue Putri, Ni Kadek Sri Adnyani Alit; Yowani, Sagung Chandra
Innovative: Journal Of Social Science Research Vol. 5 No. 4 (2025): Innovative: Journal Of Social Science Research
Publisher : Universitas Pahlawan Tuanku Tambusai

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31004/innovative.v5i4.20335

Abstract

Dengue Hemorrhagic Fever (DHF) is a serious infectious disease caused by the Dengue virus, with a high morbidity and mortality rate, especially in tropical countries such as Indonesia. One sensitive and specific method for early diagnosis is Polymerase Chain Reaction (PCR), with the Non-Structural gene 1 (NS1) as the ideal molecular target. This study aims to design an in silico PCR primer that is specific to the NS1 gene of Dengue virus serotype 2 (DENV-2) strain New Guinea C (NGC). The design was done using the Primer3Plus software, and the specificity validation was done through Primer-BLAST against the NCBI database. The selected primary pair has a length of 20 bases with a melting temperature (Tm) of 60.0°C, and a GC content of 50.0% and 45.0%, respectively. The primer was able to amplify the NS1 gene segment along 258 bp specifically without exhibiting cross-amplification of the human genome or other DENV serotypes. These results suggest that the designed primer has strong potential to be further developed as a molecular diagnostic tool for early detection of DENV-2 infection.
Desain Primer Secara In Silico untuk Amplifikasi Gen Pre-S2 Virus Hepatitis B Tirtawati, Ni Putu Ayu; Yowani, Sagung Chandra
Innovative: Journal Of Social Science Research Vol. 5 No. 4 (2025): Innovative: Journal Of Social Science Research
Publisher : Universitas Pahlawan Tuanku Tambusai

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.31004/innovative.v5i4.20964

Abstract

Hepatitis B is a serious infectious disease caused by the Hepatitis B virus (HBV), which can progress to cirrhosis and hepatocellular carcinoma. Early detection of HBV infection is crucial to prevent disease progression, but the Pre-S2 gene region as a diagnostic target remains understudied. This gene plays a crucial role in viral infectivity, replication, and immune response, and its mutations are known to contribute to latent infection and the pathogenesis of liver cancer. This study aimed to design in silico primer pairs specific to the HBV Pre-S2 gene using a bioinformatics approach. The design was performed using Primer3Plus based on the HBV genome sequence from GenBank (Accession Number AB246345.1), and evaluated through physicochemical parameters such as length, melting temperature (Tm), GC content, and potential for secondary structure formation. The best candidates were then tested for specificity using Primer-BLAST against various HBV isolates. The results showed that the forward primer pair 5’-TTCCTCTTCATCCTGCTGCT-3’ and reverse primer pair 5’-AGTTTCCGTCCGAAGGTTTT-3’ were able to amplify the Pre-S2 gene with a PCR product length of 193 bp and exhibited high specificity for the HBV genome. These findings demonstrate the effectiveness of the in silico approach in designing primers for molecular detection of the HBV Pre-S2 gene and its potential applications in diagnosis, mutation research, and the development of prevention strategies.
Co-Authors A. W. Dwiputri Ade Ari Sundari Ade Ari Sundari Amelia Putri, Ni Luh Dian Saptari Arifani Siswidiasari Asmara A. A. R. Astuti, M.A.P. Ayu Nyoman Chandra Yustiana Ayu Putu Chika Iswari Anjani, Sang Cista Dewi, Ni Putu Fiona Dek Pueteri Dewi Suryani Deniariasih, N.W. Devi, Ni Wayan Antika Sri Devita Kusdianingrum Dewa Ayu Swastini Dewi Andayani Farmawati Dwicandra, N.M.O. Dyah Subadrika Warma Dewi Endang Kumolosasi Gede Bayu Surya Ekayana, I Heni Pujiastuti I Gede Ketut Sajinadiyasa I Gusti A. A. Santhi Rahmaryani I Gusti Ayu Agung Septiari I Ketut Juniarta I Ketut Tunas I Made Dira Swantara I Nengah Wirajana I Nyoman Gede Budiana I Wayan Kasa Ida Ayu Gendari Ida Ayu Ratih Dwi Nugraha Putri Ida Bagus Nyoman Putra Dwija Indra Juana Adikara Jennifer Tamara Jennifer Tamara Kadek Ratna Sari Dewi Kadek Widya Yuli Hartati Ketut Ratnayani Ketut Widyani Astuti Liangky Syane S Luh Vida Sasmitha Luk Ketut Budi Maitriani M. A. Pratiwi Made Dharmesti Wijaya Made Rai Dwitya Wiradiputra Marfu'ah, Nurul Marlia Singgih Wibowo Mirawati N.K.W. Ni Kadek Ari Cipta Pratiwi Ni Kadek Ariani Ni Ketut Sri Anggreni Ni Komang Sasi Ani Ni Made Febrianti Ni Made Yustikarini Ni Nyoman Pradnya Utari Ni Putu Ariantari Ni Putu Intan Satya Dewi Ni Putu Monica Rosdiana Dewi Paramitha Ni Wayan Sukma Pramitha Sari1 Osamu Iitsuka Pradnyaniti, D.G Putri, Ni Kadek Sri Adnyani Alit Putu Ayu Indrayathi Putu Lita Astriani Rasmaya Niruri Ratna Sari Dewi, Kadek Rini Noviyani Sang Ayu Putu Chika Iswari Anjani Saputra, Gusti Nyoman Oka Sari Dewi, Kadek Ratna Sudarma, I Wayan Ari Syamsul Arifin Tasya Pramiswari Tirtawati, Ni Putu Ayu Wijayakusuma, I Gusti Ngurah Lanang Yayanasri Yustiantara, Putu Sanna