Volume 22, Issue 1 (Spring 2025)
Sci J Iran Blood Transfus Organ 2025, 22(1): 19-29 |
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Zandi M, Sharifi Z, Ajorloo M. Design and In-Silico Evaluation of Specific Primers for the HBZ Gene of HTLV-1 to Establish a Semi-Nested PCR Method. Sci J Iran Blood Transfus Organ 2025; 22 (1) :19-29
URL: http://bloodjournal.ir/article-1-1567-en.html
URL: http://bloodjournal.ir/article-1-1567-en.html
Abstract: (454 Views)
A B S T R A C T
Background and Objectives
Human T-cell lymphotropic virus type 1 (HTLV-1) is the only human oncogenic retrovirus associated with adult T-cell leukemia/lymphoma and tropical spastic paralysis. Common serological methods for detecting this virus are ELISA and Western blot. The HBZ gene, encoded by the negative strand of the HTLV-1 provirus, does not undergo continuous mutations, unlike other viral genes. In this study, the HBZ gene of HTLV-1 was used to design specific primers and develop a semi-nested PCR assay.
Materials and Methods
In a cross-sectional study, HBZ gene sequences from various virus isolates were extracted from the NCBI database and aligned using MEGA6 software. Using Gene Runner software, the primer design was performed from the conserved region common to all strains. To evaluate the primers, parameters such as GC content, melting temperature, hairpin, and dimer structures were used calculated by OligoAnalyzer software. To examine the exact binding site of the primers, SnapGene software was used to simulate the PCR reaction and electrophoresis. Primers were screened and synthesized using the BLASTN tool in NCBI. In the laboratory stage, genomic DNA was extracted from blood samples of HTLV-1 positive and healthy individuals and electrophoresed for Semi-nested PCR reaction and evaluation of PCR products.
Results
First, the HBZ protein coding sequences from 43 viral isolates with different geographical origins were aligned, and then primers were designed from the most similar conserved regions. The primers lacked hairpin and dimer structures. The GC percentage was between 45%-60%, and the melting temperature was between 64-67°C. BLAST results showed that the designed primers were 100% capable of identifying the target gene (HBZ), and no overlap with the genomic sequences of other viruses or humans was observed. After genomic DNA extraction and PCR, the length of the desired fragment was 493 bp in the first stage and 106 bp in the second stage, which was consistent with the predicted bioinformatics results.
Conclusions
The design of HBZ gene primers utilizing bioinformatics software and the successful development of a Semi-nested PCR assay were achieved. The laboratory results confirmed the bioinformatics predictions and demonstrated the effectiveness of this method for the accurate and rapid detection of the virus.
Background and Objectives
Human T-cell lymphotropic virus type 1 (HTLV-1) is the only human oncogenic retrovirus associated with adult T-cell leukemia/lymphoma and tropical spastic paralysis. Common serological methods for detecting this virus are ELISA and Western blot. The HBZ gene, encoded by the negative strand of the HTLV-1 provirus, does not undergo continuous mutations, unlike other viral genes. In this study, the HBZ gene of HTLV-1 was used to design specific primers and develop a semi-nested PCR assay.
Materials and Methods
In a cross-sectional study, HBZ gene sequences from various virus isolates were extracted from the NCBI database and aligned using MEGA6 software. Using Gene Runner software, the primer design was performed from the conserved region common to all strains. To evaluate the primers, parameters such as GC content, melting temperature, hairpin, and dimer structures were used calculated by OligoAnalyzer software. To examine the exact binding site of the primers, SnapGene software was used to simulate the PCR reaction and electrophoresis. Primers were screened and synthesized using the BLASTN tool in NCBI. In the laboratory stage, genomic DNA was extracted from blood samples of HTLV-1 positive and healthy individuals and electrophoresed for Semi-nested PCR reaction and evaluation of PCR products.
Results
First, the HBZ protein coding sequences from 43 viral isolates with different geographical origins were aligned, and then primers were designed from the most similar conserved regions. The primers lacked hairpin and dimer structures. The GC percentage was between 45%-60%, and the melting temperature was between 64-67°C. BLAST results showed that the designed primers were 100% capable of identifying the target gene (HBZ), and no overlap with the genomic sequences of other viruses or humans was observed. After genomic DNA extraction and PCR, the length of the desired fragment was 493 bp in the first stage and 106 bp in the second stage, which was consistent with the predicted bioinformatics results.
Conclusions
The design of HBZ gene primers utilizing bioinformatics software and the successful development of a Semi-nested PCR assay were achieved. The laboratory results confirmed the bioinformatics predictions and demonstrated the effectiveness of this method for the accurate and rapid detection of the virus.
References
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