APPLICATION OF NEW DEGENERATE PRIMER SET FOR SIMULTANEOUS ISOLATION OF HYPER VARIABLE SUBUNIT OF ENV GENE FROM DISTINCT HIV-1 GENOTYPES

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FALAHI SH.; RAVANSHAD M.; KENAR KOOHI A.

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Journal: ARAK MEDICAL UNIVERSITY JOURNAL (AMUJ) Year:2011 | Volume:14 | Issue:4 (57) Page(s): 60-68

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Title

APPLICATION OF NEW DEGENERATE PRIMER SET FOR SIMULTANEOUS ISOLATION OF HYPER VARIABLE SUBUNIT OF ENV GENE FROM DISTINCT HIV-1 GENOTYPES

Author(s)

FALAHI SH. | RAVANSHAD M. | KENAR KOOHI A. | Issue Writer Certificate

Keywords

DEGENERATE PRIMERS FOR PCRQ2

V3- LOOPQ2

HIVQ2

RT-PCRQ2

Abstract

Introduction: Polymerase chain reaction is the most common technique in the field of molecular biology that use for amplification of a specific nucleic acid sequence. Degenerate primers have ability to amplify related but distinct sequences. The aim of current study was to use, two sets of degenerate primers in combination with Hemi Nested PCR for detection V3-Loop sequence of envelope gene from wide spectrum of Human Immunodeficiency Virus (HIV) subtypes.Material and Methods: In this experimental study we designed and optimized, a degenerate primer pair in combination with Hemi Nested PCR, to detect HIV-1 V3 loop from Envelop gene that has wide variations among genotypes. The developed assay was used to check, 40 HIV infected, 10 negative controls as well as 5 samples from each HCV, HBV, HGV, and TTV were analyzed using developed method.Results: after optimization, 35 out of 40 positive controls were positive using our test. None of the negative human and viral control samples showed specific band. Also, in positive samples, nonspecific bands were not detected.Conclusion: In this study moreover than standard PCR, we used two degenerate primers that could detect specific region of genome. In fact, first round of PCR product act as a template for second round inner primers and can produce smaller sequence with high sensitivity due to degeneracy. Based on the current investigation, the developed assay had advantages including product confirmation and hence more sensitivity.

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APA: Copy

FALAHI, SH., RAVANSHAD, M., & KENAR KOOHI, A.. (2011). APPLICATION OF NEW DEGENERATE PRIMER SET FOR SIMULTANEOUS ISOLATION OF HYPER VARIABLE SUBUNIT OF ENV GENE FROM DISTINCT HIV-1 GENOTYPES. ARAK MEDICAL UNIVERSITY JOURNAL (AMUJ), 14(4 (57)), 60-68. SID. https://sid.ir/paper/69461/en

Vancouver: Copy

FALAHI SH., RAVANSHAD M., KENAR KOOHI A.. APPLICATION OF NEW DEGENERATE PRIMER SET FOR SIMULTANEOUS ISOLATION OF HYPER VARIABLE SUBUNIT OF ENV GENE FROM DISTINCT HIV-1 GENOTYPES. ARAK MEDICAL UNIVERSITY JOURNAL (AMUJ)[Internet]. 2011;14(4 (57)):60-68. Available from: https://sid.ir/paper/69461/en

IEEE: Copy

SH. FALAHI, M. RAVANSHAD, and A. KENAR KOOHI, “APPLICATION OF NEW DEGENERATE PRIMER SET FOR SIMULTANEOUS ISOLATION OF HYPER VARIABLE SUBUNIT OF ENV GENE FROM DISTINCT HIV-1 GENOTYPES,” ARAK MEDICAL UNIVERSITY JOURNAL (AMUJ), vol. 14, no. 4 (57), pp. 60–68, 2011, [Online]. Available: https://sid.ir/paper/69461/en

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