The internal transcribed spacer regions (ITS) were submitted to PCR amplification using fungus-specific primers, namely ITSl (5′-TCC GTA GGT GAA CCT GCG G-3′) and ITS4 (5′-TCC TCC GCT TAT TGA TAT G-3′). The amplification was initiated by incubating the PCR reaction mixture at 95°C for 5 min, followed by 35 cycles of denaturation for 30 s at 94°C. The reaction was annealed at 50°C for 30 s and terminated with extension consisting of 1 min at 72°C and final steps of 10 min at 72°C. The PCR products were analyzed on an agarose gel (1%) and purified by the Polyethylene Glycerol- (PEG-) NaCl method. The nucleotide sequences were determined using the Big-Dye Terminator v3.1 Cycle Sequencing Kit and the automated ABI Prism1 3100-Avant Genetic Analyser (Applied Biosystems). The sequence obtained for the intergenic region rRNA. The BLAST search program (
Abi prism1 3100 avant genetic analyser
The ABI Prism 3100-Avant Genetic Analyzer is a capillary electrophoresis (CE) system designed for high-throughput DNA analysis. It features 16 capillaries and can perform a variety of applications, including DNA sequencing, fragment analysis, and microsatellite analysis.
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2 protocols using abi prism1 3100 avant genetic analyser
Fungal DNA Extraction and Sequencing
The internal transcribed spacer regions (ITS) were submitted to PCR amplification using fungus-specific primers, namely ITSl (5′-TCC GTA GGT GAA CCT GCG G-3′) and ITS4 (5′-TCC TCC GCT TAT TGA TAT G-3′). The amplification was initiated by incubating the PCR reaction mixture at 95°C for 5 min, followed by 35 cycles of denaturation for 30 s at 94°C. The reaction was annealed at 50°C for 30 s and terminated with extension consisting of 1 min at 72°C and final steps of 10 min at 72°C. The PCR products were analyzed on an agarose gel (1%) and purified by the Polyethylene Glycerol- (PEG-) NaCl method. The nucleotide sequences were determined using the Big-Dye Terminator v3.1 Cycle Sequencing Kit and the automated ABI Prism1 3100-Avant Genetic Analyser (Applied Biosystems). The sequence obtained for the intergenic region rRNA. The BLAST search program (
Molecular Identification of Fungal Strain
The partial sequence of the fungal rDNA ITS gene was submitted to PCR amplification via forward primer ITSl (5′-TCCGTAGGTGAACCTGCG-3′) and reverse primer ITS4 (5′-TCCTCCGCTTATTGATATG-3′).
The PCR was initiated by incubating the reaction mixture at 94 °C for 3 min, followed by 35 cycles of 1 min at 94 °C. The reaction was annealed at 55 °C for 1 min and terminated with extension and final steps consisting of 1 min at 72 °C and 10 min at 72 °C. The PCR products were analysed on an agarose gel and purified by the PEG-NaCl method. The nucleotide sequences were determined using the Big-Dye Terminator v3.1 Cycle Sequencing Kit and the automated ABI Prism1 3100-Avant Genetic Analyser (Applied Biosystems). The sequence obtained for the intergenic region rRNA ITS was deposited at the GenBank in NCBI under accession number KM594388.
Fungi were identified by searching the homology of ITS genes sequences of the isolate with the sequences using BLAST search algorithm.
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