Molecular Studies on Heat Shock Protein 70 Gene （Hsp70） Using ClustalW Multiple Sequence Alignment Analysis
Molecular Studies on Heat Shock Protein 70 Gene （Hsp70） Using ClustalW Multiple Sequence Alignment Analysis作者机构：Molecular Genetics Lab Biotechnology College Misr University for Science and Technology 6th of October City October 12451 Egypt Department of Genetics Faculty of Agriculture Cairo University Giza 12613 Egypt A in Shams Center for Genetics Engineering and Biotechnology Faculty of Agriculture Ain Shams University Cairo 11241 Egypt
出 版 物：《Journal of Life Sciences》 (生命科学（英文版）)
年 卷 期：2010年第4卷第6期
页 面：1-8页
学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 081704[工学-应用化学] 07[理学] 08[工学] 0817[工学-化学工程与技术] 0906[农学-兽医学] 09[农学]
主 题：ClustalW tool degenerate PCR different melting temperatures In-Silico PCR.
摘 要：Degenerate primers are particularly useful in amplifying homologous genes from different organisms. This paper describes a method for designing degenerate primers for a given multiple alignment of DNA sequences of Hsp70 gene family using ClustalW algorithm. The authors used an in silico approach to find a homology between more than one accession numbers of DNA sequences, X67711.2 was for Oryza sativa Hsp70, AY372071.1 was for Nicotiana tabacum Hsp70 and L41253.2 was for Lycopersicon esculentum Hsc70. The three accession numbers which were retrieved by the BLASTn program depend on their expected value （E-value）. Multiple sequence alignment was performed by ClustalW algorithm to produce a conserved blocks and determine the consensus region which had been used to produce the forward and reverse primer by the primer select module of DNAStar Lasergene V7 and In-Silco PCR module of FASTPCR program ver.4.0.8 was performed to detect the melting temperatures （Tm） and predict the PCR product size, The results of designed degenerate primer showed that there was a homology found between the designed primers and the DNA templates for the three accession numbers with at least 80% identity. The result of degenerate PCR showed that the three bands of the amplified PCR products of the three accession numbers were detected at the same molecular weight of marker （400 bp） with a difference about 15 pb compared to the in silco PCR product （385 pb）. In conclusion, this study focused on the importance of using the clustalW algorithm for designing the degenerate primer.
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