Detection and Protein Modelling for Consensus Region of hsp70 Gene Family in Egyptian Arundo donax

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 and detect the consensus region in gene family of hsp70 in a plant species which have not any recorded information about hsp70 gene family in the Genbank of National Centre of Biotechnology Information (NCBI) like Arando donax .The sequenced consensus sequence of Arando donax is considered a gene marker in building the genome map sequence. The BLASTn program is used 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). In silco PCR module was performed to detect the melting temperatures (Tm) and predicted the PCR product size (783 bp).The result of designed degenerate primers showed that there was a homology founded among the designed primers and the DNA templates of the recorded sequences (AY372071.1, X67711.2 and L41253.2) with at least 80% identity. The designed degenerate primers were used to isolate a consensus region of hsp70 gene family of Arando donax at the expected molecular weight (783 bp). The isolated PCR product, (783 bp) of Arando donax was sequenced and submitted to the Database of Japan (DDBJ) with accession number AB819871. The ORF finder tool translated the accession number AB819871 and gave a selected frame which used to build 3D structure model. In conclusion, this study focused on the importance of designing the degenerate primers to isolate the gene family and predict the 3D structure of gene family depending on the ORF finder tool of Genebank.