I am confused with the selection of gene for primer design using bioedit software. How I select a suitable gene sequence for further primer design? There is no primer available for my new bacterial isolate thats why use related genera of bacteria that have Pha C gene and trying to generate a primer sequence. Please give a Step wise Procedure for design a gene primer for detection of Pha C gene for new bacteria.
For design primer we need to know the sequence. If you are using related genera you shoud choose 16srna for related genera.
Well, it will depend of what do you want to do with the sequence: If it is the case of only checking the presence of the gene, you could align different phaC genes from several organisms in any software (MEGA or ClustalW) and look for conserved regions between all of them and design primers from there. Usually, 20 base primers are used, and for stability reasons, try to start and finish it with cytosine or guanine, i.e: G/CXXXXXXXXXXXXXXXXXXXG/C. As Antonio said, it would be easier to have an identification of the bacteria to help you to select which sequences will you choose to compare with.
Thank you, Mr. Guillermo Fernandez-Bunster, Mr. Arvind Singh Chandel and Mr. A.M. Fernandes for your kind suggestion.
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