PCR Primer Designer Tool Notes

PCR is utilized to study gene expression, gene cloning and gene amplification or sequencing studies.

PCR primer designing is an important process with respect to PCR.  The success of PCR mainly depends upon primer so this class will be useful for PCR. One set of primer namely right/forward/5’ and left/reverse/3’ primers required.

Inorder to design primer, first one should have the gene sequence to which PCR is going to perform. Gene sequence might be retrieved from genbank of NCBI.

For primer designing, Primer3plus tool is utilized in this lecture.

In primer3plus tool, gene sequence as raw sequence is pasted or input file is browsed.  By using default options, primer designed.  The default options actually predicted the best primer because optimum conditions like GC content, Tm and primer length were set in the default options.  After entering or loading sequence, pick primer is used to run the program.

The output of primer3plus tool provides one primer set in details and other four primer sets in brief.  Details of primer set include amplified product length, primer length, GC content, and Tm etc.  Normal file saving options might be used to save the file.

To get primer for specific length or full gene, options of primer3plus tool might be used.