A primer is a short synthetic oligonucleotide which is used in many molecular techniques from PCR to DNA sequencing. These primers are designed to have a sequence which is the reverse complement of a region of template or target DNA to which we wish the primer to anneal. Plasmid map drawing system primer design has two essential & distinct phases, physical design and selectivity design. Physical design of primers involves the consideration of factors, such as GC-content, primer length, annealing & melting temperatures, starting nucleotides & higher-order oligonucleotide structure. These factors are essential to ensure that a primer is able to bind to a template and initiate extension by the polymerase in an efficient, consistent manner. Primer selectivity refers to the ability of a primer to bind to a single location within the initial pool of DNA. For microarray validation studies, there are two broad factors determining selectivity. First, a primer should be specific to a given mRNA transcript and should not bind in a region conserved across a gene or protein family (transcriptomicselectivity). Second, the primer should be robust against contamination by genomic DNA (genomic selectivity). If either type of selectivity is poor, a primer will amplify multiple products and thereby decrease PCR efficiency & introduce a confounding effect that will reduce the sensitivity & accuracy of quantitative PCR methods.