Primer Designing for Dreb1A, A Cold Induced Gene

Primer designing for cold induced gene, DREB1A is done using Primer3 software. Seventeen sequences related to DREB1A gene were retrieved from UniGene, GenBank and RefSeq databases using Entrez. On multiple sequence alignment, a 286 bp conserved region was identified. Potential primers for the conserved region and for seventeen nucleotide sequences were determined using Primer3 . The properties of these potential primers were analyzed using Premier Biosoft’s NetPrimer tool. One forward (5’ end) and one backward (3’ end) primer having 50 to 60% GC content, 52 to 58 o C Tm and absence of secondary structures were finalized. Specificity of the primers was validated by carrying out local alignment against the NCBI’s nr database through BLAST. All the alignments showed significant alignment to DREB1A gene validating the specificity of the primers.