Identification of Conserved Sequences for PCR Primer Design by Multiple Alignments of Dot Matrix Plots

摘要

Data analysis has shown that during evolution different regions of certain genes are well conserved between species. The conserved nucleotide sequences in the related DNA or RNAcan provide information for designing consensus primer pairs for polymerase chain reactions (PCR). With a set of consensus primers directed towards conserved regions of the gene of interest, a particular cDNA sequence can be amplified from all of the species that are known to preserve the primer-targeted sequences. In addition, it is very likely that using such a primer pair, the particular cDNA can be amplified from divergent species, for which no sequence information is available. Numerous molecular biology software packages that are used on microcomputers using a variety of homology algorithms can assist in the identification of conserved regions between different DNA sequences. However, locating conserved regions that are shared by multiple, otherwise dissimilar nucleic acid sequences can be a very difficult process. Tocircumvent this problem, a novel approach of aligning dot matrix plots was developed. This method can be used to easily locate ≥14-nucleotide (nt)-long perfectly conserved sequences, which can be used to design primers for PCR.