Random amplification of polymorphic DNA with conserved sequences reveals genome-specific monomorphic amplicons: Implications in clad identification

The enzymatic amplification of genomic DNA with an arbitrary primer generat es informative band profile useful for genome analysis. We used a set of sy nthetic oligodeoxyribonucleotide primers OAT15.2 (GACA)(3.75), OAT18.2 (GAC A)(4.5), OAT(24.2) (GACA)(6), OAT36 (GACA)(9), comprising 4-9 consecutive u nits of GACA repeat, O33.15 (CACCTCTCCACCTGCC) and O33.6 (CCTCCAGCCCTCCTCCA GCCCT) for RAPD reactions of genomic DNA from different sources. The GACA b ased oligos of 15 and 18 base residues generated discernible genome specifi c amplicons whereas primers larger than 18 bases revealed smeary signals. T he other oligos O33.15 and O33.6 also generated genome specific amplicons w ith more bands compared with those obtained from OAT15.2 or OAT18.2. The pr esence of OAT15.1 (GATA)(3.75) and OAT15.2 (GACA)(3.75) sequences in differ ent genomes were ascertained by independent dot-blot hybridization prior to using them for RAPD reactions. The RAPD amplicons generated by evolutionar ily conserved primer(s) or sequences shared by many species may be useful f or clad identification in controversial systematics, comparative genome ana lysis, acid for establishing the phylogenetic status of an organism.