%0 Journal Article
%T In Silico RAPD Priming Sites in Expressed Sequences and iSCAR Markers for Oil Palm
%A Balakrishnan Vasanthakumari Premkrishnan
%A Vadivel Arunachalam
%J International Journal of Genomics
%D 2012
%I Hindawi Publishing Corporation
%R 10.1155/2012/913709
%X RAPD is a simple dominant marker system widely used in biology. Effectiveness of RAPD can be improved by selecting and redesigning primers whose priming sites occur in target sequence(s) of gene or organism at optimum distance. We developed software that uses sequences of random decamer primers and nucleotide sequence(s) as two input files. It locates the priming sites in input sequences and generates output files listing frequency and distance between priming sites. When the priming sites of a single primer occur more than once in a sequence with a distance of 200 to 2000£¿bp, the software also designs pairs of iSCAR primers. An input of 387 RAPD primers and 42,432 expressed sequences of oil palm are used as test. Wet-lab PCR results from a publication that used the same set of primers were compared with software output on priming sites. In the test sequences of oil palm covering 1.4% of genome, we found that at least 60% the primers chosen using software are sure of giving PCR amplification. We designed 641 iSCAR primers suitable for amplification of oil palm DNA. The software successfully predicted 92% (67 out of 73) of published polymorphic RAPD primers in oil palm. 1. Introduction The secret of differences between individual organism lies in their genetic material, called deoxyribonucleic acid (DNA). A genetic marker can be defined in one of the following ways: (a) a chromosomal landmark or allele that allows for the tracing of a specific region of DNA, (b) a specific piece of DNA with a known position on the genome, or (c) a gene whose phenotypic expression is usually easily discerned, used to identify an individual or a cell that carries it, or as a probe to mark a nucleus, chromosomes, or locus [1]. Genetic markers may not have a biological function, and they are inherited from one generation to next. Random amplified polymorphic (RAPD) DNA markers were introduced by Williams et al. [2] in 1990. RAPD markers can be implemented more rapidly and inexpensively than other type of markers. Prior knowledge of the DNA sequence for the targeted gene is not required, as the primers will bind somewhere in the sequence although exact location is unknown. RAPD primers are of decamer (10 base pairs) size and are randomly generated. The success of Polymerase Chain Reaction (PCR) is highly dependent on these short arbitrary oligonucleotides that hybridize onto the complementary DNA fragments. These short oligonucleotides function in pairs (one forward and one reverse primer) and are used to amplify [3] a set of DNA fragments. When choosing an arbitrary primer
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