Development of swine-specific DNA markers for biosensor-based halal authentication

ABSTRACT. The pig (Sus scrofa) mitochondrial genome was targeted to design short (15-30 nucleotides) DNA markers that would be suitable for biosensor-based hybridization detection of target DNA. Short DNA markers are reported to survive harsh conditions in which longer ones are degraded into smaller fragments. The whole swine mitochondrial-genome was in silico digested with AluI restriction enzyme. Among 66 AluI fragments, five were selected as potential markers because of their convenient lengths, high degree of interspecies polymorphism and intraspecies conservatism. These were confirmed by NCBI blast analysis and ClustalW alignment analysis with 11 different meat-providing animal and fish species. Finally, we integrated a tetramethyl rhodamine-labeled 18-nucleotide AluI fragment into a 3-nm diameter citrate-tannate coated gold nanoparticle to develop a swine-specific hybrid nanobioprobe for the determination of pork adulteration in 2.5-h autoclaved pork-beef binary mixtures. This hybrid probe detected as low as 1 % pork in deliberately contaminated autoclaved pork-beef binary 1763 ©FUNPEC-RP www.funpecrp.com.brGenetics and Molecular Research 11 (2): 1762-1772 (2012) Pig DNA markers for biosensor-based halal authentication mixtures and no cross-species detection was recorded, demonstrating the feasibility of this type of probe for biosensor-based detection of pork adulteration of halal and kosher foods. Key words: In silico digestion; Intra- and interspecies polymorphisms; Restriction enzyme; Mitochondrial genome; Amplicon length; Protein coding gene