The Completion of the Genomic Sequence of Arhodomonas sp. Seminole Supported by the Use of Polymerase Chain Reaction

Abstract

Arhodomonas sp. Seminole is a halophilic bacterium that was found in the crude-oil filled soil in Seminole, OK. After using enrichment to obtain pure culture of the bacteria, the researchers were left with a major question. What DNA sequence completed the incomplete genomic sequence? In order to answer this question, using the BLASTX program, we identified the sequence gap and used the given related protein sequences  through PrimerQuest and determined a forward and reverse primer sequence. Using a physical version of our primers, we mixed them along with several other ingredients into a mixture that allowed PCR to be performed. We put this mixture into a gel to have Agarose Gel Electrophoresis performed to create a product. After PCR was performed, the mixture we created failed in producing a PCR product. So, in conclusion, the failure in producing a PCR product could mean a variety of things including: something was performed incorrectly in the experiment, the PCR primers were designed were not compatible, or the related protein sequence we were given was not a proper match.