Sepia bandensis ink inhibits polymerase chain reactions

While cephalopods serve critical roles in ecosystems and are of significant interest in scientific studies of the nervous system, medicinal toxins, and evolutionary diversification. The absence of a genomic library and the lack of comprehensive gene analysis present challenges to conducting efficient and thorough research. One difficulty in advancing cephalopod genomics is the presence of inhibitors (such as ink) that impede the amplification of DNA samples with PCR. We tested the hypothesis that Sepia bandensis (dwarf cuttlefish) ink inhibits PCR by running PCR reactions with and without the back addition of ink to Turbo fluctuosus (marine sea snail) DNA with the inclusion of the appropriate positive and negative controls. The experimental results show that ink added to T. fluctuosus DNA extracted using two kit-based extraction methods or phenol chloroform extraction prevents the amplification of the cytochrome c oxidase subunit I (COI) mitochondrial gene. Also, while modern extraction methods like quaternary amine resin and silica column isolation failed to produce genomic products viable for PCR from S. bandensis, phenol chloroform extraction eliminated the inhibitors and resulted in successful amplification. The results of this investigation could further cephalopod genomic studies and serve as a model for experiments aiming to determine the cause of PCR inhibition.