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E-FAS, vol. 17, no. 3, pp.339-344, September, 2014
DOI. http://dx.doi.org/10.5657/FAS.2014.0339

Development of Clamping Probe for Rare DNA Detection  using Universal Primers

Meyong il Kim1, Ki-Young Lee2 and Sang-Man Cho3*
1Incheon Fisheries Research Institute, Incheon 409-871, Korea
2Department of Marine Biotechnology, Kunsan National University, Gunsan 573-701, Korea
3Department of Aquaculture and Aquatic resources, Kunsan National University, Gunsan 573-701, Korea

PCR amplification with universal primer is a useful tool for speciation of symbionts in marine eukaryote coupled with robust sepa- ration method such as denaturing high performance chromatography (DHPLC). To overcome the biased amplification, clamping PCR is recommended to suppress the amplification of host gene. In this study, we evaluated the efficiency of rare gene detection for two kinds of clamping probes which were successfully utilized for eukaryotic symbiont analysis: C3 linked nucleotide (C3) and peptide nucleic acid (PNA). PNA was 3-4 orders of magnitude higher than that of C3 tested in clamping efficiency and rare gene detection. This represented that PNA could be a more competent clamping probe for the enhancement of PCR amplification for rare symbiont genes.

Keyword : Peptide nucleic acid (PNA), Clamping PCR, Symbiont, Clamping efficiency

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