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Rep-PCR Profiling


Repetitive-element PCR (Rep-PCR) is a method for fingerprinting microbial genomes by PCR amplification of repetitive DNA elements that are widely distributed in the microbial genomes. Rep-PCR is rapidly developed and widely used in the classification of a variety of microbial genes. The technique is high-resolution, easy to perform, and can be applied to large or small numbers of samples. We provide rep-PCR profiling service to help you examine strain-specific patterns and identify microbes even on the strain level.

Our Advantages:
  • Decades of experience in genomics service and proven expertise in microbial genomics.
  • Provide exquisite gel electropherogram.
  • High-resolution and high-reproducibility data.
  • Extensive experience in handling various samples.
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Introduction to our rep-PCR profiling platform

Rep-PCR is rapidly becoming the most widely used DNA-based typing method. The repetitive sequences, including REP (repetitive extragenic palindromic) sequences, ERIC (enterobacterial repetitive intergenic consensus) sequences and BOX elements, are widely distributed in microbial genomes. They differ in distribution at the level of strains, species and genera, but are relatively conservative in evolution. The REP elements are 38-bp sequences consisting of six degenerate positions and a 5-bp variable loop between each side of a conserved palindromic stem. ERIC sequences are 126-bp elements which contain a highly conserved central inverted repeat and are located in extragenic regions of the microbial genomes. BOX elements are located within intergenic regions and can also form stem-loop structures due to their dyad symmetry. Rep-PCR uses the primers which are complementary to interspersed repetitive consensus sequences for PCR experiments, and then, DNA fragments of different sizes between repetitive elements are amplified. The PCR-products are separated by electrophoresis apparatus depending on the size of the fragments and a species (sometimes strain)-specific pattern is obtained. Isolates with similar patterns will cluster together, which is the basis of microbial ID using rep-PCR.

The microbial genome repetitive sequence PCR technology for molecular typing of microorganisms has the advantages of simplicity, rapidity and stability. Compared with plasmid profiling and genomic fingerprinting, rep-PCR shows broader species applicability and better discriminatory power. Meanwhile, Rep-PCR has considerably better discernibility than the restriction analysis of the 16S/18S rRNA gene or the 16S-23S spacer region. Some studies have shown that rep-PCR technology precedes other typing methods such as multilocus enzyme electrophoresis, biochemical characterizations, and ribotyping. Rep-PCR profiling service can be used as molecular markers for bacteria in the study of microbial DNA typing. It is also used for the identification and classification of strains and genetic relationship analysis.

Rep-PCR profiling service workflow

Sample Requirement

    1. 1.8 < OD260/280 < 2.0, no degradation or contamination.
    2. Mixed microbial genomic DNA: total amount > 1 ug, concentration > 10 ng/ul.
    3. Gram-positive bacteria are not easy to extract from a complex microbial community due to the relatively thick cell wall, and the use of conventional methods may result in the loss of strains. Please provide us with more than 10 ml of microbial solution (OD600 > 1.5) or the microbial pellet.

Sampling kits: We provide a complete range of microbial sampling kits for clients, including microbial collection products, DNA/RNA isolation kits, and accessories for storage and mailing.

Deliverables: The experimental report includes information on experimental methods, primers, PCR conditions, gel electropherogram, etc.

Reference

  1. Olive D M, Bean P. Principles and applications of methods for DNA-based typing of microbial organisms. Journal of clinical microbiology, 1999, 37(6): 1661-1669.

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