Scarab Strain Identification Kit

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SKU Product Manufacturer Price: Quantity
IS-0410-10 IS-0410-10 - Scarab Strain Identification Kit ***** 1
  • Meet Regulatory Needs – Validate the identity of your production host strains for quality control and regulatory purposes.
  • Precise Identification - PCR of unique genomic markers accurately identifies the Clean Genome® E. coli Strains, whereas phenotypic growth assays may misidentify because of the engineered secondary metabolism in the Clean Genome® strains.
  • Quickly Process Multiple Strains or Time Points – PCR detection enables an answer in hours instead of days and can be applied to multiple samples with minimal additional effort.


Researchers generating biological materials often need to validate the identity of their production host strains for Quality Control and regulatory purposes.

The Scarab Strain Identification (SSI) kit is designed to validate and verify the identity of Scarab Genomics’ Multiple Deletion Series (MDS™) Clean Genome® E. coli host strains. The MDS™ strains have been engineered by deleting over 15 % of the genome from the K12 reference strain MG1655, resulting in improved performance in many applications including production of biopharmaceuticals.

As a side effect of the numerous genomic deletions, MDS™ host strains have missing or altered genes that affect secondary metabolic characteristics (e.g. nutritional requirements) that are sometimes used in traditional microbial identification. As a result, Clean Genome® strains are not always properly identified as “E. coli” when evaluated by growth phenotype tests. One set of tests using the BiOLOG Phenotype Microarray™ metabolic panel analysis identified MDS™42 as having a 95% probability of being a Citrobacter species rather than E. coli.

This kit addresses the issues that may occur with phenotype based assays by providing a genome based approach wherein a panel of specific sequences unique to the MDS™ strains are assayed by PCR. The MDS™ strains are very distinct from other commonly used E. coli hosts due to the many genomic deletions generated during their creation. This kit uses primers designed to distinguish whether a given bacterial genomic DNA sample has or lacks a series of genomic modifications specific to the MDS™ strains.


Figure 1: Primer Validation with Positive and Negative Control Genomic DNAs and Citrobacter Genomic DNA and Expected Size Amplicon. (A) SDS-PAGE of PCR reaction products for the positive and negative controls. M = 1kb Plus DNA Ladder (Invitrogen) (B) Indicates the expected size of the resulting amplicon.


Kit Components

  • Positive Control MDS™ Strain Genomic DNA: 160 μl, sufficient for the analysis of 10 samples.
  • Positive Control ScarabXpress™ DNA: 50 μl, sufficient for the analysis of 10 samples.
  • Negative Control K12 MG1655 E. coli Genomic DNA: 160 μl, sufficient for the analysis of 10 samples.
  • Negative Control Citrobacter Genomic DNA: 160 μl, sufficient for the analysis of 10 samples.
  • SSI-specific Forward (F) and Reverse (R) Primers: 80 μl of each primer at a concentration of 5 μM, sufficient for the analysis of 10 samples.

    Forward Primers Reverse Primer
    F-SSI-Del A R-SSI-Del A
    F-SSI-Del B R-SSI-Del B
    F-SSI-Del C R-SSI-Del C
    F-SSI-Del D R-SSI-Del D
    F-SSI-Del E R-SSI-Del E
    F-SSI-Del F1 R-SSI-Del F1
    F-SSI-Del F2 R-SSI-Del F2
    F-SSI-Del G1 R-SSI-Del G1
    F-SSI-Del G2 R-SSI-Del G2
    F-SSI-Del H1 R-SSI-Del h2
    F-SSI-Del I R-SSI-Del I
    F-SSI-Del J R-SSI-Del J
    F-SSI-Del K R-SSI-Del K

  • tufA SSI Positive Control Forward (F) and Reverse (R) Primers (SSI-Pos Cntrl): 60 μl of each primer at a concentration of 5 μM, sufficient for the analysis of 10 samples.

Quality Control
SSI Identification primers sets are functionally tested using the Control Genomic DNAs and by following the procedure described in this User Protocol. The kit and reaction conditions have been validated with Phusion™ High-Fidelity DNA Polymerase from New England Biolabs. The use of other thermostable DNA polymerases may be possible provided that the proper optimization of reaction conditions is performed. Six microliters (6 μl) of the PCR amplification product is analyzed on 1.0% 1X TAE agarose gel. No products are visible when water is added in place of template DNA.

Storage Conditions
Store components at –20°C. Do not store in a frost-free freezer.

Patents & Disclaimers

Scarab is providing you with this Material subject to the non-transferable right to use the subject amount of the Material for your research at your academic institution. The Recipient agrees not to sell or otherwise transfer this Material, or anything derived or produced from the Material to a third party. NO RIGHTS ARE PROVIDED TO USE THE MATERIAL OR ANYTHING DERIVED OR PRODUCED FROM THE MATERIAL FOR COMMERCIAL PURPOSES. If the Recipient makes any changes to the chromosome of the Material that results in an invention in breach of this limited license, then Scarab will have a worldwide, exclusive, royalty-free license to such invention whether patentable or not. If the Recipient is not willing to accept the terms of this limited license, Scarab is willing to accept return of this product with a full refund, minus shipping and handling costs. For information on obtaining a license to this Material for purposes other than research, please contact Scarab’s Licensing Department. Scarab Genomics’ technology is covered by U.S. Pat. No. 6,989,265 and related foreign applications.

Clean Genome® is a registered trademark of Scarab Genomics, LLC.