Difference between revisions of "Part:BBa K4342000"
 
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<partinfo>BBa_K4342000 short</partinfo>
 
<partinfo>BBa_K4342000 short</partinfo>
  
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<h1>Usage and Biology</h1>
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<h1>Introduction</h1>  
  
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The <i>tdk/kan</i> cassette is a highly versatile sequence used for efficiently and effectively engineering the <i> Acinetobacter baylyi </i> ADP1 genome. This part contains the <i> kanR </i> and <i> tdk </i> genes which allow for the selection and counterselection of genetically engineered ADP1 cells. When this cassette is integrated into the ADP1 genome, the <i> kanR </i> gene confers resistance to kanamycin and the <i> tdk </i> gene is lethal to the cell when Azidothymidine is present (Metzgar et. al - 2004).  
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[[File:intro-part-figure.png|500px|thumb|right|]]
  
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The 2022 UT Austin iGEM team used the <i> tdk/kan </i> cassette to successfully delete a number of genes, insert DNA sequences into the ADP1 chromosome, and engineer an ADP1-based biosensor for detecting any DNA sequence of interest. The composite parts below utilized the <i> tdk/kan </i> cassette for genetic engineering.
 
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<ul>
 
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<li> <i> ACIAD2049 tdk/kan </i> Cassette </li>
 
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<li> <i> ACIAD2049 </i> Rescue Cassette</li>
 
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<li> <i> AcrB tdk/kan </i> Cassette </li>
 
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<li> <i> AcrB </i> Rescue Cassette </li>
 
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<li> <i> PbpG tdk/kan Cassette </i> </li>
 
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<li> <i> PbpG </i> Rescue Cassette </li>
 
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<li> <i> RecJ tdk/kan </i> Cassette </li>
 
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<li> <i> RecJ </i> Rescue Cassette </li>
 
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<li> Broken <i> nptII </i> Gene </li>
 
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<li> <i> nptII </i> Gene Detector Construct</li>
 
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<li> <i> TEM-1 </i> Broken Gene </li>
 
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<li> <i> TEM-1 </i> Gene Detector Construct</li>
 
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<li> <i> P. destructans </i> Detector Construct</li>
 
  
  
 +
The 2022 UT Austin iGEM Team’s Part Collection provides a number of DNA sequences and procedures for genetically engineering <i>Acinetobacter baylyi </i> ADP1. We were able to effectively engineer ADP1's genome using a two-step genetic engineering protocol. See the [https://2022.igem.wiki/austin-utexas/engineering Engineering Page] for more details on how we modified ADP1's genome. On this page, we explain how our part collection can be used alongside this two-step protocol to delete ADP1 genes, insert DNA sequences into any chromosomal location, and engineer an ADP1-based biosensor to detect any DNA sequence of interest.
 +
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<b>We hope this part collection guides future iGEM teams in engineering ADP1 and utilizing ADP1’s flexibility to tackle any challenge in synthetic biology.</b>
 +
 +
 +
 +
 +
<h1>Categorization</h1>
 +
For our parts collection, we categorize our parts into the following categories:
 +
 +
<b> Upstream </b>
 +
 +
An <b> Upstream </b> basic part is a DNA sequence directly upstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include the ACIAD2049 Upstream for <i>P. destructans</i> detector [https://parts.igem.org/Part:BBa_K4342003 (BBa_4342003)] and <i>pbpG</i> Upstream [https://parts.igem.org/Part:BBa_K4342011 (BBa_4342011)].
 +
 +
 +
<b> Downstream </b>
 +
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A <b> Downstream </b> basic part is a DNA sequence directly downstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include ACIAD2049 Downstream for <i>P. destructans</i> detector [https://parts.igem.org/Part:BBa_K4342004 (BBa_4342004)] and <i>pbpG</i> Downstream [https://parts.igem.org/Part:BBa_K4342012 (BBa_4342012)].
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<b> Integration Cassettes </b>
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An <b> "Integration" cassette </b> is a composite part consisting of an "Upstream" basic part, the <i>tdk/kan</i> basic part [https://parts.igem.org/Part:BBa_K4342000 (BBa_4342000)], and a "Downstream" basic part. These parts are designed to use in the first transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Integration cassette [https://parts.igem.org/Part:BBa_K4342019 (BBa_4342019)] and the <i>acrB</i> Integration cassette [https://parts.igem.org/Part:BBa_K4342023 (BBa_4342023)].
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<b> Rescue Cassettes </b>
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<b> "Rescue" cassette </b> is a composite part consisting of an "Upstream" basic part, an optional genetic device, and a "Downstream" basic part. These parts are designed to use in the second transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Rescue cassette [https://parts.igem.org/Part:BBa_K4342020 (BBa_4342020], Upstream + Downstream), the YFP Rescue cassette [https://parts.igem.org/Part:BBa_K4342030 (BBa_4342030], Upstream + Genetic Device + Downstream), and the <i>nptII</i> Detector Rescue cassette [https://parts.igem.org/Part:BBa_K4342031 (BBa_4342031], Upstream + Composite Part + Downstream).
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<b> Genetic Device </b>
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<b>"Genetic Device"</b> is a basic part that can be any DNA sequence to be integrated into ADP1. Examples include the <i>CymR</i> YFP [https://parts.igem.org/Part:BBa_K4342008 (BBa_4342008)] and the <i>nptII</i> Broken Gene  [https://parts.igem.org/Part:BBa_K4342015 (BBa_4342015)].
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We further categorize each part with a standardized Golden Gate Assembly (GGA) Type 1-8 Overhang [2]. Each type is ligated to a complementary type (ex. Type 2 can be ligated to Type 1 and Type 3). Moreover, some parts contain consecutive GGA Type numbers, such as Type 234. These DNA sequences start with a Type 2 Overhang and end with a Type 4 Overhang (ex. <i>tdk/kan</i> cassette [https://parts.igem.org/Part:BBa_K4342000 (BBa_4342000)].
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<b> <i>tdk/kan</i> cassette </b> is categorized as a Type 2-4 <b> Integration </b> cassette in our part collection.
 +
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<h1>Usage and Biology</h1>
 +
 +
The <i>tdk/kan</i> cassette is the keystone of our parts collection. It is a highly versatile sequence used for efficiently and effectively engineering the <i>Acinetobacter baylyi</i> ADP1 genome. This part contains the <i>kanR</i> and <i>tdk</i> genes, which allow for the selection and counterselection of genetically engineered ADP1 cells. <i>tdk</i> confers Azidothymidine (AZT) susceptibility, and <i>kanR</i> confers Kanamycin (Kan) susceptibility.[1].
 +
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The 2022 UT Austin iGEM team used the <i>tdk/kan</i> cassette to successfully delete a number of genes, insert DNA sequences into the ADP1 chromosome, and engineer an ADP1-based biosensor for detecting antibiotic resistance genes and <i>P. destructans</i>. Our design process and two-step ADP1 genetic engineering protocol can be found on the [https://2022.igem.wiki/austin-utexas/parts Parts], [https://2022.igem.wiki/austin-utexas/contribution Contribution], and [https://2022.igem.wiki/austin-utexas/engineering Engineering] pages of our Wiki.
  
 
<h1>Design</h1>
 
<h1>Design</h1>
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As seen in figure x, the tdk/kan cassette is flanked by bsaI restriction sites on both its 5’ and 3’ ends. These restriction sites produce sticky ends which can ligate to any DNA sequence possessing the necessary restriction sites with the complementary overhangs. Figure X shows how the tdk/kan cassette can be ligated to DNA sequences homologous to ADP1’s genome.
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The <b><i>tdk/kan</i> Integration</b> cassette is a 1675 bp region containing the <i>tdk</i> and <i>kanR</i> genes.
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*Please note that BsaI restriction sites have been removed to meet RFC[1000] BioBrick Assembly Compatibility. To see in-depth primer design, please see Figure 4 on the [https://2022.igem.wiki/austin-utexas/engineering Engineering Page] for more details on how to design primers containing the correct GGA Type Overhang and restriction sites.  
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===Step 1===
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The <b><i>tdk/kan</i> Integration</b> cassette is designed to allow for reliable confirmation of successful transformants on Kanamycin (Kan) via the <i>kanR</i> gene (Figure 1).
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[[File:TdkKan_Selection.png|500px|thumb|center|<b> Fig. 1. </b> First-Step Integration of the <i>tdk/kan</i> cassette in place of an ADP1 Target Gene (ACIAD2049).]]
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===Step 2===
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The <i>tdk/kan</i> cassette can subsequently be knocked out to create a 4 bp minimal scar deletion of ACIAD2049 via BsmBI digestion. During this second-step transformation, we can use a <b>Rescue</b> cassette to select for successful transformants on Azidothymidine (AZT) (Figure 2). [[File:TdkKan_Counterselection.png|500px|thumb|center|<b> Fig. 2. </b> Second-Step Removal of the <i>tdk/kan</i> cassette.]]
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==Composite Parts==
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The composite parts below utilized this part for ADP1 genetic engineering:
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<li> [https://parts.igem.org/Part:BBa_K4342019 ACIAD2049 Integration Cassette (BBa_K4342019)] </li>
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<li>[https://parts.igem.org/Part:BBa_K4342020 ACIAD2049 Rescue Cassette] (BBa_K4342020)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342021 <i>pbpG</i> Integration Cassette] (BBa_K4342021)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342022 <i>pbpG</i> Rescue Cassette] (BBa_K4342022)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342023 <i>acrB</i> Integration Cassette] (BBa_K4342023)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342024 <i>arB</i> Rescue Cassette] (BBa_K4342024)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342025 <i>recJ</i> Integration Cassette] (BBa_K4342025)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342026 <i>recJ</i> Rescue Cassette] (BBa_K4342026)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342031 <i>nptII</i> Gene Detector Rescue Cassette] (BBa_K4342031)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342032 <i>TEM-1</i> Gene Detector Rescue Cassette] (BBa_K4342032)</li>
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<li>[https://parts.igem.org/Part:BBa_K4342029 <i>P. destructans </i> Integration Cassette (BBa_K4342029)]
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<li>[https://parts.igem.org/Part:BBa_K4342033 <i>P. destructans </i> Rescue Cassette (BBa_K4342033)]
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<h1>Characterization</h1>
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[[File:tdkkan1.png|500px|thumb|center|<b> Fig. 3. </b> Growth on kanamycin plates indicate the successful integration of the <i>tdk/kan</i> cassette into ADP1's genome.]]
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[[File:tdkkan2.png|500px|thumb|center|<b> Fig. 4. </b> Growth on AZT plates indicate the successful removal of the <i>tdk/kan</i> cassette from ADP1's genome.]]
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[[File:AcrB_Deletion_Gel.png|500px|thumb|center|<b> Fig. 5. </b> PCR showing the successful deletion of the <i>acrB</i> gene, using the <i>tdk/kan</i> part.]]
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<h1>References</h1>
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[1] Metzgar, D., Bacher, J. M., Pezo, V., Reader, J., Doring, V., Schimmel, P., Marliere, P., & de Crecy-Lagard, V. (2004). Acinetobacter sp.. ADP1: An ideal model organism for genetic analysis and Genome Engineering. Nucleic Acids Research, 32(19), 5780–5790. https://doi.org/10.1093/nar/gkh881.
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[2] Lee, M.E., DeLoache, W.C., Cervantes, B., and Dueber, J.E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS synthetic biology 4, 975–986. 10.1021/sb500366v.
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<partinfo>BBa_K4342000 SequenceAndFeatures</partinfo>

Latest revision as of 02:56, 14 October 2022

tdk/kan Cassette

Introduction

Intro-part-figure.png


The 2022 UT Austin iGEM Team’s Part Collection provides a number of DNA sequences and procedures for genetically engineering Acinetobacter baylyi ADP1. We were able to effectively engineer ADP1's genome using a two-step genetic engineering protocol. See the Engineering Page for more details on how we modified ADP1's genome. On this page, we explain how our part collection can be used alongside this two-step protocol to delete ADP1 genes, insert DNA sequences into any chromosomal location, and engineer an ADP1-based biosensor to detect any DNA sequence of interest.


We hope this part collection guides future iGEM teams in engineering ADP1 and utilizing ADP1’s flexibility to tackle any challenge in synthetic biology.



Categorization

For our parts collection, we categorize our parts into the following categories:

Upstream

An Upstream basic part is a DNA sequence directly upstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include the ACIAD2049 Upstream for P. destructans detector (BBa_4342003) and pbpG Upstream (BBa_4342011).


Downstream

A Downstream basic part is a DNA sequence directly downstream of a target gene. These basic parts are homology flanks that are used for ADP1 Genetic Engineering. Examples include ACIAD2049 Downstream for P. destructans detector (BBa_4342004) and pbpG Downstream (BBa_4342012).


Integration Cassettes

An "Integration" cassette is a composite part consisting of an "Upstream" basic part, the tdk/kan basic part (BBa_4342000), and a "Downstream" basic part. These parts are designed to use in the first transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Integration cassette (BBa_4342019) and the acrB Integration cassette (BBa_4342023).


Rescue Cassettes

"Rescue" cassette is a composite part consisting of an "Upstream" basic part, an optional genetic device, and a "Downstream" basic part. These parts are designed to use in the second transformation step in ADP1 Genetic Engineering. Examples include the ACIAD2049 Rescue cassette (BBa_4342020, Upstream + Downstream), the YFP Rescue cassette (BBa_4342030, Upstream + Genetic Device + Downstream), and the nptII Detector Rescue cassette (BBa_4342031, Upstream + Composite Part + Downstream).


Genetic Device

"Genetic Device" is a basic part that can be any DNA sequence to be integrated into ADP1. Examples include the CymR YFP (BBa_4342008) and the nptII Broken Gene (BBa_4342015).


We further categorize each part with a standardized Golden Gate Assembly (GGA) Type 1-8 Overhang [2]. Each type is ligated to a complementary type (ex. Type 2 can be ligated to Type 1 and Type 3). Moreover, some parts contain consecutive GGA Type numbers, such as Type 234. These DNA sequences start with a Type 2 Overhang and end with a Type 4 Overhang (ex. tdk/kan cassette (BBa_4342000).


tdk/kan cassette is categorized as a Type 2-4 Integration cassette in our part collection.

Usage and Biology

The tdk/kan cassette is the keystone of our parts collection. It is a highly versatile sequence used for efficiently and effectively engineering the Acinetobacter baylyi ADP1 genome. This part contains the kanR and tdk genes, which allow for the selection and counterselection of genetically engineered ADP1 cells. tdk confers Azidothymidine (AZT) susceptibility, and kanR confers Kanamycin (Kan) susceptibility.[1].

The 2022 UT Austin iGEM team used the tdk/kan cassette to successfully delete a number of genes, insert DNA sequences into the ADP1 chromosome, and engineer an ADP1-based biosensor for detecting antibiotic resistance genes and P. destructans. Our design process and two-step ADP1 genetic engineering protocol can be found on the Parts, Contribution, and Engineering pages of our Wiki.

Design

The tdk/kan Integration cassette is a 1675 bp region containing the tdk and kanR genes.

  • Please note that BsaI restriction sites have been removed to meet RFC[1000] BioBrick Assembly Compatibility. To see in-depth primer design, please see Figure 4 on the Engineering Page for more details on how to design primers containing the correct GGA Type Overhang and restriction sites.

Step 1

The tdk/kan Integration cassette is designed to allow for reliable confirmation of successful transformants on Kanamycin (Kan) via the kanR gene (Figure 1).

Fig. 1. First-Step Integration of the tdk/kan cassette in place of an ADP1 Target Gene (ACIAD2049).

Step 2

The tdk/kan cassette can subsequently be knocked out to create a 4 bp minimal scar deletion of ACIAD2049 via BsmBI digestion. During this second-step transformation, we can use a Rescue cassette to select for successful transformants on Azidothymidine (AZT) (Figure 2).
Fig. 2. Second-Step Removal of the tdk/kan cassette.


Composite Parts

The composite parts below utilized this part for ADP1 genetic engineering:

  • ACIAD2049 Integration Cassette (BBa_K4342019)
  • ACIAD2049 Rescue Cassette (BBa_K4342020)
  • pbpG Integration Cassette (BBa_K4342021)
  • pbpG Rescue Cassette (BBa_K4342022)
  • acrB Integration Cassette (BBa_K4342023)
  • arB Rescue Cassette (BBa_K4342024)
  • recJ Integration Cassette (BBa_K4342025)
  • recJ Rescue Cassette (BBa_K4342026)
  • nptII Gene Detector Rescue Cassette (BBa_K4342031)
  • TEM-1 Gene Detector Rescue Cassette (BBa_K4342032)
  • P. destructans Integration Cassette (BBa_K4342029)
  • P. destructans Rescue Cassette (BBa_K4342033)

    Characterization

    Fig. 3. Growth on kanamycin plates indicate the successful integration of the tdk/kan cassette into ADP1's genome.
    Fig. 4. Growth on AZT plates indicate the successful removal of the tdk/kan cassette from ADP1's genome.
    Fig. 5. PCR showing the successful deletion of the acrB gene, using the tdk/kan part.


    References

    [1] Metzgar, D., Bacher, J. M., Pezo, V., Reader, J., Doring, V., Schimmel, P., Marliere, P., & de Crecy-Lagard, V. (2004). Acinetobacter sp.. ADP1: An ideal model organism for genetic analysis and Genome Engineering. Nucleic Acids Research, 32(19), 5780–5790. https://doi.org/10.1093/nar/gkh881.

    [2] Lee, M.E., DeLoache, W.C., Cervantes, B., and Dueber, J.E. (2015). A highly characterized yeast toolkit for modular, multipart assembly. ACS synthetic biology 4, 975–986. 10.1021/sb500366v.



    Assembly Compatibility:
    • 10
      INCOMPATIBLE WITH RFC[10]
      Illegal XbaI site found at 719
    • 12
      COMPATIBLE WITH RFC[12]
    • 21
      INCOMPATIBLE WITH RFC[21]
      Illegal BamHI site found at 713
      Illegal XhoI site found at 875
    • 23
      INCOMPATIBLE WITH RFC[23]
      Illegal XbaI site found at 719
    • 25
      INCOMPATIBLE WITH RFC[25]
      Illegal XbaI site found at 719
    • 1000
      COMPATIBLE WITH RFC[1000]