Difference between revisions of "Part:BBa K676001:Design"

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===Design Notes===
 
===Design Notes===
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Cloned it from the bacteriophage genome by PCR using synthesised primers.
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The gyrase binding sites (GBS) or strong gyrase sites and are found to be about 280bp ( Mu phage SGS) according to Oram(2003). In the 280bp DNA sequence, approximately 130bp will be wrapped around the tetrameric enzyme in a way similar to nuclesome formation.
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By using bioinformatics software and websites such as NCBI , eurofins operons  and the Mu GBS sequence from Oram (2003) , we have designed the appropriate forward and reverse primers to extract and amplify the 280 bp sequence from the Mu phage DNA template which was kindly provided by the Department of Molecular Biosciences .
 +
 
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Here are the forward and reverse primers we had designed to PCR the GBS :
 +
Forward primer: CGGTACACCCGATATGGCA
 +
Reverse primer: Cattcagtgcggcaatgc
  
 
===Source===
 
===Source===
  
−
Mu bacteriophage genome
+
Wild type Mu bacteriophage genome
  
 
===References===
 
===References===
 +
Mark Oram , Alison J. Howells, Anthony Maxwell and Martin L . Pato (2003)A biochemical analysis of the interaction of DNA gyrase with the bacteriophage Mu , pSC101 and pBR322 Strong gyrase Sites ; the role of DNA sequence in modulating gyrase supercoiling and biological activity ; Molecular Microbiology 50(1).333-347

Latest revision as of 22:21, 9 October 2011

Gyrase Binding Site from Mu Bacteriophage


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal AgeI site found at 191
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

The gyrase binding sites (GBS) or strong gyrase sites and are found to be about 280bp ( Mu phage SGS) according to Oram(2003). In the 280bp DNA sequence, approximately 130bp will be wrapped around the tetrameric enzyme in a way similar to nuclesome formation.

By using bioinformatics software and websites such as NCBI , eurofins operons and the Mu GBS sequence from Oram (2003) , we have designed the appropriate forward and reverse primers to extract and amplify the 280 bp sequence from the Mu phage DNA template which was kindly provided by the Department of Molecular Biosciences .

Here are the forward and reverse primers we had designed to PCR the GBS : Forward primer: CGGTACACCCGATATGGCA Reverse primer: Cattcagtgcggcaatgc

Source

Wild type Mu bacteriophage genome

References

Mark Oram , Alison J. Howells, Anthony Maxwell and Martin L . Pato (2003)A biochemical analysis of the interaction of DNA gyrase with the bacteriophage Mu , pSC101 and pBR322 Strong gyrase Sites ; the role of DNA sequence in modulating gyrase supercoiling and biological activity ; Molecular Microbiology 50(1).333-347