Difference between revisions of "Part:BBa K2194000:Design"
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===Design Notes=== | ===Design Notes=== | ||
| − | Primers used to PCR amplify <i>chrR</i> from the <i>Escherichia coli</i> MG1655 genome: <p> | + | Primers used to PCR amplify <i>chrR</i> from the <i>Escherichia coli</i> MG1655 genome*: <p> |
| − | 5’ | + | 5’ <b>CGATCGTCTCACTCGA</b>ATGTCTGAAAAATTGCAGGTG 3’ </p><p> |
| − | 5' | + | 5'<b>GCATCGTCTCACTCTGCCA</b>TTAGATCTTAACTCGCTGAATAAACTC 3'</p> |
| − | + | <p></p> | |
| − | Primers used for PCR site-directed mutagenesis (in addition to the primers used to amplify <i>chrR</i> from the genome:<p> | + | Primers used for PCR site-directed mutagenesis (in addition to the primers used to amplify <i>chrR</i> from the genome*:<p> |
| − | 5' ATGCCGTCTCA<u>A</u><b>ATCACCTGCGCCAGATTC | + | 5' <b>ATGCCGTCTCA<u>A</u></b>ATCACCTGCGCCAGATTC 3'</p><p> |
| − | 5' ATGCCGTCTCAGAT<u>T</u>CTG | + | 5' <b>ATGCCGTCTCAGAT<u>T</u>CTG</b>ACAGCGCGCGCCGCC 3'</p> |
| − | + | <p></p> | |
The primers for PCR site-directed mutagenesis incorporate BsmBI recognition sites into the overhangs so that the two resulting PCR fragments can be assembled using a Golden Gate reaction. This process generates the sequence for <i>chrR6</i> without any scars around the site of PCR mutagenesis. | The primers for PCR site-directed mutagenesis incorporate BsmBI recognition sites into the overhangs so that the two resulting PCR fragments can be assembled using a Golden Gate reaction. This process generates the sequence for <i>chrR6</i> without any scars around the site of PCR mutagenesis. | ||
| + | <p></p> | ||
| + | *The primer overhangs are <b>bolded</b> and the part of the primer that introduces the mutation is <u>underlined</u>. | ||
===Source=== | ===Source=== | ||
Revision as of 01:33, 1 November 2017
chrR6 Chromate Reductase Enzyme
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal BglII site found at 570
- 23COMPATIBLE WITH RFC[23]
- 25INCOMPATIBLE WITH RFC[25]Illegal AgeI site found at 337
- 1000INCOMPATIBLE WITH RFC[1000]Illegal BsaI site found at 3
Illegal BsaI.rc site found at 583
Design Notes
Primers used to PCR amplify chrR from the Escherichia coli MG1655 genome*:5’ CGATCGTCTCACTCGAATGTCTGAAAAATTGCAGGTG 3’
5'GCATCGTCTCACTCTGCCATTAGATCTTAACTCGCTGAATAAACTC 3'
Primers used for PCR site-directed mutagenesis (in addition to the primers used to amplify chrR from the genome*:5' ATGCCGTCTCAAATCACCTGCGCCAGATTC 3'
5' ATGCCGTCTCAGATTCTGACAGCGCGCGCCGCC 3'
The primers for PCR site-directed mutagenesis incorporate BsmBI recognition sites into the overhangs so that the two resulting PCR fragments can be assembled using a Golden Gate reaction. This process generates the sequence for chrR6 without any scars around the site of PCR mutagenesis.
- The primer overhangs are bolded and the part of the primer that introduces the mutation is underlined.
Source
We sourced the nucleotide sequence for chrR from the Escherichia coli MG1655 genome NCBI database (entry NC_000913.3:3894652-3895218). We used this sequence to design primers to PCR amplify the sequence from purified Escherichia coli MG1655 genome. Then, we designed primers to incorporate a single nucleotide change so that the 128th codon of the sequence changed from TAT → AAT (Try-->Asn).