Melbourne/Blue Photosensor Background
From 2007.igem.org
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== Preliminaries == | == Preliminaries == | ||
| - | Restriction Site Analysis - [http://tools.neb.com/NEBcutter2/index.php|NEB cutter] | + | Restriction Site Analysis - [http://tools.neb.com/NEBcutter2/index.php| NEB cutter] |
| - | Sequence Translation - [http://au.expasy.org/tools/dna.html|Translate] | + | Sequence Translation - [http://au.expasy.org/tools/dna.html| Translate] |
| - | Sequence Aligment - [http://www.jalview.org/download.html|JalView] | + | Sequence Aligment - [http://www.jalview.org/download.html| JalView] |
| - | PCR primer design - [http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html|NetPrimer] | + | PCR primer design - [http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html| NetPrimer] |
Revision as of 12:04, 6 August 2007
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The background to the design of the blue photosensor is included here. Specifically the design for the chimeric fusion protein that will be the key link in blue light pathway
Contents |
Preliminaries
Restriction Site Analysis - [http://tools.neb.com/NEBcutter2/index.php| NEB cutter]
Sequence Translation - [http://au.expasy.org/tools/dna.html| Translate]
Sequence Aligment - [http://www.jalview.org/download.html| JalView]
PCR primer design - [http://www.premierbiosoft.com/netprimer/netprlaunch/netprlaunch.html| NetPrimer]
Sequences and Restriction Sites
SopII
sensory rhodopsin II
DNA, AA, [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sopII genbank]
- No IGEM restriction sites
- HaeII (@168) present
HtrII
sensory rhodopsin II transducer
DNA, AA, [http://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=3702851&ordinalpos=1&itool=EntrezSystem2.PEntrez.Gene.Gene_ResultsPanel.Gene_RVDocSum genbank]
- No IGEM restriction sites
- No useful restriction site
SopII/HtrII fusion
DNA, AA (frame 2 in Translate - only SopII + HtrII + Linker included in link), linker = TSASA SNGASA,
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sopII genbank]
- No IGEM restriction sites
- Use site from SopII (this is the one that will be used)
ComP
two-component sensor histidine kinase
DNA (includes IGEM forward and reverse primers (VF2 + VR) and IGEM prefix and suffix, AA, [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sopII genbank]
SpeI (@927) deleted HaeII (@1902) inserted
ComA
sensory rhodopsin II transducer
DNA, AA, [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=search&term=sopII genbank]
SpeI (@12) deleted HaeII (@433) inserted
Chimera Design
Overview
Refer to 4 PCR primer method here, 2001 paper
SopII Analysis
transmembrane photoreceptor, requires all-trans retinal as substrate... linked to HtrII insert TM analysis here. reference the three papers cited in background
HtrII Analysis
Yeh!!!! sequence analysis.
ComP Analysis
Chosen Fusion
File:Seq align.jpg Media:Example.ogg
