Template:SBB10Project-15924: Difference between revisions
JCAnderson (talk | contribs) (New page: Your Name<br>{{SBB10_ProjectGeneralNotes}}==sbb11: sleeping beauty 5'TR== Source: Synthetic Target Sequence: agttgaagtcggaagtttacatacacttaagttggagtcatt...) |
No edit summary |
||
Line 1: | Line 1: | ||
[[Template:SBB10Indiv-15924 | Your Name]]<br>{{SBB10_ProjectGeneralNotes}}==sbb11: sleeping beauty 5'TR== | [[Template:SBB10Indiv-15924 | Your Name]]<br> | ||
{{SBB10_ProjectGeneralNotes}} | |||
==sbb11: sleeping beauty 5'TR== | |||
Source: Synthetic Target Sequence: agttgaagtcggaagtttacatacacttaagttggagtcattaaaactcgtttttcaactacaccacaaatttcttgttaacaaacaatagttttggcaagtcagttaggacatctactttgtgcatgacacaagtcatttttccaacaattgtttacagacagattatttcacttataattcactgtatcacaattccagtgggtcagaagtttacatacactaa | |||
Vector: pBjk2741 | |||
Short description: sleeping beauty 5'TR | |||
{{SBB10_CisElement}} | |||
{{SBB10_sleepingBeauty}} | |||
{{SBB10_GeneSynthesisRequired}} | |||
==sbb13: PhiC31 Integrase== | |||
Source: pBca9523-Bca1623, pBca9523-Bca1659 | |||
Target Sequence: DTYAGAYDRQSRERENSSAASPATQRSANEDKAADLQREVERDGGRFRFVGHFSEAPGTSAFGTAERPEFERILNECRAGRLNMIIVYDVSRFSRLKVMDAIPIVSELLALGVTIVSTQEGVFRQGNVMDLIHLIMRLDASHKESSLKSAKILDTKNLQRELGGYVGGKAPYGFELVSETKEITRNGRMVNVVINKLAHSTTPLTGPFEFEPDVIRWWWREIKTHKHLPFKPGSQAAIHPGSITGLCKRMDADAVPTRGETIGKKTASSAWDPATVMRILRDPRIAGFAAEVIYKKKPDGTPTTKIEGYRIQRDPITLRPVELDCGPIIEPAEWYELQAWLDGRGRGKGLSRGQAILSAMDKLYCECGAVMTSKRGEESIKDSYRCRRRKVVDPSAPGQHEGTCNVSMAALDKFVAERIFNKIRHAEGDEETLALLWEAARRFGKLTEAPEKSGERANLVAERADALNALEELYEDRAAGAYDGPVGRKHFRKQQAALTLRQQGAEERLAELEAAEAPKLPLDQWFPEDADADPTGPKSWWGRASVDDKRVFVGLFVDKIVVTKSTTGRGQGTPIEKRASITWAKPPTDDDEDDAQDGTEDVAA | |||
Vector: pBjk2741 | |||
Short description: <phiC31> | |||
Genbank reference: X59938.1 | |||
Flavor: {<part>} | |||
{{SBB10_DNAModEnzyme}} | |||
{{SBB10_phiC31}} | |||
__NOTOC__ |
Revision as of 22:34, 2 February 2010
Welcome to your project page!
For each part listed, you should:
- Design oligos to make your part
- Write up proper construction files and put it on the Construction Files page
- Put your oligos on the Oligo Log page
- Put your parts into Clotho
You should design your construction strategy to put your part into plasmid vectorName-Bca1144 (Where vectorName is indicated for each part) using EcoRI and BamHI or just BamHI or BglII for EIPCR. The maps for all plasmids involved in our project can be downloaded here.
Several references have been provided to give you some background on the biology of your part.
Also, use the link above left to upload a picture of yourself, your name, and anything else you'd like.
Finally, you should create a notebook on the main page of the wiki
sbb11: sleeping beauty 5'TR
Source: Synthetic Target Sequence: agttgaagtcggaagtttacatacacttaagttggagtcattaaaactcgtttttcaactacaccacaaatttcttgttaacaaacaatagttttggcaagtcagttaggacatctactttgtgcatgacacaagtcatttttccaacaattgtttacagacagattatttcacttataattcactgtatcacaattccagtgggtcagaagtttacatacactaa Vector: pBjk2741 Short description: sleeping beauty 5'TR
This part encodes a DNA cis element
DNA cis elements are sequences that are bound by DNA binding domains, replication proteins, or DNA modification enzymes. The proteins sometimes just stick to them, and other times they perform some sort of DNA chemistry on them.
This part is associated with sleeping beauty transposon devices
Sleeping Beauty transposase is a popular enzyme that generates protein-DNA complexes called transposomes from DNAs flanked by "terminal repeats". These terminal repeats, or TR's, are specific cis elements. The transposomes are highly reactive and insert the DNA contained within them randomly into other DNAs (such as a genome).
You should read the following papers
References: DOI 10.1007/s10989-007-9114-z, PMID 19412179
This part requires Gene Synthesis
To make this part, you'll use gene synthesis. You may use the tools at GeneDesign to design your oligos for making this part by the PCA method. The protocol is here.
sbb13: PhiC31 Integrase
Source: pBca9523-Bca1623, pBca9523-Bca1659 Target Sequence: DTYAGAYDRQSRERENSSAASPATQRSANEDKAADLQREVERDGGRFRFVGHFSEAPGTSAFGTAERPEFERILNECRAGRLNMIIVYDVSRFSRLKVMDAIPIVSELLALGVTIVSTQEGVFRQGNVMDLIHLIMRLDASHKESSLKSAKILDTKNLQRELGGYVGGKAPYGFELVSETKEITRNGRMVNVVINKLAHSTTPLTGPFEFEPDVIRWWWREIKTHKHLPFKPGSQAAIHPGSITGLCKRMDADAVPTRGETIGKKTASSAWDPATVMRILRDPRIAGFAAEVIYKKKPDGTPTTKIEGYRIQRDPITLRPVELDCGPIIEPAEWYELQAWLDGRGRGKGLSRGQAILSAMDKLYCECGAVMTSKRGEESIKDSYRCRRRKVVDPSAPGQHEGTCNVSMAALDKFVAERIFNKIRHAEGDEETLALLWEAARRFGKLTEAPEKSGERANLVAERADALNALEELYEDRAAGAYDGPVGRKHFRKQQAALTLRQQGAEERLAELEAAEAPKLPLDQWFPEDADADPTGPKSWWGRASVDDKRVFVGLFVDKIVVTKSTTGRGQGTPIEKRASITWAKPPTDDDEDDAQDGTEDVAA Vector: pBjk2741 Short description: <phiC31> Genbank reference: X59938.1 Flavor: {<part>}
This part encodes a DNA modifying enzyme
Different DNA modification enzymes are needed in different flavors, so take special note of what type this one should be. DNA modification enzymes are often toxic to E. coli, so you may have some difficulty making this part. Make careful note in your notebook about the size distribution of colonies you get on your plates and the ratio of red to white colonies.
This part is associated with phiC31 integration devices
phiC31 is a bacteriophage integrase. It is somewhat similar in mechanism to Cre recombinase, but it acts on the asymmetric sites attB and attP. It causes these sequences to be recombined to generate attL and attR sequences. This system is useful for integrating large DNAs site-specifically into genomes.
You should read the following papers
References: PMID 14996222, PMID 19002165, PMID 19439387, PMID 12034816