Missouri Western State University 2006
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== '''hix BioBricks''' == | == '''hix BioBricks''' == | ||
| + | ''' Hey, it's your Davidon pals.We noticed that your biobricks do not have the Not1 site between E and X in the prefix and S and P in the suffix''' | ||
x-hix-s-p | x-hix-s-p | ||
Revision as of 19:15, 1 June 2006
Front Row (left to right) Adam Brown, Trevor Butner, Brad Ogden, Marian Broderick, Todd Eckdahl.
Back Row (left to right) Jeff Poet, Eric Jessen, Kelly Malloy
Contents |
Students
• Marian Broderick [1]
• Adam Brown [2]
• Trevor Butner [3]
• Lane Heard [4]
• Eric Jessen [5]
• Kelly Malloy [6]
• Brad Ogden [7]
• Kayla Ragsdale [8]
Faculty
• Todd Eckdahl [http://staff.missouriwestern.edu/~eckdahl/], Department of Biology, [9]
• Jeff Poet [http://staff.missouriwestern.edu/~poet/], Department of Computer Science, Mathematics, and Physics, [10]
Shipping Address: Todd Eckdahl, Biology Department, Missouri Western State University, 4525 Downs Drive, Saint Joseph, MO, 64507
Research Links
Goodman et al. 1973-1979. The Pancake Problems [http://www.math.uiuc.edu/~west/openp/pancake.html]
Nanassy and Hughes. 1998. In Vivo Identification of Intermediate Stages of the DNA Inversion Reaction Catlyzed by the Salmonella Hin Recombinase [http://www.genetics.org/cgi/content/abstract/149/4/1649]
Lim et al. 1997. Hin-mediated Inversion on Positively Supercoiled DNA [http://www.jbc.org/cgi/content/full/272/29/18434]
Hughes et al. 1992. Sequence-specific interaction of the Salmonella Hin recombinase in both major and minor grooves of DNA [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=1628628]
Nanassy and Hughes. 2001. Hin Recombinase Mutants Functionally Disrupted in Interactions with Fis [http://jb.asm.org/cgi/content/full/183/1/28?view=long&pmid=11114897]
Lee et al. 1998. In Vivo Assay of Protein-Protein Interactions in Hin-Mediated DNA Inversion [http://jb.asm.org/cgi/content/abstract/180/22/5954]
Merickel et al. 1998. Communication between Hin recombinase and Fis regulatory subunits during coordinate activation of Hin-catalyzed site-specific DNA inversion [http://www.genesdev.org/cgi/content/abstract/12/17/2803]
Haykinson and Johnson. 1993. DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=8508775]
Vasquez et al. 2004. Tangle Analysis of Gin Site-specific Recombination [http://math.berkeley.edu/~mariel/Vazquez_Gin04.pdf]
Merickel and Johnson. 2004. Topological analysis of Hin-catalysed DNA recombination in vivo and in vitro [http://www.blackwell-synergy.com/doi/abs/10.1046/j.1365-2958.2003.03890.x]
R.C. Johnson and M.F. Bruist. 1989. Intermediates in Hin-mediated DNA inversion: a role for Fis and the recombinational enhancer in the strand exchange reaction [http://www.pubmedcentral.gov/picrender.fcgi?tool=pmcentrez&blobtype=pdf&artid=400990]
Lim and Simon. 1992. The Role of Negative Supercoiling in Hin-mediated Site-Specific Recombination[http://www.jbc.org/cgi/content/abstract/267/16/11176]
The Pancake Tossing World Record[http://www.recordholders.org/en/records/pancake.html]
Cool site for Breakfast [http://www.cut-the-knot.org/SimpleGames/Flipper.shtml]
iGEM iDeas
Powerpoint with two possible project ideas. [http://staff.missouriwestern.edu/~eckdahl/Research/Synthetic_Biology_2006/IGEMideas%2005-29-06.ppt]
Parts to Make:
HixL: TTCTGGAAAA CCAAGGTTTT TGATAA
HixR: TTATCAAAAA CCTTCCAAAA GGAAAA
HixC: TTATCAAAAA CCATGGTTTT TGATAA
HixC1: TTCTGGAAAACC AT CCAAAAGGAAAA
Steps
1. Design/Order DNA – Hix L, R, & C
- Want to do a Left to Right BioB addition: Promoter + RBS w/AmpR -->Hix site-->
Term-->Hix(C)site-->TetR + Term
2. On receiving – restrict/ligate BioBricks into plasmid w/resistance gene on one side
a. Promoter, RBS BioB
b. TetR BioB (Backwards)
c. Term BioB
3. Transform E. coli
E = G/AATC
X = T/CTAGA
P = CGAT/CG
S = A/CTAGT
hix BioBricks
Hey, it's your Davidon pals.We noticed that your biobricks do not have the Not1 site between E and X in the prefix and S and P in the suffix
x-hix-s-p
HixL
G/AATC T/CTAGA TTCTTGAAAACCAAGGTTTTTGATAA A/CTAGT CGAT/CG
HixR
G/AATC T/CTAGA TTATCAAAAACCTTCCAAAAGGAAAA A/CTAGT CGAT/CG
HixC
G/AATC T/CTAGA TTATCAAAAACCATGGTTTTTGATAA A/CTAGT CGAT/CG
Process of Creating Synthetic Pancake:
