Davidson 2006

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('''Current Course of Action''')
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*Isolating genomic DNA from Salmonella typhimurium
*Isolating genomic DNA from Salmonella typhimurium
*Ordered olioges for recombinational enhancer and primers for the hin gene
*Ordered olioges for recombinational enhancer and primers for the hin gene
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==Pancake Simulator aka The Lancelator==
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[[randompancakeflipper.m]]

Revision as of 19:51, 6 June 2006

Logo.gif

DC team.JPG
Malcolm, Laurie, Sabriya, Erin, Lance.


Contents

Students

• Sabriya Rosemond [1] is a rising junior biology major at Hampton University in VA.

• Erin Zwack [2] is a rising junior biology major at Davidson College in NC.

• Lance Harden [3] is a rising sophomore at Davidson College, who might major in math.


Faculty

• A. Malcolm Campbell [http://www.bio.davidson.edu/campbell Department of Biology], [4]

• Laurie J. Heyer [http://www.davidson.edu/math/heyer/ Department of Mathematics], [5]

Papers of Interest

• [http://www.bio.davidson.edu/courses/synthetic/papers/Sanders_04.pdf Stepwise Dissection of the Hin-catalyzed Recombination Reaction from Synapsis to Resolution. Erin R. Sanders and Reid C. Johnson]

• [http://www.molcells.org/home/journal/article_read.asp?volume=16&number=3&startpage=377 The Effects of Ethidium Bromide and Mg++ Ion on Strand Exchange in the Hin-mediated Inversion Reaction. Hee Jung Lee et al.] Excellent description of Hin recombination mechanism.

• [http://www.jbc.org/cgi/reprint/267/16/11183 The Effects of Symmetrical Recombination Site hixC on Hin Recombinase Function. Heon Man Lim et al.]

• [http://www.pubmedcentral.gov/articlerender.fcgi?tool=pubmed&pubmedid=3457367 The role of the loxP spacer region in P1 site-specific recombination. Ronald H.Hoess et al.]

• [http://www.biomedcentral.com/1471-2164/7/73 A high-throughput screen identifying sequence and promiscuity characteristics of the loxP spacer region in Cre-mediated recombination. Perseus I Missirlis et al.]

• [http://nar.oxfordjournals.org/cgi/content/full/30/13/2764 Non-contact positions impose site selectivity on Cre recombinase. Andreas W. Rufer and Brian Sauer]

• [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=103771 Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid]

• [http://www.jbc.org/cgi/content/full/272/29/18434 Hin-mediated Inversion on Positively Supercoiled DNA]

• [http://jb.asm.org/cgi/content/full/185/3/1097 Plasmid DNA Supercoiling and Gyrase Activity in Escherichia coli Wild-Type and rpoS Stationary-Phase Cells]


Project Description



E hop.jpg



Parts Created

Davidson Parts

Questions

General Questions

Math Questions

Biology Questions

Assembly Issues

  • What is the list of DNA parts that we will need for the first stage, second stage, entire project?
  • ERIN and SABRIYA Which DNA parts exist in the registry?Answer1More Parts
  • ERIN and SABRIYAWhich DNA parts will have to be designed? Will they be synthesized or produced by PCR?

loxP sites Hin/Hix CRE gene Degradation Tags

  • Which plasmids will be used from the registry?
  • Where would biobricks be located?
  • MALCOLM What is the protocol for assembly for the first stage (restriction digestions, ligations, transformations)?
  1. http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents
  2. [[http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg2+ concentration]]
  3. http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel
  4. http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs
  5. http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes
  6. http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers
  7. Shrimp alkaline phosphatase URL to come
  8. Ligation URL to come
  9. http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Transformation http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version
  10. Promega miniprep URL to come

Current Course of Action

Plasmids

  • pSB1A3
      • amp resistant
      • copy number:100-300
      • size:2157 empty
  • pSB1AC3
      • part-BBAp1000
      • copy number:100-3000
      • amp and CmR resistant
      • contains device that provides CmR
      • size:3844 ( with device) 3005 (without device)
  • pSB1AK3
      • part BBa_|13535
      • copy number:100-300
      • amp and kan resistance
      • contains a device for screening test
      • size: 3457 (with device) 3189 (without device)
  • Transform bacteria We are using Salmonella typhimurium for the Hin protein as it was the referenced species in all of the literature.
  • Create RE biobrick (completed)
  • Isolating genomic DNA from Salmonella typhimurium
  • Ordered olioges for recombinational enhancer and primers for the hin gene

Pancake Simulator aka The Lancelator

randompancakeflipper.m

Personal tools
Past/present/future years