The What's and How's

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* <u>ERIN and SABRIYA</u>Which DNA parts will have to be designed?  Will they be synthesized or produced by PCR? <br>
* <u>ERIN and SABRIYA</u>Which DNA parts will have to be designed?  Will they be synthesized or produced by PCR? <br>
[[loxP sites]] [[Hin/Hix]] [[CRE gene]] [[Degradation Tags]]
[[loxP sites]] [[Hin/Hix]] [[CRE gene]] [[Degradation Tags]]
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* Which plasmids will be used from the registry? <br>
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* Where would biobricks be located?<br>
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]
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* <u>MALCOLM</u> What is the protocol for assembly for the first stage (restriction digestions, ligations, transformations)? <br>
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# [http://partsregistry.org/Assembly:Standard_assembly Standard Assembly]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html '''Compatibility of Plasmids''']
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg<sup>2+</sup> concentration]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/anneal_oligos.html Building dsDNA with Oligos]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pcr.html Setting up PCR mixtures]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg<sup>2+</sup> concentration]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes]]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Clean_Concentrate.html Clean and Concentrate DNA (after PCR, before digestion)]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/clean_short.html Clean DNA (short protocol)]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/SAP.html Shrimp Alkaline Phosphatase]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/gelpure.html Gel Purification]]
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# [[Double Digest Guide]]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/ligation.html Ligation Protocol]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/clean_short.html Ethanol Precipitate DNA (short protocol)]
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# [[http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Transformation]] [[http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version]]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers]
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# Promega miniprep URL to come
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/SAP.html Shrimp Alkaline Phosphatase]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Qiagen_gelpure.html Qiagen QIAquick Gel Purification]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/QIAQuick_recycle.html Qiagen QIAquick Column Regeneration Protocol]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/gelpure.html ElectroElute Gel Purification]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/ligation.html Ligation Protocol]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Heat Shock Transformation] OR [http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version of Heat Shock]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Zippy_Transformation.html Zippy Transformation]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/ColonyPCR_Screening.html Colony PCR to Screen for Successful Ligations]
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# [http://www.bio.davidson.edu/courses/Molbio/Protocols/miniprepPrmega.html Promega miniprep]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/Tranformation_list.html Choices for Transformation: Heat Shock vs. Zyppy]
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#[http://www.bio.davidson.edu/courses/Molbio/Protocols/MiniPrep_list.html Choices for Mini-Preps: Promega vs. Zyppy]

Latest revision as of 13:45, 20 June 2007

  • 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

  1. [http://www.bio.davidson.edu/courses/Molbio/Protocols/reagents.html Common molecular reagents]
  2. [http://partsregistry.org/Assembly:Standard_assembly Standard Assembly]
  3. [http://www.bio.davidson.edu/courses/Molbio/Protocols/ORIs.html Compatibility of Plasmids]
  4. [http://www.bio.davidson.edu/courses/Molbio/Protocols/anneal_oligos.html Building dsDNA with Oligos]
  5. [http://www.bio.davidson.edu/courses/Molbio/Protocols/pcr.html Setting up PCR mixtures]
  6. [http://www.bio.davidson.edu/courses/Molbio/Protocols/magnesium.html PCR and Mg2+ concentration]
  7. [http://www.bio.davidson.edu/courses/Molbio/Protocols/Clean_Concentrate.html Clean and Concentrate DNA (after PCR, before digestion)]
  8. [http://www.bio.davidson.edu/courses/Molbio/Protocols/pourgel.html Pouring an agarose gel]
  9. [http://www.bio.davidson.edu/courses/Molbio/Protocols/molwt.html Calculate MWs]
  10. [http://www.bio.davidson.edu/courses/Molbio/Protocols/digestion.html Digest DNA with restriction enzymes]
  11. Double Digest Guide
  12. [http://www.bio.davidson.edu/courses/Molbio/Protocols/clean_short.html Ethanol Precipitate DNA (short protocol)]
  13. [http://www.bio.davidson.edu/courses/Molbio/Protocols/gels2002/1kbladder.pdf 1kb MW markers]
  14. [http://www.bio.davidson.edu/courses/Molbio/Protocols/SAP.html Shrimp Alkaline Phosphatase]
  15. [http://www.bio.davidson.edu/courses/Molbio/Protocols/Qiagen_gelpure.html Qiagen QIAquick Gel Purification]
  16. [http://www.bio.davidson.edu/courses/Molbio/Protocols/QIAQuick_recycle.html Qiagen QIAquick Column Regeneration Protocol]
  17. [http://www.bio.davidson.edu/courses/Molbio/Protocols/gelpure.html ElectroElute Gel Purification]
  18. [http://www.bio.davidson.edu/courses/Molbio/Protocols/ligation.html Ligation Protocol]
  19. [http://www.bio.davidson.edu/courses/Molbio/Protocols/Promegacompcells.pdf Heat Shock Transformation] OR [http://www.bio.davidson.edu/courses/Molbio/Protocols/transformation.html Short version of Heat Shock]
  20. [http://www.bio.davidson.edu/courses/Molbio/Protocols/Zippy_Transformation.html Zippy Transformation]
  21. [http://www.bio.davidson.edu/courses/Molbio/Protocols/ColonyPCR_Screening.html Colony PCR to Screen for Successful Ligations]
  22. [http://www.bio.davidson.edu/courses/Molbio/Protocols/miniprepPrmega.html Promega miniprep]
  23. [http://www.bio.davidson.edu/courses/Molbio/Protocols/Tranformation_list.html Choices for Transformation: Heat Shock vs. Zyppy]
  24. [http://www.bio.davidson.edu/courses/Molbio/Protocols/MiniPrep_list.html Choices for Mini-Preps: Promega vs. Zyppy]
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