Talk:CH391L/S13/DnaAssembly

Gabriel Wu 23:39, 27 January 2013 (EST): Minor point: Companies like biomatik are not included on the genspace list. Is it necessary to make a wiki page with a "more" comprehensive list?

Gabriel Wu 00:49, 28 January 2013 (EST): This is a nice anecdotal piece of information that shows some concrete numbers for what DNA synthesis might have cost in June 2011. Unfortunately, it's not really appropriate for the main wiki page, but I post it here to live for eternity! Also, if anyone finds a more legitimate way of presenting this kind of data on the main page, then this comment might actually be useful. [1]

• Aurko Dasgupta 20:51, 7 February 2013 (EST):I don't have any clear idea of the kind of budgets one should expect for making a 3000bp plasmid in lab, but getting 1 millimole of plasmid for ~$1200 actually sounds like a decent deal. Would it be reasonable to say that the labor and materials to make such a plasmid would amount to more than $1200, assuming a few mistakes along the way?
  • Max E. Rubinson 22:47, 7 February 2013 (EST):That's probably an issue between you and your boss.

Gabriel Wu 13:10, 4 February 2013 (EST): These are notes to myself. They help illustrate techniques in cloning or trends in DNA synthesis

• Rob Carlson website and nature biotech paper on "The Changing Economics of DNA synthesis," report
  
• Practical example of DNA synthesis genscript, blog idt
  
• biobricks
  
• TA-TOPO
  
• TA cloning
  
• USER
  
• Red recombineering
  
• Cre/LoxP
  
• LIC
  
• In-Fusion
  
• Nathan's SLIC explanation
  
• TAR
  
• MAGIC
  

Gabriel Wu 18:23, 4 February 2013 (EST): Added an introduction motivating the page. Explaining the need for "putting together" DNA.

• Neil R Gottel 13:11, 7 February 2013 (EST):I was looking into Ginkgo Bioworks because this article at sciencenews mentioned they rely heavily on their own special CAD tools when designing their organisms, and found their blog. It hasn't been updated in a year, but their last post was talking about how slow and variable the turn-around times are for gene synthesis. They've got a chart showing the length of each order, and the time it took between when the order was placed, and when it was received. Some of their genes (or "synthons" as they call it, since some sequences are not whole genes) took more than two months to synthesize!

Thomas Wall 20:23, 7 February 2013 (EST): I had a formatting issue Gabe, You put CPEC and splice under gibson cloning, making it look like it is a subset of that when I think you mean for it to be a subset of overlap cloning.

Thomas Wall 20:31, 7 February 2013 (EST): This is a cool extension of CPEC I want to potentially start using in my lab (http://www.ncbi.nlm.nih.gov/pubmed/21293463)

Assembling nonstandard bases

• Catherine I. Mortensen 22:07, 6 February 2013 (EST): I noticed you mentioned that nontraditional bases could be assembled... I'm taking genetics now so I may learn about this soon but could you give an example when a nontraditional base would be useful? I assume a nontraditional base refers to another purine or pyrimidine?
  • Yunle Huang 10:02, 7 February 2013 (EST): One example I found was 2-Aminopurine. 2-Aminopurine is a fluorescent nucleic acid analogues can be used in nucleic acid research. Since it pairs with both thymine and cytosine, it can also be used for mutagenesis. http://www.pnas.org/content/83/15/5434
  • Benjamin Gilman 16:02, 7 February 2013 (EST): Unnatural bases are often used in synthetic DNA oligos to broaden the range of binding interactions or chemistry available (like what Somalogic has done with DNA aptamers). Are there any applications where genes with synthetic, unnatural bases were used in vivo?
    • Aurko Dasgupta 20:34, 7 February 2013 (EST):So I'm guessing they handle stuff like promoter/transcription factor binding affinity? Unless you use some kind of unnatural tRNA as well, I doubt you'd be able get that stuff translated.

iGEM connection

• Jeffrey E. Barrick 00:35, 7 February 2013 (EST):Someone mentioned that CPEC was started as an iGEM project. Can you like to the relevant team website as part of the topic so that we can take a look at it?
  • Max E. Rubinson 22:43, 7 February 2013 (EST):I don't know if CPEC was started as an iGEM project, but this group at Duke (where the method was developed) used CPEC to assemble a metabolic pathway for the production of plastic polymers in E. coli.
• Thomas Wall 20:33, 7 February 2013 (EST): http://2009.igem.org/Team:Duke