Questions and Answers

From OpenWetWare
Revision as of 17:03, 19 January 2009 by Leo Tang (talk | contribs)
Jump to: navigation, search

Post new questions at the top of the list

About Trizol

I want to make some homemade Trizol. However I find something very wired in the protocols in Openwetware([[1]]). In protocols Guanidinium Thioyanate(W.M. 118.2) final concentration is 0.8M, but 118.2g is used in 1L Trizol. Ammonium thiocyanate (W.M. 76.1) is 76.1g in Trizol, however, they said the final concentration is 0.4M. I can not understant that. Thank you for your answer!

Does anybody have experience in red recombinase? We are recently get started and have little experience in primer design. When add the homology sequence, the primer is long, what should we do if the primer have a high Tm, or too much hairpin and Dimer? How do set the PCR parameters?

Automatic colony counter

Does anybody have access (or know about access to) an automatic colony counter? I'm looking for a way to count colonies of different colors. Please email with any information. Thanks.


  • Reshma 11:45, 11 December 2006 (EST): You could try emailing the biostuff list to reach a wider MIT-specific audience. You may also be able to do something by just taking a photo of your plate and do some sort of image analysis to count colonies. I've never done this but it shouldn't be that different from what people do to identify cells from microscope images. Though that might be an overly complex solution to your problem. Not sure.

Vector LoxP sites flanking two antibiotic marker genes for use in E.coli

I am in need of a low-copy vector (1 to 2 per cell) which carries two antibiotic marker genes. (preferably one sensitive such rpsL, and one resistant such at Tetracycline, Chloramphenicol, etc.) and are FLANKED between two LoxP sites so as once i express Cre recombinase i get recombination between the lox sites and removal of the antibiotic sites. I have rpsL gene at the lab, also i have tetracycline. So even if the plasmid doesn';t carry any antibiotic genes, but has LoxP it would be o.k and i may move in with my construct by subcloning between the sites but that would entail more work... :) Anyone in a position to help? I would also be very happy,whoever wishes,to collaborate and explain better my underlying project. email address:


RBS prediction

Is there an online or otherwise easy to use tool for finding RBS sites?


I've used TIGR's software to do RBS prediction. The program is called RBS finder. Also, if you have a specific sequence you want to test, you can use Stormo's work:

  1. Barrick D, Villanueba K, Childs J, Kalil R, Schneider TD, Lawrence CE, Gold L, and Stormo GD. Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res. 1994 Apr 11;22(7):1287-95. PubMed ID:8165145 | HubMed [stormo1994]

Of couse, this is all for E. coli --Sri Kosuri 19:22, 23 March 2006 (EST)

Homologous recombination in E. coli

If anyone has experience with homologous recombination in E. coli please check out the Standard E. coli Strain for BioBricks project and annotate the page with your feedback and comments. Please include any protocols or materials information you might have on the appropriate pages and link to them from the standard strain project page as well. Any and all advice is appreciated.


See Standard E. coli Strain for BioBricks for comments. Can add more detail later.--Kathleen