User:Anthony Salvagno/Notebook/Research/2010/12/15/New Tweezer Construct: Designing the DNA: Difference between revisions

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===Temp Area===
===Temp Area===
This search is quite the struggle. Nothing seems to be able to locate the entire string that I listed above in any plasmid. I don't know if that is because there is some trick to the search that I'm not getting or if the plasmid databases I'm using is limited. I also don't know how to search for any restriction site that give me the 4 base overhang I need. This is complicated, but I feel like it shouldn't be.

Revision as of 13:28, 15 December 2010

How should I organize this page? I don't think I currently have a planning category. Should I make one? With that said I'm going to be building a new unzipping/stretching construct. We want to use a new plasmid that we can buy cheaply. Perhaps one with the same BstXI site as pRL574 so that we don't have to redesign the adapter (but I think I want to make that anyway because I want to add a few biotin more to the adapter to enhance microsphere attachment). I will start by finding a plasmid with that site and then design 2 or more PCR reactions (4.4kb reaction and 1.1kb reaction).

The Search for a Plasmid

The conditions:

  • cheap
  • contains exact BstXI cut site from pRL574

According to my Fermentas Reviewer tool (see the notebook homepage) the sequence I need to find in any plasmid I wish to build around is:

  • 5' - CCAACGAT | CTGG - 3' where the line is where BstXi snips. The overhang is CGAT meaning any compliment (like the one in our adapter) is 5' - ATCG.

Temp Area

This search is quite the struggle. Nothing seems to be able to locate the entire string that I listed above in any plasmid. I don't know if that is because there is some trick to the search that I'm not getting or if the plasmid databases I'm using is limited. I also don't know how to search for any restriction site that give me the 4 base overhang I need. This is complicated, but I feel like it shouldn't be.

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