User:Anthony Salvagno/Notebook/Research/2010/01/20/Preplanning for Jasper PCR

Resuspending Oligos
I will want 100uM DNA solutions which is 100pmol/ul. Here is my information:

So if you notice on the sheet, I made a mistake. I added the volume I was supposed to add to R3 to F5 so essentially I halved the concentration. Another thing to note, my nanodrop readings were way off. Somehow I got the right concentrations at the end. I don't know how it worked out, but it did. Good for me.

Protocol for Fang
Essentially I used the nanodrop (which measures absorbence of light to determine how much DNA is in solution). Using various formulas (mostly division) I obtained the numbers you see in the spreadsheet above. Since I want 100uM solution I basically divide my pmol by 100 to get the amount of ul I need to add to my DNA powder. The information for pmol and ug comes from some data sheets that Alpha DNA kindly provides.

When I add my buffer (0.1x Tris in this case) I swoosh the buffer up and down to get the DNA into suspension in the buffer. Then I just pipette 1ul out and place on the pedestal of the nanodrop. I make my measurements and record the data. Then I do the calculations you see above and voila!

Next to set up the PCR...

PCR Preplanning
BTW, I am using abbreviations for my primers. Example: pbrF2825-Cy3 is shortened to F3 for quick writing. So my primers are: F3, F5, R3, F5.

Take note of the PCR settings table. I don't really know what my times should be but I'm going with 30s annealing and 10s extension. The rule of thumb is 1min per 1kb but I have about 100kb so that is 6s and I upped it to 10 to be safe. I feel like 30s annealing is too long, but who knows. Maybe I should up that to 1min like I usually do. I'll decide tomorrow.