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How to read / interpret a DNA ladder

Discussion of all aspects of biological molecules, biochemical processes and laboratory procedures in the field.

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How to read / interpret a DNA ladder

Postby marinebiologist26 » Sun Oct 18, 2009 8:41 am

Hey guys,

New to the forum! Writing a lab report on a marine alga Griffithsia traversii, and need help interpreting the results of the DNA ladder we produced in last weeks lab. I'm a fourth yr undergrad marine major and haven't done much of DNA before. DNA was extracted using CTAB buffer, electrophoresis in agarose gel, and amplified using PCR. I've attached a pic of the sample, DNA ladder is on the far right, samples read from right to left, my DNA band is sample to the immediate left of ladder. From what i can tell it seemed to have worked quite well?

However, I don't know how to interpret results or what I can say about the extracting/results in my report. We are not genotyping or anything like that. So fairly basic.. Any help is greatly appreciated!!

Thanks :-)
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samples56-59and68-69.jpg
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Postby JackBean » Sun Oct 18, 2009 10:07 am

First thing, which you can definitely say is, that your DNA ladder is totally useless and your teacher didn't prepare for the lab, as s/he should.
Anyway, the mobility has some dependence on size of DNA, so you can extrapolate it, althrough it won't be so accurate.
Basically, the log M = a.x, where x is how the DNA has gone and a is some constant describing your experiment. Let's say, that you have 50/5; 100/4.5; 200/4; 300/3.5 (first is the size in base pairs, second is the distance in cm), so you will put it into graph and see, what will be your dependence (remember to put there log of the size, otherwise it will be logaritmic and not linear). In this way, you can find out, how large should be your amplicon, whether it has correct size ;)
So, you can say, that samples 56, 57 and 59 didn't work at all, and sample 69 did work best (maybe it did contain only most of DNA in the beginning? Did you check the concentration?)
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Postby MrMistery » Sun Oct 18, 2009 12:47 pm

The correct answer would be "My teacher is a lazy bastard who didn't take the 2 minutes to check what the size specifications are for the ladder and for the expected PCR product".
"As a biologist, I firmly believe that when you're dead, you're dead. Except for what you live behind in history. That's the only afterlife" - J. Craig Venter
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Re:

Postby JackBean » Sun Oct 18, 2009 1:01 pm

MrMistery wrote:The correct answer would be "My teacher is a lazy bastard who didn't take the 2 minutes to check what the size specifications are for the ladder and for the expected PCR product".

:lol: :lol:
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Postby Darwin420 » Sun Oct 18, 2009 6:57 pm

Yea...epic fail on the ladder.
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