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Did my EcoRI restriction digestion work? picture included!

ecori restriction digestion

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49 replies to this topic

#46 ascacioc

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Posted 31 August 2012 - 12:00 PM

In the words of Trof, anything measured by nanodrop under 10 ng/uL is a number randomly generated. I would say it is too little to trust what you have there.

#47 Papaver

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Posted 01 September 2012 - 02:32 AM

Hi,

so it can work with such low amounts,I did it once with ~ 1 ng/µl. Usually I work with amounts of 4 - 15 ng/µl and it always works fine. Just do the same protocol as before, maybe with less vector concentration (20-30 is thoroughly enough)...and using therefore more in the transformation mix.

But in parallel I would repeat the digestion using more template and set up two or three reactions at the same time if you have enough template...otherwise prep new vector. Then you would have enough for ligation.

#48 Fluffy

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Posted 01 September 2012 - 06:04 PM

Hello,

Thanks for the replies, ascacioc and Papaver.
In regards to making a new insert digestion with template sounds like an idea to me and will do that in parallel to my other work.

On the other hand, Papaver, you mentioned I can use the same protocol that we agreed on earlier which was
DD pET14b vector 2.5uL
DD insert 5.5uL
5X ligase buffer 1.5uL
T4 DNA ligase 0.5uL

I didn't understand what you mean by less vector concentration? So I shouldn't use 2.5uL? Do you mean I use less, wouldn't that mean I would have to add water to make up 10uL
Also last time I added 2uL of my ligation for transformation mix, do you suggest using more this time?

Thanks again

#49 Papaver

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Posted 02 September 2012 - 02:24 AM

HI Fluffy,
by using less I meant the total amount of DNA. You always have to adjust your protocol to your DNA concentrations.
Helpful therefore is: use vector concentrations of 20-50 ng; a molar ratio of insert: vector = 4:1; final buffer concentrations has to be 1x, use 0.5 - 1 µl ligase.
The final volume of you ligation mix does not have to be 10 µl. You can vary it in a way you need it. You may also read the recommendations of the company you got the ligase from.

So this time it would be better to use less vector DNA because you will need more insert DNA.
Try this: 2 µl vector (~ 40 ng)
11 µl insert (~ 16.5-22 ng)
1.5 µl 10xbuffer (= 1x)
0.5 µl ligase
If you still have only 5x ligase buffer, then: 4 µl of 5x buffer, 2.5 µl of vector, 13 µl insert and 0.5 µl ligase.

You also can vary the volume for your transformation. If you want to make sure you get some colonies, do two or three transformation at the same time using, let's say 1 µl, 2µl and 3µl of DNA. When I had difficulties with my cloning (usually when I had to use some old plasmids) I used to transform up to 10 µl (for 200 µl competent cells). When I remember right, the volume of your competent cells was 50 µl. So do not add more than 5 µl (which would be 10 % of the total volume).

#50 Fluffy

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Posted 10 September 2012 - 10:14 AM

Thanks Papaver. Had a vacation. Did those ligations today and hope for the best!





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