Agarose gel electrophoresis

hlo
i have obtained the area under the intensity curve, but i couldn’t able to relate it with the concentration of DNA loaded in the gel.
is there any equations to relate the area of the intensity curve and the concentration of DNA…

and is there any other parametes other than finding the DNA concentration by gel electrophoresis?

Hi Muhilraj1 and welcome to the forum :slight_smile:

I would not try to determine DNA concentration using this method, is there any reason you cannot do spectrophotometry? You could also purify the bands in the gel and measure the absolute concentration of DNA, but this of course far more work and is usually done using kits (which are never cheap).

If you are just using an image of the gel the only way to determine concentration is comparing to bands of known concentration, and consider that this concentration is weight/volume so the size of the DNA fragments matter.

What do you mean by other parameters? Parameters for what? Maybe you can share your image and your workflow?

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thanks Sverre,
I am in thought of creating a new plugin which could analyse the gel and give the concentration of DNA present in the band.
can you please say me what are the other things than I can consider for analyzing the gel

I doubt that this will be necessary, at most a short script or macro could automate the whole procedure. But for an efficient manual approach you can look at the analyze gels tools.

It is a simple matter of measuring the intensity in the different bands and making comparisons… but maybe you can explain why you need to do it this way? i.e. quantifying DNA from agarose gels.

Whats wrong with NanoDrop?

Because it is the task given to me by my Professor.

He asked me to create a plugin in imageJ that analyses the image and gives the concentration of the sample present in each band.

Can you please enlighten me about NanoDrop???
its new to me

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I don’t see the point in writing a new plugin in Java for something that can be easily written in the macro language. Or if you prefer, any of the scripting languages available in Fiji (ImageJ distribution) including Groovy, Python, Javascript etc.

Look at the Analyze Gels tools i linked in my last reply and combine this with the macro recorder, or just do something similar and record your actions using the macro recorder. Once you have the core functionality you can adapt it to work on whole directories of images etc.


NanoDrop is a simple spectrophotometer that you find in most labs that do anything in molecular biology. Simply put it measures the absorbance of light in one drop of DNA solution at 260nm and calculates the concentration of DNA based on this. It can also quantify common contaminants, such as RNA. it is fast, easy to use and cheap. Agarose gels are easy to use and cheap, but far from fast :wink:

thankyou so much Sverre