Not so easy, at least not with measurements in the UV-range, because of many contaminations other than DNA. If the amounts spent for testing are not the problem, you could think about the classical colourimetric determination of deoxyribose in your cell extracts or similar, using the traditional diphenylamine test. It is fairly easy to do, pretty specific for DNA and yields a nice light blue colour that can easily be measured in simple filter photometers. Quantification of DNA is very accurate even in raw cell extracts.

Best wishes, Johannes.

Probably the faster and easy way to measure DNA concentration is using a spectrophotometer. But you can have wrong measures if there is some contamination on the sample, like phenolic compounds, proteins or free nucleic acids. To have a reliable measure of DNA concentration is better to use quantification assays with dyes molecules that bind to DNA molecules in a specific way and perform the quantification through comparison with a standard curve. PicoGreen (invitrogen) is a good kit to measure DNA concentration.

We can use Nanodrop..

Different DNA isolation methods often produce different amounts of contaminants (phenol, free nucleotides, etc) absorbing at the same wavelength used for spectrophotometry. OD260 nm is not a good method to compare yields in this case; fluorometry with dsDNA-specific dyes is a better alternative.

But in any case, and since you only want to compare relative yields, would it not be faster and cheaper to compare the results by gel electrophoresis?

It also seems to me that agarose gel is a good choice since you do not have to worry about small RNAs in your sample.

I would suggest gel electroscopes, however, if you are sure you will get pure DNA then Nanodrop could be an alternative.

I totally agree with Alejandro Martin that Nanodrop is measuring DNA and RNA at 260, as nucleic acids and that won't give us a reliable measurement.

Thanks for you all, in terms of using gel electrophoesis comparing DNA concentration of the bands visually with hyper ladder that I have used, would be scientifically acceptable?

It all depends on how you process the data and what conclusions you draw from it. For instance, simply running all samples in a gel without comparing to a standard would be perfectly acceptable if all you did were to point out "method A yields more DNA than method B". Running a concentration ladder and visually comparing the samples lets you assign concentration ranges, but not much else. And if you run the samples at concentrations within the dynamic range of EtBr staining, then image the gel under non-saturating conditions, integrate the signals and prepare some sort of standard curve via non-linear regression, probably you will be able to determine relatively accurate concentrations with 95% confidence intervals.

we use to go for both Nano drop as well as Agarose Gel (to detect that we are having our desired Product, or if product is degraded or not .as degraded DNA will give several bands or smear ... )

Not so easy, at least not with measurements in the UV-range, because of many contaminations other than DNA. If the amounts spent for testing are not the problem, you could think about the classical colourimetric determination of deoxyribose in your cell extracts or similar, using the traditional diphenylamine test. It is fairly easy to do, pretty specific for DNA and yields a nice light blue colour that can easily be measured in simple filter photometers. Quantification of DNA is very accurate even in raw cell extracts.

Best wishes, Johannes.

Mohammed,

This is an important question and one that is also of interest to myself and colleagues. I am not sure what your sample source, or target species is. We are looking at human saliva so we are concerned with determining the amount of human vs bacterial DNA in our extractions. Historically, we have used the Nanodrop, but like earlier comments suggest, this is not helpful in identifying the human vs bacterial components/ratio. We have also used bioanalyzer, with mixed results, and this method is not endorsed (by Agilent Tech) for differentiating human vs bacterial DNA. Currently, we use these plus Qubit dsDNA and gel electrophoresis to assess DNA samples. We have found Nanodrop and Qubit measurements from the same sample to be inconsistent, so this is another concern. If you simply want to see which extraction yields more intact DNA, I'd go with the agarose gel. I'd be interested to know how you proceed.

Nanodrop (ND-1000 Software) spectrophotometry analysis will do, to determine the purity and quantity of the DNA.

Quant-iT™ PicoGreen® dsDNA Assay Kit is the most accurate for measuring dubble-stranded DNA concentrations. It binds only to dubble-stranded DNA, not to RNA, oligonucleotides or protein.