What are you planning to use the DNA for? If you are doing routine cloning, spectrophotometric methods (http://bitesizebio.com/13501/dna-concentration-purity/) should be fine. If you are quantifying DNA for generation of a library for sequencing, you may want to use a more accurate and sensitive assay based on intercolating dye such as a Qubit system.

Hi Pankaj, i totally agree with Eric Ultraviolet (UV) spectrophotometry by measuring the optical densities of the purified nucleic acid at 260 nm and 280 nm (A260 and A280) is preferred through which concentration and purity are determined. But the problem is associated with small volumes of extracted DNA in such case a nanodrop is required although it measure the concentration of DNA and associated nucleotides and oligonucleotides.

regards

well, UV spectrophotometry measures nucleotides, oligonucleotides and RNA as well, they both (UV spectroscopy and nanodrop) work on the same principle, just the setup is little different.

The best method really depends on your amount of the DNA and the purity and the usage. You can determine amount of your DNA on agarose gel (by comparison to marker) or you can use the spectrophotometry (where proteins, RNA, nucleotides etc interfere) or you can use fluorometry.