I think both gives you a same kind of values, but if you relay go for the any downstream high-through put  experiment then definitely go for Qubit RNA quantification kit, in which dyes provided in the kit directly binds to the RNA but not to the DNA or protein presents in the samples and also give you a accurate and even quantify very low quantity of RNA by using Qubit HS RNA kit.

I complitely agree with Abhijit. In my experince Qubit from Invitrogen (Broad range or High Sensitivity kit) allows to quantified the DNA better than Nanodrop, expecially when the concentration is low.

I will tell you if you want very accurate in your measurement you should go for PicoGreen, even though this techniques are not as straight as Nano  

Dear Karuppiah,

Check the sensitivity, reproducibility and accuracy (including stray light) of each of spectrophotometer.

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Ade Kujore

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Cecil Instruments Limited

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It's better to use nanodrop for very low quantities of the samples. but it's really necessary to have uniform concentration of the DNA or RNA that you're quantifying through out the sample stock.

I'd prefer nanodrop from thermo fisher scientific to quantify such samples. If you don't have any choice , go for the eppendorf spectrophotometer and check the optical density twice or thrice at least to make sure you get precise quantities.

Good Luck

The Nanodrop measures only the absorption. Since also RNA, dsDNA and ssDNA absorb at the same wavelenght (260 nm) your measurement might be not very accurate, if your solution is not 'clean'/pure. Also other chemicals that are in your sample might absorb at 260 nm and mess with your concentration measurement.

Kits that are mesauring by fluorescence (like the mentioned PicoGreen, Qubit or AccuClear kits) are more specific and most of the kits can also quantify up to lower concentrations than the Nanodrop. Disadvantage are the higher volumes needed for those kits (e.g. 10 ul per measurement with the AccuClear, so already 30 uL for a triplo, which is recommended). If possible, you can dilute your sample (since the kit is more sensitive than the Nanodrop)...

So for speed and only an indication I would go for the Nanodrop. For more accuracy and low concentrations I would go for a fluorescence quantification kit.