NanoDrop v. Plate Reader - Fight! (Mar/23/2011 )

Hey everyone! I have a question concerning the accuracy of the NanoDrop v. plate reader spectrophotometers. My PI and the PhD student in my lab swear up and down about how amazing the plate reader is, and how "untrustworthy" the NanoDrop is. I, on the other hand, feel the exact opposite! I much prefer the NanoDrop; I've never (not once) gotten reliable results from the plate reader (e.g. 10 ng/uL DNA from a Maxiprep.....are you kidding?!)
Normally, we dilute our samples by either 1:100 or 1:200 dilution factor, and send them to the plate reader. Subsequently, we use the extinction coefficient, the 260 reading and the dilution factor to calculate our concentration. When I use the NanoDrop, I find it much easier to accurately obtain my concentrations.
My boss and the PhD student mention how the NanoDrop pedestal is "dirty" because you need to directly place your sample on the reader. I always wash the pedestal in between samples and seem to get reliable results.

So, I'm wondering: which do you guys prefer, the NanoDrop or a 96-well plate reader, and why?

For small numbers of samples, definitely the Nanodrop. For large numbers of samples, picogreen in a plate reader, robotically prepared.

Wiping both of the pedestals well (the pedastal on the base and on the arm) after each sample and there won't be a problem with the nanodrop. I've done thousands of samples and only once have I had a problem -- this was measuring a sample of high concentration (800ng/ul) followed by one I knew to be low concentration (~50ng/ul) and the low concentration sample came out higher than expected. I measured again and got a more accurate result. I have double checked many samples and the results are always within 10ng/ul of each other at the most.

Before the nanodrop came along, I always had inconsistent results diluting samples and measuring using "old-fashioned" spectrophotometers, to the point that I stopped using them and estimated from ladders on a gel instead. As suggested by phage434, using fluorescent stains seems to be about as accurate as the nanodrop, does have some advantages in that there are markers for DNA, RNA single stranded, etc. And, as phage434 states, for a high number of samples, working in plates with robotics or at least multi-channel pipettes is easier than the NanoDrop.

Does anyone have any experience with the LabChip DS? It is a high-throughput microfluidic spectophotometer with chips in 96 well SBS plate format. It is basically a "high-throughput" nanodrop from what I can understand. I was nervous about the comsumable cost for the microfluidic chips, but as it turns out they are way cheaper than picogreen. I'm awaiting a demo, but I wanted to see if anyone has heard of this? The instrument is made by a Belgian company Trinean, but is distributed in the US by Caliepr Life Sciences.

http://www.caliperls.com/products/labchip-ds.htm

Thanks!

phage434 on Wed Mar 23 15:24:34 2011 said:

Agree, the microplate reader should be done with a standard curve because its OD is not correct compared to a spectrometry such as nanodrop when using OD 260nm.

We got Tecan spectrofotometer with NanoQuant plate, you put 2 ul of sample on the 16-positions plate similar to Nanodrop. We usually have around 10 samples, so it's quicker than Nanodrop, but the spectrophotometr is multifunctional, it can read 96-wells, kinetic assays, temperature incubation. Good thing is you can only wipe it with dH2O like Nanodrop, but also take the plate out and clean it in the ultrasonic bath when you got concentration reads from empty positions, which happens when you measure proteins sometimes. I'm not sure, how you can clean Nanodrop.

the nanodrop guides do suggest cleaning solutions for such samples but over all i too have never had any problems using the nanodrop for dna as well as protein samples.... i m not against the microplate reader as well.. tecan is a good one trof but i personally love the biotek plate readers.. very robust!!!