Quantification of DNA from plant samples

[newmanreb]

Hi all, we are thinking of upgrading our gDNA quantification method from the agarose gel method to the NanoDrop. I've been trying to research online what quantification methods are best for DNA extracted from plant tissues, including wood and decayed wood, because I know these extracts can introduce unique contaminants that would not be present in something like blood, for example. I haven't found much information online about this topic specifically, just lots of discussions about NanoDrop vs. Qubit vs. qPCR quantification, etc. I think the NanoDrop will be a good move for us but I was wondering if anyone out there with expertise in plant DNA extracts has a favorite quantification method. Thank you! 

[CharonY]

A few points regarding the NanoDrop. It is convenient and you use a tiny amount of sample. But for precise quantification it is not very useful regardlesss of contamination in the sample. Considering the low volumes you pipet, the DNA (and other stuff) is often not homogenously distributed. So drop-to-drop variation is often very high and we generally do not use it beyond rough purity estimates, regardless of the sample.

That being said, one big question is whether your goal is accurate absolute DNA quantification, reproducible quantification and/or also knowledge on purity. And of course the type of extraction you use, the buffer and additives and so on can influence you quantification in various ways all on top of your source material. Then there are experimental conditions (such as concentration regime, are samples limited, what is the budget, how much time to invest, cost of downstream applications etc.) which all determine which methods are more useful or not. 

[Arete]

I hate the Nanodrop with a passion. So many failed library preps due to poor quantification - especially if you have any contaminants in your sample, which it sounds like you may. It's very simple and easy to use, but the data from a Qubit is superior - we just bought a Qubit flex, which takes 8 strip tubes instead of a single sample. 

Of course it depends on what you're doing downstream with your DNA - are you just doing PCR/Sanger, whole genome sequencing, cDNA, etc. If you're just doing standard PCR, Nanodrop data will be fine and save you a lot of time on gels, but if you're doing any sort of illumina/PacBio/Nanopore library prep, you'd want super clean extractions, like phenol chloroform extractions, and be prepared to have a high failure rate - which given the cost of library prep/sequencing kits, is going to make the $3K for a Qubit worth it pretty fast.