Also, is there a non-spectrophotometeric way to determine purity of total RNA? I am working with plant samples.
For my experiments, I quantify DNA using fluorometry, which is very reliable and accurate. You can stain your DNA with Picogreen, which stains only double-stranded DNA, and read in a fluorometer (excitation around 488nm and emission around 510).
In this article you will see it in more detail
http://www.ncbi.nlm.nih.gov/pubmed/16673882
Regarding the RNA, I thin you can apply a similar approach, but using a different staining, maybe some sort of Sybr Green.
It's important to mention that for low concentrated DNA/RNA (below 50ng/ul), Nanodrop is not very reliable. In the range of 2ng/ul - 10 ng/ul it is too much misleading. And it will also detect debris, primers, etc. If you need to be accurate, doing a standard curve in a fluorometer is the way to go. Of course, it all depends of what you want to do with your DNA/RNA. If it's just inserting amplicon in a plasmid, or something similarly simple, nanodrop or agarose gel will work properly.
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