Using Nanodrop for UV/Vis analysis of compounds at limited amounts
In short, i would say that you cant use Nanodrop for such work. Here is why:

From a quick google search it appears that a nanodrop is a UV-Vis spectrometer that can measure very small amounts of liquid. Looks like that  bio-sciences people (I am not a biologist or biochemist) use it to quantify nucleic acids by knowing the approximate molar absorptivity for DNA, RNA etc. at a specific wavelenth, measuring the sample's absorption at that wavelength, and applying the Beer-Lambert law assuming that the only compounds that absorb in the wavelenght that measurement takes place in their sample are the nucleic acids (which i guess is a fair assumption for such samples). 

However, I am not sure from your question if you want to measure nucleic acid content in a sample also containing alkaloids as part of the sample matrix or you want to quantify the various alkaloids in your sample. 

I think you must mean the latter since you mention GC-MS in which case the nanodrop seems to be a poor choice: UV-Vis spectroscopy in general is a technique with very low resolution in terms of compound separation due to the broadness of the peaks in the absorption spectra. If you had only a few alkaloids in your mixture (which i dont think you do) maybe you could use nanodrop or a normal UV-Vis spectrometer followed by a lot of calibration and absorption band decomvolution in order to identify and quantify each component. If on the other hand you have a complex mixture (which is usually the case with natural extracts) any kind of UV-Vis spectroscopy will fall short. Even NMR spectroscopy which has a much higher resolution would struggle.

This is why GC-MS seems to be the best way for such work: the GC separates the mixture in simpler mixtures (or in the pure compounds if your sample is not too complicated) and then the MS identifies and quantifies the compounds present in each fraction. So i think that you will either need to find more sample or further optimize your GC-MS method to increase sensitivity.

I hope this helps.