For any kind of sequencing now a days companies prefer to use fluorescence based quantification. Nanodrop results are not trust worthy. So I recommend to use qubit or similar or bioanalyzer.

Yes, I use both Qubit and Nandodrop. The first one for quantification and the second one to check those parameters as Qubit only tell the concentration but not 260/280 nor 260/230

I would say it depends on the underlying contaminants which are causing the low 260/230... i.e. whether or not they are inhibitors for your particular restriction enzymes. If you are starting with high molecular weight DNA (more important than DNA purity in my opinion), and a test digest of your samples yields a good fragment distribution (i.e. a nice smear on the gel), then I would say you are ready to go :). So, an easy test would be to check for consistent digest across samples.

Typically I just perform an additional pre-digest bead purification for samples which fail to digest (or don't digest well, suggesting maybe some sort of inhibitor). So, my process is this (keep in mind I am doing ddRAD, so no random shear step):

1. Run samples on gel, verify HMW DNA

2. Digest samples (plates of 48 or 96)

3. Run digests on gel (verify digest)

3b. Bead-purify samples which both failed to digest

3c. Re-digest those samples

4. Ampure cleanup all post-digest samples

5... (remainder of library prep)

Thanks Tyler for your response. I think that the low 260/230 is because of some residual NaCl of the purifying procedure. Maybe these remains of salt can affect the enzyme activity (I will use Sbf1 or EcoRI). I will take note of your recommendations, thank you very much!

Hi Ignacio, Both of those should show some level of salt inhibition. If you get poor digest performance, you can increase digest length (although this comes with higher prob of off-target cuts), or bead purify the DNA and re-do the digest.