Firstly it is unusual to determine 260/230 ratios: 260/280 is normal. If indeed you have determined 260/230, in the absence of anything that interferes this should be about 2.5, so are you sure you haven't misread the decimal place?

Secondly, ethanol does not absorb at 260 or 280nm, so is not expected to interfere with assessment of purity by the 260/280 ratio. The best test is to try sequencing: if it doesn't work, you MIGHT have ethanol problems!

Thirdly, removing ethanol by Robert's method is preferred, but if you don't have the apparatus, just flip the tube lid and lie the tube on a heating block (this allows the ethanol vapour to flow out) . If your sequencing involves amplification using taq or similar, you can set the block at 70degrees.  Ideally you should dry to constant weight, if you have a suitable balance.

Use a vacuum dryer equipped with a microfuge. First, put your samples into the microfuge, start spinning then turn on the vacuum. In a couple of minutes you get rid of the ethanol. Turn off the vacuum first. Stop the spinning second and remove your ethanol-free samples.

You can re-precipitate your DNA with 0.3M NaAcetate and 0.7vol isopropanol at -20degC for 30min - then collect the ppt by centrifugation, wash this ppt with 70% ethanol (be sure to visibly dislodge the pellet during vortexing, to remove salts), recentrifuge the pellet ppt. Finally discard the wash and dry the pellet in a 37deg incubator to complete dryness (takes 30mins to 1hr, VERY important) - resuspend in TE and use. This will make sure u do not have any ethanol contamination. 

Firstly it is unusual to determine 260/230 ratios: 260/280 is normal. If indeed you have determined 260/230, in the absence of anything that interferes this should be about 2.5, so are you sure you haven't misread the decimal place?

Secondly, ethanol does not absorb at 260 or 280nm, so is not expected to interfere with assessment of purity by the 260/280 ratio. The best test is to try sequencing: if it doesn't work, you MIGHT have ethanol problems!

Thirdly, removing ethanol by Robert's method is preferred, but if you don't have the apparatus, just flip the tube lid and lie the tube on a heating block (this allows the ethanol vapour to flow out) . If your sequencing involves amplification using taq or similar, you can set the block at 70degrees.  Ideally you should dry to constant weight, if you have a suitable balance.

I agree wholeheartedly with Geoff. Ethanol would not cause a change in A260/A230 measurements. If your DNA is not working in downstream molecular biology applications, it may require additional clean up to remove contaminating protein or RNA (this would be apparent in your A260/A280 ratio). It might be helpful to post all the details of your protocol to get the best feedback on how to optimize.

Thank you very much for your replies. The protocol is like this:

1. Carry out the plaque amplification procedure described above. After the first centrifugation in Step 4, transfer 500 μl of the phage-containing supernatant to a fresh microfuge tube.

2. Add 200 μl of 20% PEG/2.5 M NaCl. Invert several times to mix, and let stand for 10–20 minutes at room temperature.

3. Microfuge at 14,000 rpm for 10 minutes at 4°C and discard the supernatant. Phage pellet may not be visible.

4. Re-spin briefly. Carefully pipet away and discard any remaining supernatant.

5. Suspend the pellet thoroughly in 100 μl of Iodide Buffer by vigorously tapping the tube. Add 250 μl of ethanol and incubate 10–20 minutes at room temperature. Short incubation at room temperature will preferentially precipitate single-stranded phage DNA, leaving most phage protein in solution.

6. Spin in a microfuge at 14,000 rpm for 10 minutes at 4°C, and discard the supernatant. Wash the pellet with 0.5 ml of 70% ethanol (stored at –20°C), re-spin, discard the supernatant, and briefly dry the pellet under vacuum.

7. Suspend the pellet in 30 μl of TE buffer. The template can be suspended in H2O instead of TE if desired, but this is not recommended for long-term storage. In TE buffer, the phage DNA should be stable indefinitely at –20°C.

8. Quantitate product by agarose gel electrophoresis. 5 μl of resuspended template should give a band of comparable intensity to 0.5 μg of purified single-stranded M13mp18 DNA.

I dried my samples overnight at room temperature without any heating steps because we dont have vacuum drier.

My 260/280 ratio is around 1.5-1.7. The DNA amount that I obtained best is 95 ng/ul. Should I continue to sequencing, or should I use additional steps to purify DNA?

Thank you in advance for your helps.

I would try the sequencing as is. If it doesn't work, try a phenol chloroform extraction of the DNA. Make sure your concentration is based on the extinction coefficient for single-stranded DNA.

thank you very much