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Water quality

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posted on Thu, Jan 7 2010 9:08 PM

I have found that the image quality of adsorbates on mica (e.g. DNA molecules) depends on the purity of the water used to prepare solutions and to rinse the mica disks.

I like to use water from a local Milli-Q system, but sometimes the water quality is not good enough. Can anyone suggest a commercial source of water?

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replied on Thu, Jan 7 2010 9:10 PM

We have used quite successfully Ultrapure MilliQ water for imaging of
single molecules. If the filter cartridge/membrane were not changed as
recommended, there is a good chance that water gets contaminated. We do
not change those as frequently as the manufacturer recommends (too
expensive), and therefore, we have to monitor quality of this water.

We found three quite simple tests:

1. pH of good water should be around 7. If it is below ~6 or above ~7.5,
there is a good chance that it is contaminated.

2. Light scattering: should be none. The device to check it is very
simple, and can be assembled within an hour. It is a cuvette for
fluorescence, which you fill with water to analyze. Put it under
anoptical microscope with an objective with working distance >~1mm (>
than wall thickness of the cuvette) . Then you illuminate water in your
cuvette from the side with a laser (a good laser pointer might be
sufficient). If there are any particulate contamination there, you will
see it (starting from the size of a few nm). (P.S. Definitely, one
should be caution about using lasers, and not trying to send it directly
to your eyes.)

3. (probably the most accurate), just look at Raman spectra (a regular
fluorescent spectrometer should work). Contaminated water has specific
signatures that are very easy to recognize.

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replied on Thu, Jan 7 2010 9:12 PM

Yes, the quality of miiliQ water can be rather low for low height, dry samples like DNA. Note that it depends a lot on how well the miiliQ machine is maintained! I've compared the quality of various waters, for this aplication, and the best is Sigma

"Water for Molecular Biology"

It's around 40 Euros a litre.

This is mentioned at

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replied on Thu, Jan 7 2010 9:14 PM

We have had the exact same problem in our lab; that is, imaging DNA on mica in air,

and finding particulates on the surface. We spent a long time trying to get to the bottom of it,

 and to the best of our knowledge the impurities actually come from two different sources.

 When making control samples incubated and washed with water from various sources (MilliQ,

 distilled, tap etc.) we noticed a variation between and within sources, and found that BPC Grade

water from Sigma (W3513 - Biotechnology Performance Certified) gave the cleanest and most

reproducible results. The other source of impurities we found was the nitrogen stream used to

dry the samples after washing. What exactly these particulates are we never found out, but by

 running the nitrogen through a simple, home-made bubble trap, they largely went away.

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