Cloudy DNA

Gregory Poon mk.poon at utoronto.ca
Mon Aug 23 11:43:30 EST 2004


If you are preparing the calf thymus DNA from fibres, they are quite
difficult to rehydrate and are also very much contaminated with proteins
(and who knows what else).  When I did this a few years ago, I had to use a
sonicator to clarify the solution, and then try to clean the stuff up by
phenol extraction, etc.  I wouldn't trust the UV data too much until you
have the solution clarified since there will be a lot of scattering in the
suspension.

On the other hand, Invitrogen sells a fairly pure calf thymus solution at 10
mg/mL and it's fairly cheap (something like $100 for 5 mL); wouldn't this be
concentrated enough for your purposes?

Gregory

"Aaron Engelhart" <aaron.engelhart at gmail.com> wrote in message
news:afd496b4.0408230123.33877bd6 at posting.google.com...
> We do some work with calf thymus DNA at high concentrations (3-7
> millimolar) in milliliter quantities for spectrophotometry/transient
> absorption spectroscopy purposes. One problem is that it seems to be
> fairly cloudy above the millimolar level. This is the cheapest source
> of DNA, so I like to use it for obvious reasons before doing
> experiments on synthetic oligos or polyG-polyC, etc, but the
> cloudiness is a problem. I have done some work with phenol extraction,
> which seems to help a bit, but with significant product loss. Every
> time I do a phenol extraction, there is a bit of whitish gunk at the
> interface. I don't understand the mechanics of this completely, or
> exactly what it is. There's some obvious product loss from leaving a
> bit of the supernatant behind to avoid taking up the impurity, but my
> understanding is that the dsDNA stays in the aqeuous phase and the
> proteins go into the organic phase. A260/280 ratio looks fine (and
> unchanged!) before and after extraction. Does anyone have a good way
> to clear up CTDNA/know what this is? TIA,
>
> Aaron





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