Questions about DNA recovery by silica binding

David F. Spencer dspencer at
Thu Oct 16 11:43:19 EST 1997

In article <Pine.SUN.3.95L.971014000013.1252A-100000 at>,
Wilson <netson at> wrote:

> Dear all,
>         I would like to use homemake silica to recover DNA from agarose
> gel.  I know that DNA can bind to the silica under high salt
> concentration.  Almost all protocol are suggested that high concentration
> of NaI is used to dissolve agarose gel and provide the high salt condition
> for the DNA binding.  Is it possible to use other salt such as NaCl, KCl
> etc to substitute NaI (if my DNA is in agarose gel or in TE)?  Is there
> any advantage of using NaI rather than other salt? 

You must use a chaotropic salt to solubilize agarose gels and chlorides are
not very effective.  NaI is still the most common salt used for this
purpose but there are variations that use sodium perchlorate, and of course
guanidinium isothiocyanate is used in other preparative procedures that
involve DNA binding to silica; GTC would not however be the most obvious
choice for purifying DNA from agarose.

If you track down an old physical chemistry text such as Glasstone that
gives the Hofmeister series (also called the lyotropic series) then you can
find other possible suitable salts.  The series includes both cations and
anions; technically the most effective chaotropic salt would be predicted
to be cesium thiocyanate but I believe you will have to settle for
something less exotic.

Dave Spencer

David F. Spencer, PhD
Dept. Of Biochemistry
Dalhousie University
Halifax, Nova Scotia

dspencer at
dspencer at

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