Questions about DNA recovery by silica binding

Hiranya Roychowdhury hroychow at NMSU.EDU
Fri Oct 17 10:43:37 EST 1997

At 05:43 PM 10/16/97 +0100, David F. Spencer wrote:
>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

Also, the -thiocyanite salts tend to produce nicks in DNA, and hence may not
be suitable for certain manipulations.

Dr. Hiranya Sankar Roychowdhury
Plant Genetic Engineering Lab.
New Mexico State University
Las Cruces, NM 88003
Ph. (505) 646-5785
hroychow at

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